From 7dcdc4bc553329504625a1b0a7ac664351277292 Mon Sep 17 00:00:00 2001 From: Laurent Gatto Date: Mon, 30 Sep 2024 08:14:42 +0200 Subject: [PATCH] update cv --- DESCRIPTION | 2 +- NEWS | 4 + src/pwiz/data/common/CVTranslator.cpp | 471 +++++++------ src/pwiz/data/common/CVTranslator.hpp | 132 ++-- src/pwiz/data/common/cv.cpp | 614 ++++++++++++++-- src/pwiz/data/common/cv.hpp | 396 ++++++++++- src/pwiz/data/common/psi-ms.obo | 979 +++++++++++++++++++++++--- 7 files changed, 2115 insertions(+), 483 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index aa06e48d3..dde2511c6 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: mzR Type: Package Title: parser for netCDF, mzXML and mzML and mzIdentML files (mass spectrometry data) -Version: 2.39.0 +Version: 2.39.1 Author: Bernd Fischer, Steffen Neumann, Laurent Gatto, Qiang Kou, Johannes Rainer Authors@R: c( person("Steffen", "Neumann", email="sneumann@ipb-halle.de", role=c("aut","cre")), diff --git a/NEWS b/NEWS index b51734c7e..59c1ffc5b 100644 --- a/NEWS +++ b/NEWS @@ -1,3 +1,7 @@ +CHANGES IN VERSION 2.39.1 +------------------------- +o Update CV translator, adds support for Astral + CHANGES IN VERSION 2.37.3 ------------------------- o Fix compilation on Windows/aarch64 (#290), thanks to Tomas Kalibera for the patch diff --git a/src/pwiz/data/common/CVTranslator.cpp b/src/pwiz/data/common/CVTranslator.cpp index c600be24b..9ddd8abf1 100644 --- a/src/pwiz/data/common/CVTranslator.cpp +++ b/src/pwiz/data/common/CVTranslator.cpp @@ -1,234 +1,237 @@ -// -// $Id$ -// -// -// Original author: Darren Kessner -// -// Copyright 2008 Spielberg Family Center for Applied Proteomics -// Cedars-Sinai Medical Center, Los Angeles, California 90048 -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// -// - - -#define PWIZ_SOURCE - -#include "CVTranslator.hpp" -#include "boost/algorithm/string/predicate.hpp" -#include "pwiz/utility/misc/Std.hpp" - - -namespace pwiz { -namespace data { - - -using namespace pwiz::cv; - - -// -// default extra translations -// - - -namespace { - -struct ExtraEntry -{ - const char* text; - CVID cvid; -}; - -ExtraEntry defaultExtraEntries_[] = -{ - {"ITMS", MS_ion_trap}, - {"FTMS", MS_FT_ICR}, -}; - -size_t defaultExtraEntriesSize_ = sizeof(defaultExtraEntries_)/sizeof(ExtraEntry); - -} // namespace - - -// -// CVTranslator::Impl -// - - -class CVTranslator::Impl -{ - public: - - Impl(); - void insert(const string& text, CVID cvid); - CVID translate(const string& text) const; - - private: - - typedef map Map; - Map map_; - - void insertCVTerms(); - void insertDefaultExtraEntries(); -}; - - -CVTranslator::Impl::Impl() -{ - insertCVTerms(); - insertDefaultExtraEntries(); -} - - -namespace { - - -inline char alnum_lower(char c) -{ - // c -> lower-case, whitespace, or + - return isalnum(c) ? static_cast(tolower(c)) : c == '+' ? c : ' '; -} - -inline char alnum_lower_regex(char c) -{ - // c -> lower-case, whitespace, +, or _ for things that appear to be part of a regex - return isalnum(c) ? static_cast(tolower(c)) : c == '+' ? c : '_'; -} - -string preprocess(const string& s) -{ - string result = s; - if (bal::starts_with(s, "(?<=")) // Looks like a regex - { - transform(result.begin(), result.end(), result.begin(), alnum_lower_regex); - } - else - { - transform(result.begin(), result.end(), result.begin(), alnum_lower); - } - return result; -} - - -string canonicalize(const string& s) -{ - // remove non-alnum characters - istringstream iss(preprocess(s)); - - // remove whitespace around tokens - vector tokens; - copy(istream_iterator(iss), istream_iterator(), back_inserter(tokens)); - - // concatenate with underscores - ostringstream oss; - copy(tokens.begin(), tokens.end(), ostream_iterator(oss, "_")); - - return oss.str(); -} - - -} // namespace - - -bool shouldIgnore(const string& key, CVID value, CVID cvid) -{ - return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || - key=="pi_" && value==MS_PI && cvid==UO_pi || // MS_PI==photoionization, UO_pi==3.14 - key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point - key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 - cvid == UO_volt_second_per_square_centimeter); // conflict between 1002814 200010007 (volt-second per square centimeter) -} - - -bool shouldReplace(const string& key, CVID value, CVID cvid) -{ - return false; -} - - -void CVTranslator::Impl::insert(const string& text, CVID cvid) -{ - string key = canonicalize(text); - - if (map_.count(key)) - { - if (shouldIgnore(key, map_[key], cvid)) - return; - - if (!shouldReplace(key, map_[key], cvid)) - { - throw runtime_error("[CVTranslator::insert()] Collision: " + - lexical_cast(map_[key]) + " " + - lexical_cast(cvid)); - } - } - - map_[key] = cvid; -} - - -CVID CVTranslator::Impl::translate(const string& text) const -{ - Map::const_iterator it = map_.find(canonicalize(text)); - if (it != map_.end()) - return it->second; - return CVID_Unknown; -} - - -void CVTranslator::Impl::insertCVTerms() -{ - for (vector::const_iterator cvid=cvids().begin(); cvid!=cvids().end(); ++cvid) - { - const CVTermInfo& info = cvTermInfo(*cvid); - - if (info.isObsolete) continue; - - if (!(bal::starts_with(info.id, "MS") || - bal::starts_with(info.id, "UO"))) continue; - - // insert name - insert(info.name, *cvid); - - // insert synonyms - if (*cvid < 100000000) // prefix == "MS" - { - for (vector::const_iterator syn=info.exactSynonyms.begin(); - syn!=info.exactSynonyms.end(); ++syn) - insert(*syn, *cvid); - } - } -} - - -void CVTranslator::Impl::insertDefaultExtraEntries() -{ - for (const ExtraEntry* it=defaultExtraEntries_; - it!=defaultExtraEntries_+defaultExtraEntriesSize_; ++it) - insert(it->text, it->cvid); -} - - -// -// CVTranslator -// - - -PWIZ_API_DECL CVTranslator::CVTranslator() : impl_(new Impl) {} -PWIZ_API_DECL void CVTranslator::insert(const string& text, CVID cvid) {impl_->insert(text, cvid);} -PWIZ_API_DECL CVID CVTranslator::translate(const string& text) const {return impl_->translate(text);} - - -} // namespace data -} // namespace pwiz - +// +// $Id$ +// +// +// Original author: Darren Kessner +// +// Copyright 2008 Spielberg Family Center for Applied Proteomics +// Cedars-Sinai Medical Center, Los Angeles, California 90048 +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. +// +// + + +#define PWIZ_SOURCE + +#include "CVTranslator.hpp" +#include "boost/algorithm/string/predicate.hpp" +#include "pwiz/utility/misc/Std.hpp" + + +namespace pwiz { +namespace data { + + +using namespace pwiz::cv; + + +// +// default extra translations +// + + +namespace { + +struct ExtraEntry +{ + const char* text; + CVID cvid; +}; + +ExtraEntry defaultExtraEntries_[] = +{ + {"ITMS", MS_ion_trap}, + {"FTMS", MS_FT_ICR}, +}; + +size_t defaultExtraEntriesSize_ = sizeof(defaultExtraEntries_)/sizeof(ExtraEntry); + +} // namespace + + +// +// CVTranslator::Impl +// + + +class CVTranslator::Impl +{ + public: + + Impl(); + void insert(const string& text, CVID cvid); + CVID translate(const string& text) const; + + private: + + typedef map Map; + Map map_; + + void insertCVTerms(); + void insertDefaultExtraEntries(); +}; + + +CVTranslator::Impl::Impl() +{ + insertCVTerms(); + insertDefaultExtraEntries(); +} + + +namespace { + + +inline char alnum_lower(char c) +{ + // c -> lower-case, whitespace, or + + return isalnum(c) ? static_cast(tolower(c)) : c == '+' ? c : ' '; +} + +inline char alnum_lower_regex(char c) +{ + // c -> lower-case, whitespace, +, or _ for things that appear to be part of a regex + return isalnum(c) ? static_cast(tolower(c)) : c == '+' ? c : '_'; +} + +string preprocess(const string& s) +{ + string result = s; + if (bal::starts_with(s, "(?<=")) // Looks like a regex + { + transform(result.begin(), result.end(), result.begin(), alnum_lower_regex); + } + else + { + transform(result.begin(), result.end(), result.begin(), alnum_lower); + } + return result; +} + + +string canonicalize(const string& s) +{ + // remove non-alnum characters + istringstream iss(preprocess(s)); + + // remove whitespace around tokens + vector tokens; + copy(istream_iterator(iss), istream_iterator(), back_inserter(tokens)); + + // concatenate with underscores + ostringstream oss; + copy(tokens.begin(), tokens.end(), ostream_iterator(oss, "_")); + + return oss.str(); +} + + +} // namespace + + +bool shouldIgnore(const string& key, CVID value, CVID cvid) +{ + return (key=="unit_" && value==MS_unit_OBSOLETE && cvid==UO_unit || + key=="pi_" && value==MS_PI && cvid==UO_pi || // MS_PI==photoionization, UO_pi==3.14 + key=="pi_" && value==MS_PI && cvid==MS_pI || // MS_pI==isoelectric point + key=="de_" && value==MS_DE && cvid==1001274 || // conflict between 1000246 and 1001274 + cvid == UO_volt_second_per_square_centimeter); // conflict between 1002814 200010007 (volt-second per square centimeter) +} + + +bool shouldReplace(const string& key, CVID value, CVID cvid) +{ + return false; +} + + +void CVTranslator::Impl::insert(const string& text, CVID cvid) +{ + string key = canonicalize(text); + + if (map_.count(key)) + { + if (shouldIgnore(key, map_[key], cvid)) + return; + + if (map_[key] == cvid) // ignore exact synonyms that only differ before canonicalization + return; + + if (!shouldReplace(key, map_[key], cvid)) + { + throw runtime_error("[CVTranslator::insert()] Collision: " + key + " " + + lexical_cast(map_[key]) + " " + + lexical_cast(cvid)); + } + } + + map_[key] = cvid; +} + + +CVID CVTranslator::Impl::translate(const string& text) const +{ + Map::const_iterator it = map_.find(canonicalize(text)); + if (it != map_.end()) + return it->second; + return CVID_Unknown; +} + + +void CVTranslator::Impl::insertCVTerms() +{ + for (vector::const_iterator cvid=cvids().begin(); cvid!=cvids().end(); ++cvid) + { + const CVTermInfo& info = cvTermInfo(*cvid); + + if (info.isObsolete) continue; + + if (!(bal::starts_with(info.id, "MS") || + bal::starts_with(info.id, "UO"))) continue; + + // insert name + insert(info.name, *cvid); + + // insert synonyms + if (*cvid < 100000000) // prefix == "MS" + { + for (vector::const_iterator syn=info.exactSynonyms.begin(); + syn!=info.exactSynonyms.end(); ++syn) + insert(*syn, *cvid); + } + } +} + + +void CVTranslator::Impl::insertDefaultExtraEntries() +{ + for (const ExtraEntry* it=defaultExtraEntries_; + it!=defaultExtraEntries_+defaultExtraEntriesSize_; ++it) + insert(it->text, it->cvid); +} + + +// +// CVTranslator +// + + +PWIZ_API_DECL CVTranslator::CVTranslator() : impl_(new Impl) {} +PWIZ_API_DECL void CVTranslator::insert(const string& text, CVID cvid) {impl_->insert(text, cvid);} +PWIZ_API_DECL CVID CVTranslator::translate(const string& text) const {return impl_->translate(text);} + + +} // namespace data +} // namespace pwiz + diff --git a/src/pwiz/data/common/CVTranslator.hpp b/src/pwiz/data/common/CVTranslator.hpp index 57d6b6552..c08b63111 100644 --- a/src/pwiz/data/common/CVTranslator.hpp +++ b/src/pwiz/data/common/CVTranslator.hpp @@ -1,66 +1,66 @@ -// -// $Id$ -// -// -// Original author: Darren Kessner -// -// Copyright 2008 Spielberg Family Center for Applied Proteomics -// Cedars-Sinai Medical Center, Los Angeles, California 90048 -// -// Licensed under the Apache License, Version 2.0 (the "License"); -// you may not use this file except in compliance with the License. -// You may obtain a copy of the License at -// -// http://www.apache.org/licenses/LICENSE-2.0 -// -// Unless required by applicable law or agreed to in writing, software -// distributed under the License is distributed on an "AS IS" BASIS, -// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -// See the License for the specific language governing permissions and -// limitations under the License. -// -// - - -#ifndef _CVTRANSLATOR_HPP_ -#define _CVTRANSLATOR_HPP_ - - -#include "pwiz/utility/misc/Export.hpp" -#include "cv.hpp" -#include "boost/shared_ptr.hpp" - - -namespace pwiz { -namespace data { - - -/// translates text to CV terms -class PWIZ_API_DECL CVTranslator -{ - public: - - /// constructor -- dictionary includes all - /// CV term names and exact_synonyms - CVTranslator(); - - /// insert a text-cvid pair into the dictionary - void insert(const std::string& text, cv::CVID cvid); - - /// translate text -> CVID - cv::CVID translate(const std::string& text) const; - - private: - class Impl; - boost::shared_ptr impl_; - CVTranslator(CVTranslator&); - CVTranslator& operator=(CVTranslator&); -}; - - -} // namespace data -} // namespace pwiz - - -#endif // _CVTRANSLATOR_HPP_ - +// +// $Id$ +// +// +// Original author: Darren Kessner +// +// Copyright 2008 Spielberg Family Center for Applied Proteomics +// Cedars-Sinai Medical Center, Los Angeles, California 90048 +// +// Licensed under the Apache License, Version 2.0 (the "License"); +// you may not use this file except in compliance with the License. +// You may obtain a copy of the License at +// +// http://www.apache.org/licenses/LICENSE-2.0 +// +// Unless required by applicable law or agreed to in writing, software +// distributed under the License is distributed on an "AS IS" BASIS, +// WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +// See the License for the specific language governing permissions and +// limitations under the License. +// +// + + +#ifndef _CVTRANSLATOR_HPP_ +#define _CVTRANSLATOR_HPP_ + + +#include "pwiz/utility/misc/Export.hpp" +#include "cv.hpp" +#include "boost/shared_ptr.hpp" + + +namespace pwiz { +namespace data { + + +/// translates text to CV terms +class PWIZ_API_DECL CVTranslator +{ + public: + + /// constructor -- dictionary includes all + /// CV term names and exact_synonyms + CVTranslator(); + + /// insert a text-cvid pair into the dictionary + void insert(const std::string& text, cv::CVID cvid); + + /// translate text -> CVID + cv::CVID translate(const std::string& text) const; + + private: + class Impl; + boost::shared_ptr impl_; + CVTranslator(CVTranslator&); + CVTranslator& operator=(CVTranslator&); +}; + + +} // namespace data +} // namespace pwiz + + +#endif // _CVTRANSLATOR_HPP_ + diff --git a/src/pwiz/data/common/cv.cpp b/src/pwiz/data/common/cv.cpp index 4a0120e96..8273ddac1 100644 --- a/src/pwiz/data/common/cv.cpp +++ b/src/pwiz/data/common/cv.cpp @@ -117,6 +117,7 @@ const TermInfo termInfos_[] = {NCIT_Property_or_Attribute, "NCIT:0320189", "Property or Attribute", "A distinguishing quality or prominent aspect of a person, object, action, process, or substance.", false}, {NCIT_Temporal_Qualifier, "NCIT:0321514", "Temporal Qualifier", "Terms used to indicate units of time or other terms associated with time.", false}, {NCIT_Duration, "NCIT:0325330", "Duration", "The period of time during which something continues.", false}, + {NCIT_Number, "NCIT:0325337", "Number", "A numeral or string of numerals expressing value, quantity, or identification.", false}, {NCIT_Action, "NCIT:0325404", "Action", "A thing done.", false}, {NCIT_Characteristic, "NCIT:0325447", "Characteristic", "The distinguishing qualities or prominent aspect of a person, object, action, process, or substance.", false}, {NCIT_Qualifier, "NCIT:0341009", "Qualifier", "A term that helps define and render a concept unique.", false}, @@ -157,7 +158,7 @@ const TermInfo termInfos_[] = {MS_vendor_OBSOLETE, "MS:1000030", "vendor", "Name of instrument vendor.", true}, {MS_instrument_model, "MS:1000031", "instrument model", "Instrument model name not including the vendor's name.", false}, {MS_customization, "MS:1000032", "customization", "Free text description of a single customization made to the instrument; for several modifications, use several entries.", false}, - {MS_deisotoping, "MS:1000033", "deisotoping", "The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution.", false}, + {MS_deisotoping, "MS:1000033", "deisotoping", "The removal of isotope peaks to represent the ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution.", false}, {MS_charge_deconvolution, "MS:1000034", "charge deconvolution", "The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions.", false}, {MS_peak_picking, "MS:1000035", "peak picking", "Spectral peak processing conducted on the acquired data to convert profile data to centroided data.", false}, {MS_scan_mode_OBSOLETE, "MS:1000036", "scan mode", "OBSOLETE.", true}, @@ -460,7 +461,7 @@ const TermInfo termInfos_[] = {MS_Linked_Scan_at_Constant_B_1__E_E0___1_2___E_OBSOLETE, "MS:1000333", "Linked Scan at Constant B[1-(E/E0)]^1/2 / E", "A linked scan performed on a sector instrument that incorporates at least one electric sector plus one magnetic sector placed in either order. The accelerating voltage is fixed while scanning the magnetic field, B, and electric field, E, simultaneously, so as to maintain the quantity B[1-(E/E0)]1/2/E at a constant value. This linked scan records a constant neutral mass loss (or gain) spectrum of dissociation or other reactions occurring in a field free region preceding the two sectors. E0 is the electric field required to transmit the singly charged analog of the desired neutral fragment. The term B[1-(E/E0)]1/2/E linked scan.", true}, {MS_MS_MS_in_Time_OBSOLETE, "MS:1000334", "MS/MS in Time", "A tandem mass spectrometry method in which product ion spectra are recorded in a single m/z analyzer (such as a Paul Ion Trap or FTMS) in discreet steps over time. Ions in a specific m/z range are selected, dissociated, and the product ions analyzed sequentially in time.", true}, {MS_MS_MS_in_Space_OBSOLETE, "MS:1000335", "MS/MS in Space", "A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition.", true}, - {MS_neutral_loss, "MS:1000336", "neutral loss", "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID: 21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type).", false}, + {MS_neutral_loss, "MS:1000336", "neutral loss", "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID:21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type).", false}, {MS_nth_generation_product_ion_OBSOLETE, "MS:1000337", "nth generation product ion", "Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated.", true}, {MS_nth_generation_product_ion_scan_OBSOLETE, "MS:1000338", "nth generation product ion scan", "The specific scan functions or processes that record the appropriate generation of product ion or ions of any m/z selected precursor ions.", true}, {MS_nth_generation_product_ion_spectrum_OBSOLETE, "MS:1000339", "nth generation product ion spectrum", "The mass spectrum recorded from any mass spectrometer in which the appropriate scan function can be set to record the appropriate generation product ion or ions of m/z selected precursor ions.", true}, @@ -518,6 +519,7 @@ const TermInfo termInfos_[] = {MS_ion_pair_formation_OBSOLETE, "MS:1000391", "ion-pair formation", "The reaction of a molecule to form both a positive ion and negative ion fragment among the products.", true}, {MS_ionization_efficiency, "MS:1000392", "ionization efficiency", "The ratio of the number of ions formed to the number of electrons, molecules or photons used.", false}, {MS_laser_desorption_ionization, "MS:1000393", "laser desorption ionization", "The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material.", false}, + {MS_no_sequence_database, "MS:1000394", "no sequence database", "No reference sequence database was used in the search process to determine the identified peptide sequence, for example as with de novo sequencing.", false}, {MS_liquid_secondary_ionization, "MS:1000395", "liquid secondary ionization", "The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization.", false}, {MS_membrane_inlet, "MS:1000396", "membrane inlet", "A semi-permeable membrane separator that permits the passage of gas sample directly to the mass spectrometer ion source.", false}, {MS_microelectrospray, "MS:1000397", "microelectrospray", "Electrospray ionization at a solvent flow rate of 300-800 nL/min where the flow is a result of a mechanical pump. See nanoelectrospray.", false}, @@ -783,6 +785,7 @@ const TermInfo termInfos_[] = {MS_QSTAR_XL, "MS:1000657", "QSTAR XL", "Applied Biosystems|MDS SCIEX QSTAR XL.", false}, {MS_4800_Proteomics_Analyzer, "MS:1000658", "4800 Proteomics Analyzer", "Applied Biosystems|MDS SCIEX 4800 Proteomics Analyzer.", false}, {MS_4000_Series_Explorer_Software, "MS:1000659", "4000 Series Explorer Software", "SCIEX or Applied Biosystems software for data acquisition and analysis.", false}, + {MS_Xevo_MRT_MS, "MS:1000660", "Xevo MRT MS", "Waters Corporation Xevo MRT Mass Spectrometer.", false}, {MS_GPS_Explorer, "MS:1000661", "GPS Explorer", "SCIEX or Applied Biosystems software for data acquisition and analysis.", false}, {MS_LightSight_Software, "MS:1000662", "LightSight Software", "SCIEX or Applied Biosystems|MDS SCIEX software metabolite identification.", false}, {MS_ProteinPilot_Software, "MS:1000663", "ProteinPilot Software", "SCIEX or Applied Biosystems|MDS SCIEX software for protein ID and quant.", false}, @@ -952,6 +955,7 @@ const TermInfo termInfos_[] = {MS_isolation_window_target_m_z, "MS:1000827", "isolation window target m/z", "The primary or reference m/z about which the isolation window is defined.", false}, {MS_isolation_window_lower_offset, "MS:1000828", "isolation window lower offset", "The extent of the isolation window in m/z below the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z.", false}, {MS_isolation_window_upper_offset, "MS:1000829", "isolation window upper offset", "The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z.", false}, + {MS_precision, "MS:1000830", "precision", "Precision is the degree of how close repeated measurements are to each other. This can, for example, be expressed using the standard deviation.", false}, {MS_sample_preparation, "MS:1000831", "sample preparation", "Properties of the preparation steps which took place before the measurement was performed.", false}, {MS_MALDI_matrix_application, "MS:1000832", "MALDI matrix application", "Attributes to describe the technique how the sample is prepared with the matrix solution.", false}, {MS_matrix_application_type, "MS:1000833", "matrix application type", "Describes the technique how the matrix is put on the sample target.", false}, @@ -989,7 +993,7 @@ const TermInfo termInfos_[] = {MS_empirical_formula, "MS:1000865", "empirical formula", "A chemical formula which expresses the proportions of the elements present in a substance.", false}, {MS_molecular_formula, "MS:1000866", "molecular formula", "A chemical compound formula expressing the number of atoms of each element present in a compound, without indicating how they are linked.", false}, {MS_structural_formula, "MS:1000867", "structural formula", "A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other.", false}, - {MS_SMILES_formula, "MS:1000868", "SMILES formula", "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.", false}, + {MS_SMILES_string, "MS:1000868", "SMILES string", "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string.", false}, {MS_collision_gas_pressure, "MS:1000869", "collision gas pressure", "The gas pressure of the collision gas used for collisional excitation.", false}, {MS_4000_QTRAP_OBSOLETE, "MS:1000870", "4000 QTRAP", "SCIEX or Applied Biosystems|MDS SCIEX QTRAP 4000.", true}, {MS_SRM_software, "MS:1000871", "SRM software", "Software used to predict, select, or optimize transitions or analyze the results of selected reaction monitoring runs.", false}, @@ -2725,6 +2729,8 @@ const TermInfo termInfos_[] = {MS_list_of_integers, "MS:1002712", "list of integers", "A list of xsd:integer.", false}, {MS_list_of_floats, "MS:1002713", "list of floats", "A list of xsd:float.", false}, {MS_FLASHDeconv, "MS:1002714", "FLASHDeconv", "Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics.", false}, + {MS_temperature_chromatogram, "MS:1002715", "temperature chromatogram", "Representation of temperature versus time.", false}, + {MS_measured_element, "MS:1002716", "measured element", "The component or dimension of an object being measured, for example the temperature of an instrument component over time.", false}, {MS_Pegasus_BT, "MS:1002719", "Pegasus BT", "LECO bench-top GC time-of-flight mass spectrometer.", false}, {MS_MSPathFinder, "MS:1002720", "MSPathFinder", "PNNL top-down/bottom-up analysis software for identifying peptides and proteoforms in fragmentation mass spectra.", false}, {MS_MSPathFinder_SpecEValue, "MS:1002721", "MSPathFinder:SpecEValue", "MSPathFinder spectral E-value.", false}, @@ -3107,7 +3113,7 @@ const TermInfo termInfos_[] = {MS_MaxQuant_DIA_PEP, "MS:1003101", "MaxQuant-DIA PEP", "PSM evidence PEP probability from MaxQuant-DIA algorithm.", false}, {MS_NIST_msp_comment, "MS:1003102", "NIST msp comment", "Term for a comment field withing the NIST msp file format", false}, {MS_ion_annotation_format, "MS:1003103", "ion annotation format", "Annotation format used for annotating individual spectrum ion peaks.", false}, - {MS_peptide_ion_annotation_format, "MS:1003104", "peptide ion annotation format", "Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions.", false}, + {MS_mzPAF_peptide_ion_annotation_format, "MS:1003104", "mzPAF peptide ion annotation format", "Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions.", false}, {MS_crosslinked_peptide_ion_annotation_format, "MS:1003105", "crosslinked peptide ion annotation format", "Annotation format designed specifically for crosslinked peptide ion peaks.", false}, {MS_glycan_ion_annotation_format, "MS:1003106", "glycan ion annotation format", "Annotation format designed specifically for glycan ion peaks.", false}, {MS_lipid_ion_annotation_format, "MS:1003107", "lipid ion annotation format", "Annotation format designed specifically for lipid ion peaks.", false}, @@ -3329,11 +3335,11 @@ const TermInfo termInfos_[] = {MS_Lipid_shorthand_identification_confidence___Complete_structure, "MS:1003326", "Lipid shorthand identification confidence - Complete structure", "Lipid shorthand identification confidence level 'Complete structure'.", false}, {MS_number_of_identified_protein_groups, "MS:1003327", "number of identified protein groups", "The number of protein groups that pass the threshold to be considered identified with sufficient confidence.", false}, {MS_number_of_identified_proteoforms, "MS:1003328", "number of identified proteoforms", "The number of proteoforms that pass the threshold to be considered identified with sufficient confidence.", false}, - {MS_loop_link_spectrum_identification_item, "MS:1003329", "loop-link spectrum identification item", "Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a loop-link.", false}, + {MS_looplink_spectrum_identification_item, "MS:1003329", "looplink spectrum identification item", "Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a looplink.", false}, {MS_noncovalently_associated_peptides_search, "MS:1003330", "noncovalently associated peptides search", "Noncovalently associated peptides search performed. Noncovalently associated peptides are two different peptides which were not crosslinked but stayed associated with each other throughout the workflow, due to noncovalent interactions.", false}, {MS_noncovalently_associated_peptides_spectrum_identification_item, "MS:1003331", "noncovalently associated peptides spectrum identification item", "Noncovalently associated peptides spectrum identification item.", false}, {MS_identification_based_on_multiple_spectra, "MS:1003332", "identification based on multiple spectra", "Provides an identifier to encode identifications based on multiple spectra.", false}, - {MS_regular_expression_for_encoding_identifications_based_on_multiple_spectra_, "MS:1003333", "regular expression for encoding identifications based on multiple spectra.", "^(?[0-9]+)(?::(?P|C))$", false}, + {MS_regular_expression_for_encoding_identifications_based_on_multiple_spectra_, "MS:1003333", "regular expression for encoding identifications based on multiple spectra.", "^(?[0-9]+)(?::(?P|C))?$", false}, {MS_parent_term_for_PSM_level_scores_for_identifications_based_on_multiple_spectra, "MS:1003334", "parent term for PSM-level scores for identifications based on multiple spectra", "Parent term for PSM-level scores for identifications based on multiple spectra.", false}, {MS_regular_expression_for_PSM_level_scores_for_identifications_based_on_multiple_spectra, "MS:1003335", "regular expression for PSM-level scores for identifications based on multiple spectra", "^(?[0-9]+):(?[-+]?[0-9]+(?:[.][0-9]+)?(?:[Ee][-+]?[0-9]+))$", false}, {MS_posterior_error_probability_from_identification_based_on_multiple_spectra, "MS:1003336", "posterior error probability from identification based on multiple spectra", "PEP score for identifications based on multiple spectra.", false}, @@ -3357,6 +3363,61 @@ const TermInfo termInfos_[] = {MS_middle_down_proteomics, "MS:1003354", "middle-down proteomics", "study of proteins via the use of mass spectrometers to measure the masses and abundances of large protein fragments after partial digestion of denatured proteins.", false}, {MS_bottom_up_proteomics, "MS:1003355", "bottom-up proteomics", "study of proteins via the use of mass spectrometers to measure the masses and abundances of peptides after complete digestion of denatured proteins.", false}, {MS_Orbitrap_Ascend, "MS:1003356", "Orbitrap Ascend", "Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers.", false}, + {MS_ANN_SoLo, "MS:1003357", "ANN-SoLo", "ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up open modification searching by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate and the shifted dot product score to sensitively match modified spectra to their unmodified counterpart.", false}, + {MS_XCorr_rank, "MS:1003358", "XCorr rank", "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the XCorr score.", false}, + {MS_exact_p_value, "MS:1003359", "exact p-value", "A p-value for the XCorr score, calculated using dynamic programming.", false}, + {MS_refactored_XCorr, "MS:1003360", "refactored XCorr", "A modified version of the XCorr score that is made amenable to dynamic programming calculation of p-values by changing a max operation to a sum.", false}, + {MS_res_ev_score, "MS:1003361", "res-ev score", "The residue-evidence (res-ev) score measures the quality of a match between a peptide and observed spectrum using a method similar to XCorr, but considering all pairs of observed peaks.", false}, + {MS_res_ev_rank, "MS:1003362", "res-ev rank", "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the res-ev score.", false}, + {MS_res_ev_p_value, "MS:1003363", "res-ev p-value", "The residue-evidence p-value is computed from the residue-evidence score using a dynamic programming procedure.", false}, + {MS_combined_p_value, "MS:1003364", "combined p-value", "A p-value that is computed by taking the product of the exact p-value and the res-ev p-value and then adjusting for dependencies between them.", false}, + {MS_combined_p_value_rank, "MS:1003365", "combined p-value rank", "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the combined p-value.", false}, + {MS_tailor_score, "MS:1003366", "tailor score", "A calibrated version of the XCorr score, computed by dividing the XCorr by the 99th percentile of the distribution of all scores for a particular spectrum.", false}, + {MS_monoisotopic_mass_deisotoping, "MS:1003367", "monoisotopic mass deisotoping", "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's monoisotopic mass. It is done in conjunction with the charge state deconvolution.", false}, + {MS_most_abundant_mass_deisotoping, "MS:1003368", "most abundant mass deisotoping", "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's most abundant isotopic mass. It is done in conjunction with the charge state deconvolution.", false}, + {MS_average_mass_deisotoping, "MS:1003369", "average mass deisotoping", "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's average mass. It is done in conjunction with the charge state deconvolution.", false}, + {MS_reduction_to_summed_singly_charged_peak_list, "MS:1003370", "reduction to summed singly charged peak list", "The summing of peaks corresponding to the same mass at multiple charge states and presented as singly charged m/z.", false}, + {MS_SelexION_compensation_voltage, "MS:1003371", "SelexION compensation voltage", "The voltage applied in the SelexION device to allow certain ions to transmit through to the mass spectrometer.", false}, + {MS_specification_document_extension_version, "MS:1003372", "specification document extension version", "The versioning of a an extension to a specification document that the current file requires to be read correctly. The version should encode the name of the extension, and some ordinal expression of its revision, preferably in semantic versioning notation. Signals that readers that do not know this extension should return an appropriately informative error if they do not think they can or should try to interpret the file.", false}, + {MS_mzIdentML_extension_version, "MS:1003373", "mzIdentML extension version", "The versioning of an mzIdentML extension document.", false}, + {MS_Open_Chromatography_Binary_OCB_format, "MS:1003374", "Open Chromatography Binary OCB format", "ChemClipse/OpenChrom file format.", false}, + {MS_Conversion_to_OCB, "MS:1003375", "Conversion to OCB", "Conversion of a file format to Open Chromatography Binary OCB file format.", false}, + {MS_ChemClipse, "MS:1003376", "ChemClipse", "ChemClipse is part of the Eclipse Science project. Primarily developed by Lablicate GmbH.", false}, + {MS_OpenChrom, "MS:1003377", "OpenChrom", "OpenChrom is an Open Source software for data processing and analysis. Based upon Eclipse ChemClipse.", false}, + {MS_Orbitrap_Astral, "MS:1003378", "Orbitrap Astral", "Thermo Scientific Orbitrap Astral mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral analyzer.", false}, + {MS_asymmetric_track_lossless_time_of_flight_analyzer, "MS:1003379", "asymmetric track lossless time-of-flight analyzer", "A TOF-like mass analyzer with asymmetric ion mirrors to direct ions into transversal asymmetric oscillations and ion foil shapes and maintains ion packet for transmission and resolution.", false}, + {MS_Xevo_G3_QTof, "MS:1003380", "Xevo G3 QTof", "Waters Corporation Xevo G3 QTof quadrupole time-of-flight mass spectrometer.", false}, + {MS_ACQUITY_RDa_Detector, "MS:1003381", "ACQUITY RDa Detector", "Waters Corporation RDa time-of-flight mass detector.", false}, + {MS_waters_connect, "MS:1003382", "waters_connect", "Waters Corporation waters_connect software for liquid chromatography and mass spectrometry acquisition and processing.", false}, + {MS_timsTOF_Ultra, "MS:1003383", "timsTOF Ultra", "Bruker Daltonics' timsTOF Ultra.", false}, + {MS_semantic_version_regexp, "MS:1003384", "semantic version regexp", "v?(\\d+)\\.(\\d+)\\.(\\d+)(?:-(\\S+))?", false}, + {MS_mzIdentML_crosslinking_extension_document_version, "MS:1003385", "mzIdentML crosslinking extension document version", "The versioning of the crosslinking mzIdentML extension document.", false}, + {MS_Spectra, "MS:1003386", "Spectra", "Bioconductor package Spectra for mass spectrometry data representation and processing.", false}, + {MS_MetaboAnnotation, "MS:1003387", "MetaboAnnotation", "Bioconductor package MetaboAnnotation for annotation of untargeted metabolomics data.", false}, + {MS_CompoundDb, "MS:1003388", "CompoundDb", "Bioconductor package CompoundDb for creation, usage and maintenance of public or library-specific annotation databases and spectra libraries.", false}, + {MS_mzTab_M, "MS:1003389", "mzTab-M", "Expanded tabular result format for metabolomics experiments reporting quantitative summary data, MS features and identification evidence.", false}, + {MS_crosslinker_cleavage_characteristics, "MS:1003390", "crosslinker cleavage characteristics", "Signifies that the crosslinker is cleavable and on cleavage can leave a given stub. The pattern specifies three slots ::.", false}, + {MS_crosslinker_cleavage_regular_expression, "MS:1003391", "crosslinker cleavage regular expression", "^(?[A-Za-z]):(?[+-]?[0-9]+(\\.[0-9]+)?([eE][+-]?[0-9]+(\\.[0-9]+)?)?):(?[A-Za-z]+)$", false}, + {MS_search_modification_id, "MS:1003392", "search modification id", "A unique identifier within an in mzIdentML document denoting a search modification rule. The same modification may be present multiple times with different id values to reflect different specificities or neutral losses.", false}, + {MS_search_modification_id_ref, "MS:1003393", "search modification id ref", "A reference to a `search modification id` in the current mzIdentML document that defines the properties of this modification instance.", false}, + {MS_SelexION_separation_voltage, "MS:1003394", "SelexION separation voltage", "RF voltage applied in the SelexION device to separate ions in trajectory based on the difference in their mobility between the high field and low field portions of the applied RF.", false}, + {MS_Q_Exactive_GC_Orbitrap, "MS:1003395", "Q Exactive GC Orbitrap", "Q Exactive GC Orbitrap GC-MS/MS hybrid quadrupole Orbitrap mass spectrometer.", false}, + {MS_8890_GC_MS, "MS:1003396", "8890 GC/MS", "Agilent 8890 Gas Chromatograph System.", false}, + {MS_timsTOF_fleX_MALDI_2, "MS:1003397", "timsTOF fleX MALDI-2", "Bruker Daltonics' timsTOF fleX MALDI-2.", false}, + {MS_deconvoluted_data, "MS:1003398", "deconvoluted data", "The data contained in this file have been processed to remove, collapse, or label one or more dimensions of the original dataset, such as charge deconvolution or ion mobility deconvolution. To determine the type of deconvolution done, the reader should consult the appropriate section of the file, such as the data processing methods in an mzML file.", false}, + {MS_quality_control_software, "MS:1003399", "quality control software", "Software that creates or manipulates QC-related data.", false}, + {MS_rmzqc, "MS:1003400", "rmzqc", "An R package for reading, validating, and writing mzQC files.", false}, + {MS_jmzqc, "MS:1003401", "jmzqc", "A Java package for reading, validating, and writing mzQC files.", false}, + {MS_pymzqc, "MS:1003402", "pymzqc", "A Python package for reading, validating, and writing mzQC files.", false}, + {MS_InChI, "MS:1003403", "InChI", "IUPAC International Chemical Identifier.", false}, + {MS_timsTOF_HT, "MS:1003404", "timsTOF HT", "Bruker Daltonics' timsTOF HT.", false}, + {MS_mzRecal, "MS:1003405", "mzRecal", "MS1 recalibration using identified peptides as internal calibrants.", false}, + {MS_spectrum_clustering_software, "MS:1003406", "spectrum clustering software", "Software designed to group multiple mass spectra by high similarity, generally with the goal of grouping replicate spectra derived from the same analyte.", false}, + {MS_Scout, "MS:1003407", "Scout", "Identifying crosslinked peptides in complex protein mixtures", false}, + {MS_Scout_score, "MS:1003408", "Scout score", "Scout identification search engine score", false}, + {MS_Stellar, "MS:1003409", "Stellar", "Thermo Scientific Stellar mass spectrometer contains a quadrupole mass filter, a collision cell, and a quadrupole linear ion trap mass analyzer.", false}, + {MS_electron_beam_energy, "MS:1003410", "electron beam energy", "The kinetic energy of the electron beam used in dissociation methods induced by a free electron beam, such as electron-capture dissociation (ECD), electron-detachment dissociation (EDD), and electron-activated dissociation (EAD).", false}, + {NCIT_Number_of_Occurrences, "NCIT:3150827", "Number of Occurrences", "The number of times something happened.", false}, {MS_PSI_MS_CV_Quality_Control_Vocabulary, "MS:4000000", "PSI-MS CV Quality Control Vocabulary", "PSI Quality Control controlled vocabulary term.", false}, {MS_QC_metric, "MS:4000001", "QC metric", "Parent term for QC metrics, each metric MUST have this as an ancestor in its is_a relations.", false}, {MS_QC_metric_value_type, "MS:4000002", "QC metric value type", "The QC metric type describes what type the corresponding metric is. Possible types are single value, n-tuple, table, or matrix.", false}, @@ -3428,8 +3489,8 @@ const TermInfo termInfos_[] = {MS_batch_corrected_identified_MS1_feature_area_principal_component_analysis_result, "MS:4000094", "batch-corrected identified MS1 feature area principal component analysis result", "A table with the PCA results of identified MS1 feature areas after batch-correction.", false}, {MS_slowest_frequency_for_MS_level_1_collection, "MS:4000095", "slowest frequency for MS level 1 collection", "The slowest acquisition speed with which precursor MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used.", false}, {MS_slowest_frequency_for_MS_level_2_collection, "MS:4000096", "slowest frequency for MS level 2 collection", "The slowest acquisition speed with which product MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used.", false}, - {MS_MS1_signal_jump__10x__count, "MS:4000097", "MS1 signal jump (10x) count", "The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans. An unusual high count of signal jumps or falls can indicate ESI stability issues.", false}, - {MS_MS1_signal_fall__10x__count, "MS:4000098", "MS1 signal fall (10x) count", "The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans. An unusual high count of signal jumps or falls can indicate ESI stability issues.", false}, + {MS_MS1_signal_jump__10x__count, "MS:4000097", "MS1 signal jump (10x) count", "The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans.", false}, + {MS_MS1_signal_fall__10x__count, "MS:4000098", "MS1 signal fall (10x) count", "The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans.", false}, {MS_number_of_empty_MS1_scans, "MS:4000099", "number of empty MS1 scans", "Number of MS1 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks).", false}, {MS_number_of_empty_MS2_scans, "MS:4000100", "number of empty MS2 scans", "Number of MS2 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks).", false}, {MS_number_of_empty_MS3_scans, "MS:4000101", "number of empty MS3 scans", "Number of MS3 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks).", false}, @@ -3447,11 +3508,11 @@ const TermInfo termInfos_[] = {MS_MS2_peak_density_distribution_sigma, "MS:4000113", "MS2 peak density distribution sigma", "From the distribution of peak densities in MS2, the sigma value", false}, {MS_MS2_peak_density_distribution_low_outliers, "MS:4000114", "MS2 peak density distribution low outliers", "From the distribution of peak densities in MS2, the list of outliers below a in-file defined threshold", false}, {MS_MS2_peak_density_distribution_high_outliers, "MS:4000115", "MS2 peak density distribution high outliers", "From the distribution of peak densities in MS2, the list of outliers above a in-file defined threshold", false}, - {MS_precursor_intensity_distribution_quantiles, "MS:4000116", "precursor intensity distribution quantiles", "From the distribution of precursor intensities, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3", false}, - {MS_precursor_intensity_distribution_mean, "MS:4000117", "precursor intensity distribution mean", "From the distribution of precursor intensities, the mean", false}, - {MS_precursor_intensity_distribution_sigma, "MS:4000118", "precursor intensity distribution sigma", "From the distribution of precursor intensities, the sigma value", false}, - {MS_precursor_intensity_distribution_low_outliers, "MS:4000119", "precursor intensity distribution low outliers", "From the distribution of precursor intensities, the list of outliers below a in-file defined threshold", false}, - {MS_precursor_intensity_distribution_high_outliers, "MS:4000120", "precursor intensity distribution high outliers", "From the distribution of precursor intensities, the list of outliers above a in-file defined threshold", false}, + {MS_MS2_precursor_intensity_distribution, "MS:4000116", "MS2 precursor intensity distribution", "From the distribution of MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3.", false}, + {MS_MS2_precursor_intensity_distribution_mean, "MS:4000117", "MS2 precursor intensity distribution mean", "From the distribution of MS2 precursor intensities, the mean", false}, + {MS_MS2_precursor_intensity_distribution_sigma, "MS:4000118", "MS2 precursor intensity distribution sigma", "From the distribution of MS2 precursor intensities, the sigma value", false}, + {MS_MS2_precursor_intensity_distribution_low_outliers, "MS:4000119", "MS2 precursor intensity distribution low outliers", "From the distribution of precursor intensities, the list of outliers below a in-file defined threshold", false}, + {MS_MS2_precursor_intensity_distribution_high_outliers, "MS:4000120", "MS2 precursor intensity distribution high outliers", "From the distribution of precursor intensities, the list of outliers above a in-file defined threshold", false}, {MS_MS1_signal_to_noise_ratio_quantiles, "MS:4000121", "MS1 signal-to-noise ratio quantiles", "From the distribution of signal-to-noise ratio in MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3", false}, {MS_MS1_signal_to_noise_ratio_mean, "MS:4000122", "MS1 signal-to-noise ratio mean", "From the distribution of signal-to-noise ratio in MS1, the mean", false}, {MS_MS1_signal_to_noise_ratio_sigma, "MS:4000123", "MS1 signal-to-noise ratio sigma", "From the distribution of signal-to-noise ratio in MS1, the sigma value", false}, @@ -3473,13 +3534,46 @@ const TermInfo termInfos_[] = {MS_MS2_ion_collection_time_low_outliers, "MS:4000139", "MS2 ion collection time low outliers", "From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers below a in-file defined threshold", false}, {MS_MS2_ion_collection_time_high_outliers, "MS:4000140", "MS2 ion collection time high outliers", "From the distribution of ion injection times (MS:1000927) for MS2, the list of outliers above a in-file defined threshold", false}, {MS_outlier_threshold_criterion, "MS:4000141", "outlier threshold criterion", "The definition of the outlier criteria applied.", false}, - {MS_Tukey_s_fence, "MS:4000142", "Tukey's fence", "Defines outliers with Tukey's fence as <(Q1-x*IQR) for low outliers and >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5", false}, - {MS_Tukey_s_fence_high_outliers, "MS:4000143", "Tukey's fence high outliers", "Defines high outliers with Tukey's fence as >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5", false}, - {MS_Tukey_s_fence_low_outliers, "MS:4000144", "Tukey's fence low outliers", "Defines low outliers with Tukey's fence as <(Q1-x*IQR) for low outliers, where x is defined by the term's value. The default is x=1.5", false}, - {MS_Z_score_threshold, "MS:4000145", "Z-score threshold", "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3", false}, - {MS_Z_score_threshold_high_outliers, "MS:4000146", "Z-score threshold high outliers", "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3", false}, - {MS_Z_score_threshold_low_outliers, "MS:4000147", "Z-score threshold low outliers", "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3", false}, - {MS_algorithmical_threshold, "MS:4000148", "algorithmical threshold", "Defines outliers algorithmically, where a single value threshold might not be applicable or p.r.n. multivariate decision making is applied. The value of the term should name the algorithmical method used", false}, + {MS_Tukey_s_fence, "MS:4000142", "Tukey's fence", "Defines outliers with Tukey's fence as <(Q1-x*IQR) for low outliers and >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5.", false}, + {MS_Tukey_s_fence_high_outliers, "MS:4000143", "Tukey's fence high outliers", "Defines high outliers with Tukey's fence as >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5.", false}, + {MS_Tukey_s_fence_low_outliers, "MS:4000144", "Tukey's fence low outliers", "Defines low outliers with Tukey's fence as <(Q1-x*IQR) for low outliers, where x is defined by the term's value. The default is x=1.5.", false}, + {MS_Z_score_threshold, "MS:4000145", "Z-score threshold", "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3.", false}, + {MS_Z_score_threshold_high_outliers, "MS:4000146", "Z-score threshold high outliers", "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3.", false}, + {MS_Z_score_threshold_low_outliers, "MS:4000147", "Z-score threshold low outliers", "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3.", false}, + {MS_algorithmical_threshold, "MS:4000148", "algorithmical threshold", "Defines outliers algorithmically, where a single value threshold might not be applicable or p.r.n. multivariate decision making is applied. The value of the term should name the algorithmical method used.", false}, + {MS_iRT_calibration_formula, "MS:4000149", "iRT calibration formula", "A polynomial formula to calibrate retention time based on iRT reference peptides. The order of the values corresponds to polynomial terms. I.e. a linear equation is represented by a two-tuple consisting of (slope, intercept). More general, the position in the n_tuple indicates the power of `x`: position `n → x^0`, position `n - 1 → x^1`, position `n - 2 → x^2`, etc.", false}, + {MS_iRT_calibration_adjusted_r_squared, "MS:4000150", "iRT calibration adjusted r-squared", "The goodness of fit statistic between observed retention times and iRT calibrated retention times.", false}, + {MS_MsQuality, "MS:4000151", "MsQuality", "MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data.", false}, + {MS_MS2_precursor_median_m_z_of_identified_quantification_data_points, "MS:4000152", "MS2 precursor median m/z of identified quantification data points", "Median m/z value for MS2 precursors of all quantification data points after user-defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_interquartile_RT_period_for_identified_quantification_data_points, "MS:4000153", "interquartile RT period for identified quantification data points", "The interquartile retention time period, in seconds, for all quantification data points after user-defined acceptance criteria are applied over the complete run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_rate_of_the_interquartile_RT_period_for_identified_quantification_data_points, "MS:4000154", "rate of the interquartile RT period for identified quantification data points", "The rate of identified quantification data points for the interquartile retention time period, in identified quantification data points per second. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_area_under_TIC, "MS:4000155", "area under TIC", "The area under the total ion chromatogram.", false}, + {MS_area_under_TIC_RT_quantiles, "MS:4000156", "area under TIC RT quantiles", "The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple.", false}, + {MS_extent_of_identified_MS2_precursor_intensity, "MS:4000157", "extent of identified MS2 precursor intensity", "Ratio of 95th over 5th percentile of MS2 precursor intensity for all quantification data points after user-defined acceptance criteria are applied. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_median_of_TIC_values_in_the_RT_range_in_which_the_middle_half_of_quantification_data_points_are_identified, "MS:4000158", "median of TIC values in the RT range in which the middle half of quantification data points are identified", "Median of TIC values in the RT range in which half of quantification data points are identified (RT values of Q1 to Q3 of identifications). These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_median_of_TIC_values_in_the_shortest_RT_range_in_which_half_of_the_quantification_data_points_are_identified, "MS:4000159", "median of TIC values in the shortest RT range in which half of the quantification data points are identified", "Median of TIC values in the shortest RT range in which half of the quantification data points are identified. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_MS2_precursor_intensity_range, "MS:4000160", "MS2 precursor intensity range", "Minimum and maximum MS2 precursor intensity recorded.", false}, + {MS_identified_MS2_precursor_intensity_distribution, "MS:4000161", "identified MS2 precursor intensity distribution", "From the distribution of identified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_unidentified_MS2_precursor_intensity_distribution, "MS:4000162", "unidentified MS2 precursor intensity distribution", "From the distribution of unidentified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_identified_MS2_precursor_intensity_distribution_mean, "MS:4000163", "identified MS2 precursor intensity distribution mean", "From the distribution of identified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_unidentified_MS2_precursor_intensity_distribution_mean, "MS:4000164", "unidentified MS2 precursor intensity distribution mean", "From the distribution of unidentified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_identified_MS2_precursor_intensity_distribution_sigma, "MS:4000165", "identified MS2 precursor intensity distribution sigma", "From the distribution of identified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_unidentified_MS2_precursor_intensity_distribution_sigma, "MS:4000166", "unidentified MS2 precursor intensity distribution sigma", "From the distribution of unidentified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_ratio_of_1__over_2__of_all_MS2_known_precursor_charges, "MS:4000167", "ratio of 1+ over 2+ of all MS2 known precursor charges", "The ratio of 1+ over 2+ MS2 precursor charge count of all spectra.", false}, + {MS_ratio_of_1__over_2__of_identified_MS2_known_precursor_charges, "MS:4000168", "ratio of 1+ over 2+ of identified MS2 known precursor charges", "The ratio of 1+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_ratio_of_3__over_2__of_all_MS2_known_precursor_charges, "MS:4000169", "ratio of 3+ over 2+ of all MS2 known precursor charges", "The ratio of 3+ over 2+ MS2 precursor charge count of all spectra.", false}, + {MS_ratio_of_3__over_2__of_identified_MS2_known_precursor_charges, "MS:4000170", "ratio of 3+ over 2+ of identified MS2 known precursor charges", "The ratio of 3+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_ratio_of_4__over_2__of_all_MS2_known_precursor_charges, "MS:4000171", "ratio of 4+ over 2+ of all MS2 known precursor charges", "The ratio of 4+ over 2+ MS2 precursor charge count of all spectra.", false}, + {MS_ratio_of_4__over_2__of_identified_MS2_known_precursor_charges, "MS:4000172", "ratio of 4+ over 2+ of identified MS2 known precursor charges", "The ratio of 4+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_mean_MS2_precursor_charge_in_all_spectra, "MS:4000173", "mean MS2 precursor charge in all spectra", "Mean MS2 precursor charge in all spectra", false}, + {MS_mean_MS2_precursor_charge_in_identified_spectra, "MS:4000174", "mean MS2 precursor charge in identified spectra", "Mean MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_median_MS2_precursor_charge_in_all_spectra, "MS:4000175", "median MS2 precursor charge in all spectra", "Median MS2 precursor charge in all spectra", false}, + {MS_median_MS2_precursor_charge_in_identified_spectra, "MS:4000176", "median MS2 precursor charge in identified spectra", "Median MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability.", false}, + {MS_contaminant_protein_abundance_fraction, "MS:4000177", "contaminant protein abundance fraction", "The fraction of total protein abundance in a mass spectrometry run or a group of runs which can be attributed to a user-defined list of contaminant proteins (e.g. using the cRAP contaminant database).", false}, + {MS_precursor_ppm_deviation_mean, "MS:4000178", "precursor ppm deviation mean", "The mean of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied", false}, + {MS_precursor_ppm_deviation_sigma, "MS:4000179", "precursor ppm deviation sigma", "The standard deviation of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied", false}, + {MS_table_of_missed_cleavage_counts, "MS:4000180", "table of missed cleavage counts", "The number of identified peptides with corresponding number of missed cleavages after user-defined acceptance criteria are applied. The number of missed cleavages per peptide is given in the 'number of missed cleavages' column, the respective count of such peptides identified in the 'Number of Occurrences' column. The highest 'missed cleavages' row is to be interpreted as that number of missed cleavages or higher.", false}, + {MS_identified_MS2_quarter_RT_fraction, "MS:4000181", "identified MS2 quarter RT fraction", "The interval used for acquisition of the first, second, third, and fourth quarter of all identified MS2 events divided by retention time duration.", false}, {UNIMOD_unimod_root_node, "UNIMOD:0", "unimod root node", "The root node of the unimod modifications ontology.", false}, {UNIMOD_Acetyl, "UNIMOD:1", "Acetyl", "Acetylation.", false}, {UNIMOD_Amidated, "UNIMOD:2", "Amidated", "Amidation.", false}, @@ -4994,6 +5088,17 @@ const TermInfo termInfos_[] = {UNIMOD_Di_L_Gln_N___propargyl_L_Gln_desthiobiotin, "UNIMOD:2069", "Di_L-Gln_Nγ-propargyl-L-Gln_desthiobiotin", "Dimodification of L-Gln and Nγ-propargyl-L-Gln probe with clicked desthiobiotin-azide.", false}, {UNIMOD_L_Gln, "UNIMOD:2070", "L-Gln", "Monomodification with glutamine.", false}, {UNIMOD_Glyceroyl, "UNIMOD:2072", "Glyceroyl", "Glyceroylation.", false}, + {UNIMOD_N6pAMP, "UNIMOD:2073", "N6pAMP", "Plain N6-Propargyl-AMP modified proteins without any clicked enrichment tag.", false}, + {UNIMOD_DABCYL_C2_maleimide, "UNIMOD:2074", "DABCYL-C2-maleimide", "DABCYL-C2-maleimide Thiol-reactive dye for fluorescence labelling of proteins.", false}, + {UNIMOD_NBF, "UNIMOD:2079", "NBF", "Thiol blocking reagent.", false}, + {UNIMOD_DCP, "UNIMOD:2080", "DCP", "Dimedone-Based Chemical Probes.", false}, + {UNIMOD_Ethynyl, "UNIMOD:2081", "Ethynyl", "Ethynlation of cysteine residues.", false}, + {UNIMOD_QQTGG, "UNIMOD:2082", "QQTGG", "SUMOylation leaving QQTGG.", false}, + {UNIMOD_Pyro_QQTGG, "UNIMOD:2083", "Pyro-QQTGG", "SUMOylation leaving Pyro-QQTGG.", false}, + {UNIMOD_NQTGG, "UNIMOD:2084", "NQTGG", "SUMOylation leaving NQTGG.", false}, + {UNIMOD_DVFQQQTGG, "UNIMOD:2085", "DVFQQQTGG", "SUMOylation by Endogenous SUMO2/3 following Lys C and Asp-N serial digestion.", false}, + {UNIMOD_iST_NHS_specific_cysteine_modification, "UNIMOD:2086", "iST-NHS specific cysteine modification", "Preomics iST-NHS Kit specific cysteine modification.", false}, + {UNIMOD_Label_13C_2_15N_1_, "UNIMOD:2088", "Label:13C(2)15N(1)", "13C(2) 15N(1) Silac label.", false}, {UO_unit, "UO:0000000", "unit", "A unit of measurement is a standardized quantity of a physical quality.", false}, {UO_length_unit, "UO:0000001", "length unit", "A unit which is a standard measure of the distance between two points.", false}, {UO_mass_unit, "UO:0000002", "mass unit", "A unit which is a standard measure of the amount of matter/energy of a physical object.", false}, @@ -5463,6 +5568,7 @@ CVIDPair relationsIsA_[] = {NCIT_Statistical_Technique, NCIT_Technique}, {NCIT_Temporal_Qualifier, NCIT_Qualifier}, {NCIT_Duration, NCIT_Temporal_Qualifier}, + {NCIT_Number, NCIT_Property_or_Attribute}, {NCIT_Action, NCIT_Activity}, {NCIT_Characteristic, NCIT_Property_or_Attribute}, {NCIT_Qualifier, NCIT_Property_or_Attribute}, @@ -5719,6 +5825,7 @@ CVIDPair relationsIsA_[] = {MS_electron_ionization, MS_ionization_type}, {MS_ionization_efficiency, MS_source_attribute}, {MS_laser_desorption_ionization, MS_desorption_ionization}, + {MS_no_sequence_database, MS_database_file_formats}, {MS_liquid_secondary_ionization, MS_ionization_type}, {MS_membrane_inlet, MS_inlet_type}, {MS_microelectrospray, MS_electrospray_ionization}, @@ -5947,6 +6054,7 @@ CVIDPair relationsIsA_[] = {MS_4000_Series_Explorer_Software, MS_acquisition_software}, {MS_4000_Series_Explorer_Software, MS_analysis_software}, {MS_4000_Series_Explorer_Software, MS_data_processing_software}, + {MS_Xevo_MRT_MS, MS_Waters_instrument_model}, {MS_GPS_Explorer, MS_SCIEX_software}, {MS_GPS_Explorer, MS_acquisition_software}, {MS_GPS_Explorer, MS_analysis_software}, @@ -6203,6 +6311,7 @@ CVIDPair relationsIsA_[] = {MS_isolation_window_target_m_z, MS_isolation_window_attribute}, {MS_isolation_window_lower_offset, MS_isolation_window_attribute}, {MS_isolation_window_upper_offset, MS_isolation_window_attribute}, + {MS_precision, MS_mass_analyzer_attribute}, {MS_sample_preparation, MS_object_attribute}, {MS_matrix_solution, MS_MALDI_matrix_application}, {MS_matrix_solution_concentration, MS_MALDI_matrix_application}, @@ -6235,7 +6344,7 @@ CVIDPair relationsIsA_[] = {MS_empirical_formula, MS_chemical_formula}, {MS_molecular_formula, MS_chemical_formula}, {MS_structural_formula, MS_chemical_formula}, - {MS_SMILES_formula, MS_chemical_formula}, + {MS_SMILES_string, MS_structural_formula}, {MS_collision_gas_pressure, MS_precursor_activation_attribute}, {MS_4000_QTRAP_OBSOLETE, MS_SCIEX_instrument_model}, {MS_SRM_software, MS_software}, @@ -6734,6 +6843,7 @@ CVIDPair relationsIsA_[] = {MS_X_Tandem, MS_analysis_software}, {MS_SpectraST, MS_analysis_software}, {MS_SpectraST, MS_library_creation_software}, + {MS_SpectraST, MS_spectrum_clustering_software}, {MS_Mascot_Parser, MS_analysis_software}, {MS_null_terminated_ASCII_string, MS_binary_data_type}, {MS_SCIEX_TOF_TOF_nativeID_format, MS_native_spectrum_identifier_format}, @@ -6847,6 +6957,7 @@ CVIDPair relationsIsA_[] = {MS_Scaffold_Protein_Probability, MS_search_engine_specific_score_for_proteins}, {MS_SpectrumMill_Discriminant_Score, MS_PSM_level_search_engine_specific_statistic}, {MS_FAIMS_compensation_voltage, MS_ion_mobility_attribute}, + {MS_FAIMS_compensation_voltage, MS_ion_selection_attribute}, {MS_FAIMS_compensation_voltage, MS_peak_attribute}, {MS_XCMS, MS_analysis_software}, {MS_XCMS, MS_data_processing_software}, @@ -8019,6 +8130,7 @@ CVIDPair relationsIsA_[] = {MS_list_of_floats, MS_list_of_type}, {MS_FLASHDeconv, MS_analysis_software}, {MS_FLASHDeconv, MS_data_processing_software}, + {MS_temperature_chromatogram, MS_chromatogram_type}, {MS_Pegasus_BT, MS_LECO_instrument_model}, {MS_MSPathFinder, MS_analysis_software}, {MS_MSPathFinder_SpecEValue, MS_PSM_level_e_value}, @@ -8269,6 +8381,7 @@ CVIDPair relationsIsA_[] = {MS_TopMG_spectral_p_value, MS_PSM_level_p_value}, {MS_TopMG_spectral_p_value, MS_PSM_level_search_engine_specific_statistic}, {MS_collisional_cross_sectional_area, MS_molecular_entity_property}, + {MS_collisional_cross_sectional_area, MS_ion_selection_attribute}, {MS_hr_ms_compound_identification_confidence_level, MS_small_molecule_identification_attribute}, {MS_isotopic_ion_MS_peak, MS_peak}, {MS_isotopomer_MS_peak, MS_isotopic_ion_MS_peak}, @@ -8431,7 +8544,7 @@ CVIDPair relationsIsA_[] = {MS_MaxQuant_DIA_PEP, MS_PSM_level_search_engine_specific_statistic}, {MS_NIST_msp_comment, MS_spectrum_attribute}, {MS_ion_annotation_format, MS_interpreted_spectrum_attribute}, - {MS_peptide_ion_annotation_format, MS_ion_annotation_format}, + {MS_mzPAF_peptide_ion_annotation_format, MS_ion_annotation_format}, {MS_crosslinked_peptide_ion_annotation_format, MS_ion_annotation_format}, {MS_glycan_ion_annotation_format, MS_ion_annotation_format}, {MS_lipid_ion_annotation_format, MS_ion_annotation_format}, @@ -8551,6 +8664,7 @@ CVIDPair relationsIsA_[] = {MS_ion_mobility_separation, MS_mass_spectrometry_acquisition_method_aspect}, {MS_adduct_deconvolution, MS_data_processing_action}, {MS_data_dependent_acquisition, MS_mass_spectrometry_acquisition_method_aspect}, + {MS_data_dependent_acquisition, MS_mass_spectrometry_acquisition_method}, {MS_ion_mobility_deconvolution, MS_data_processing_action}, {MS_data_independent_acquisition_from_dissociation_of_sequential_mass_ranges, MS_dissociation_of_sequential_mass_ranges}, {MS_data_independent_acquisition_from_dissociation_of_sequential_mass_ranges, MS_data_independent_acquisition}, @@ -8666,7 +8780,7 @@ CVIDPair relationsIsA_[] = {MS_number_of_identified_protein_groups, MS_single_value}, {MS_number_of_identified_proteoforms, MS_protein_level_identification_attribute}, {MS_number_of_identified_proteoforms, MS_single_value}, - {MS_loop_link_spectrum_identification_item, MS_crosslinking_attribute}, + {MS_looplink_spectrum_identification_item, MS_crosslinking_attribute}, {MS_noncovalently_associated_peptides_search, MS_special_processing}, {MS_noncovalently_associated_peptides_spectrum_identification_item, MS_crosslinking_attribute}, {MS_identification_based_on_multiple_spectra, MS_PSM_level_attribute}, @@ -8698,6 +8812,74 @@ CVIDPair relationsIsA_[] = {MS_middle_down_proteomics, MS_mass_spectrometry_proteomics}, {MS_bottom_up_proteomics, MS_mass_spectrometry_proteomics}, {MS_Orbitrap_Ascend, MS_Thermo_Scientific_instrument_model}, + {MS_ANN_SoLo, MS_analysis_software}, + {MS_XCorr_rank, MS_PSM_level_search_engine_specific_statistic}, + {MS_exact_p_value, MS_PSM_level_search_engine_specific_statistic}, + {MS_refactored_XCorr, MS_PSM_level_search_engine_specific_statistic}, + {MS_res_ev_score, MS_PSM_level_search_engine_specific_statistic}, + {MS_res_ev_rank, MS_PSM_level_search_engine_specific_statistic}, + {MS_res_ev_p_value, MS_PSM_level_search_engine_specific_statistic}, + {MS_combined_p_value, MS_PSM_level_search_engine_specific_statistic}, + {MS_combined_p_value_rank, MS_PSM_level_search_engine_specific_statistic}, + {MS_tailor_score, MS_PSM_level_search_engine_specific_statistic}, + {MS_monoisotopic_mass_deisotoping, MS_deisotoping}, + {MS_most_abundant_mass_deisotoping, MS_deisotoping}, + {MS_average_mass_deisotoping, MS_deisotoping}, + {MS_reduction_to_summed_singly_charged_peak_list, MS_data_processing_action}, + {MS_SelexION_compensation_voltage, MS_ion_mobility_attribute}, + {MS_SelexION_compensation_voltage, MS_ion_selection_attribute}, + {MS_SelexION_compensation_voltage, MS_peak_attribute}, + {MS_mzIdentML_extension_version, MS_specification_document_extension_version}, + {MS_Open_Chromatography_Binary_OCB_format, MS_mass_spectrometer_file_format}, + {MS_Conversion_to_OCB, MS_file_format_conversion}, + {MS_ChemClipse, MS_analysis_software}, + {MS_ChemClipse, MS_data_processing_software}, + {MS_OpenChrom, MS_analysis_software}, + {MS_OpenChrom, MS_data_processing_software}, + {MS_Orbitrap_Astral, MS_Thermo_Scientific_instrument_model}, + {MS_asymmetric_track_lossless_time_of_flight_analyzer, MS_time_of_flight}, + {MS_Xevo_G3_QTof, MS_Waters_instrument_model}, + {MS_ACQUITY_RDa_Detector, MS_Waters_instrument_model}, + {MS_waters_connect, MS_Waters_software}, + {MS_waters_connect, MS_acquisition_software}, + {MS_waters_connect, MS_analysis_software}, + {MS_waters_connect, MS_data_processing_software}, + {MS_timsTOF_Ultra, MS_Bruker_Daltonics_timsTOF_series}, + {MS_semantic_version_regexp, MS_regular_expression}, + {MS_mzIdentML_crosslinking_extension_document_version, MS_mzIdentML_extension_version}, + {MS_Spectra, MS_analysis_software}, + {MS_Spectra, MS_data_processing_software}, + {MS_MetaboAnnotation, MS_analysis_software}, + {MS_MetaboAnnotation, MS_data_processing_software}, + {MS_CompoundDb, MS_analysis_software}, + {MS_CompoundDb, MS_data_processing_software}, + {MS_CompoundDb, MS_library_creation_software}, + {MS_mzTab_M, MS_tab_delimited_text_format}, + {MS_crosslinker_cleavage_characteristics, MS_peptide_modification_details}, + {MS_crosslinker_cleavage_regular_expression, MS_regular_expression}, + {MS_search_modification_id, MS_peptide_modification_details}, + {MS_search_modification_id_ref, MS_peptide_modification_details}, + {MS_SelexION_separation_voltage, MS_ion_mobility_attribute}, + {MS_SelexION_separation_voltage, MS_ion_selection_attribute}, + {MS_SelexION_separation_voltage, MS_peak_attribute}, + {MS_Q_Exactive_GC_Orbitrap, MS_Thermo_Fisher_Scientific_instrument_model}, + {MS_8890_GC_MS, MS_Agilent_instrument_model}, + {MS_timsTOF_fleX_MALDI_2, MS_Bruker_Daltonics_timsTOF_series}, + {MS_deconvoluted_data, MS_data_file_content}, + {MS_quality_control_software, MS_data_processing_software}, + {MS_rmzqc, MS_quality_control_software}, + {MS_jmzqc, MS_quality_control_software}, + {MS_pymzqc, MS_quality_control_software}, + {MS_InChI, MS_spectrum_identification_result_details}, + {MS_InChI, MS_structural_formula}, + {MS_timsTOF_HT, MS_Bruker_Daltonics_timsTOF_series}, + {MS_mzRecal, MS_data_processing_software}, + {MS_spectrum_clustering_software, MS_software}, + {MS_Scout, MS_analysis_software}, + {MS_Scout_score, MS_PSM_level_search_engine_specific_statistic}, + {MS_Stellar, MS_Thermo_Scientific_instrument_model}, + {MS_electron_beam_energy, MS_precursor_activation_attribute}, + {NCIT_Number_of_Occurrences, NCIT_Number}, {MS_single_value, MS_QC_metric_value_type}, {MS_n_tuple, MS_QC_metric_value_type}, {MS_table, MS_QC_metric_value_type}, @@ -8740,6 +8922,7 @@ CVIDPair relationsIsA_[] = {MS_m_z_acquisition_range, MS_n_tuple}, {MS_retention_time_acquisition_range, MS_n_tuple}, {MS_number_of_chromatograms, MS_single_value}, + {MS_observed_mass_accuracy, MS_single_value}, {MS_QC_sample_metric, MS_QC_metric_category}, {MS_high_complexity_QC_sample_metric, MS_QC_sample_metric}, {MS_low_complexity_QC_sample_metric, MS_QC_sample_metric}, @@ -8783,11 +8966,11 @@ CVIDPair relationsIsA_[] = {MS_MS2_peak_density_distribution_sigma, MS_single_value}, {MS_MS2_peak_density_distribution_low_outliers, MS_n_tuple}, {MS_MS2_peak_density_distribution_high_outliers, MS_n_tuple}, - {MS_precursor_intensity_distribution_quantiles, MS_n_tuple}, - {MS_precursor_intensity_distribution_mean, MS_single_value}, - {MS_precursor_intensity_distribution_sigma, MS_single_value}, - {MS_precursor_intensity_distribution_low_outliers, MS_n_tuple}, - {MS_precursor_intensity_distribution_high_outliers, MS_n_tuple}, + {MS_MS2_precursor_intensity_distribution, MS_n_tuple}, + {MS_MS2_precursor_intensity_distribution_mean, MS_single_value}, + {MS_MS2_precursor_intensity_distribution_sigma, MS_single_value}, + {MS_MS2_precursor_intensity_distribution_low_outliers, MS_n_tuple}, + {MS_MS2_precursor_intensity_distribution_high_outliers, MS_n_tuple}, {MS_MS1_signal_to_noise_ratio_quantiles, MS_n_tuple}, {MS_MS1_signal_to_noise_ratio_mean, MS_single_value}, {MS_MS1_signal_to_noise_ratio_sigma, MS_single_value}, @@ -8808,6 +8991,7 @@ CVIDPair relationsIsA_[] = {MS_MS2_ion_collection_time_sigma, MS_single_value}, {MS_MS2_ion_collection_time_low_outliers, MS_n_tuple}, {MS_MS2_ion_collection_time_high_outliers, MS_n_tuple}, + {MS_outlier_threshold_criterion, MS_QC_non_metric_term}, {MS_Tukey_s_fence, MS_outlier_threshold_criterion}, {MS_Tukey_s_fence_high_outliers, MS_outlier_threshold_criterion}, {MS_Tukey_s_fence_low_outliers, MS_outlier_threshold_criterion}, @@ -8815,6 +8999,39 @@ CVIDPair relationsIsA_[] = {MS_Z_score_threshold_high_outliers, MS_outlier_threshold_criterion}, {MS_Z_score_threshold_low_outliers, MS_outlier_threshold_criterion}, {MS_algorithmical_threshold, MS_outlier_threshold_criterion}, + {MS_iRT_calibration_formula, MS_n_tuple}, + {MS_iRT_calibration_adjusted_r_squared, MS_single_value}, + {MS_MsQuality, MS_analysis_software}, + {MS_MS2_precursor_median_m_z_of_identified_quantification_data_points, MS_single_value}, + {MS_interquartile_RT_period_for_identified_quantification_data_points, MS_single_value}, + {MS_rate_of_the_interquartile_RT_period_for_identified_quantification_data_points, MS_single_value}, + {MS_area_under_TIC, MS_single_value}, + {MS_area_under_TIC_RT_quantiles, MS_n_tuple}, + {MS_extent_of_identified_MS2_precursor_intensity, MS_single_value}, + {MS_median_of_TIC_values_in_the_RT_range_in_which_the_middle_half_of_quantification_data_points_are_identified, MS_single_value}, + {MS_median_of_TIC_values_in_the_shortest_RT_range_in_which_half_of_the_quantification_data_points_are_identified, MS_single_value}, + {MS_MS2_precursor_intensity_range, MS_n_tuple}, + {MS_identified_MS2_precursor_intensity_distribution, MS_n_tuple}, + {MS_unidentified_MS2_precursor_intensity_distribution, MS_n_tuple}, + {MS_identified_MS2_precursor_intensity_distribution_mean, MS_single_value}, + {MS_unidentified_MS2_precursor_intensity_distribution_mean, MS_single_value}, + {MS_identified_MS2_precursor_intensity_distribution_sigma, MS_single_value}, + {MS_unidentified_MS2_precursor_intensity_distribution_sigma, MS_single_value}, + {MS_ratio_of_1__over_2__of_all_MS2_known_precursor_charges, MS_single_value}, + {MS_ratio_of_1__over_2__of_identified_MS2_known_precursor_charges, MS_single_value}, + {MS_ratio_of_3__over_2__of_all_MS2_known_precursor_charges, MS_single_value}, + {MS_ratio_of_3__over_2__of_identified_MS2_known_precursor_charges, MS_single_value}, + {MS_ratio_of_4__over_2__of_all_MS2_known_precursor_charges, MS_single_value}, + {MS_ratio_of_4__over_2__of_identified_MS2_known_precursor_charges, MS_single_value}, + {MS_mean_MS2_precursor_charge_in_all_spectra, MS_single_value}, + {MS_mean_MS2_precursor_charge_in_identified_spectra, MS_single_value}, + {MS_median_MS2_precursor_charge_in_all_spectra, MS_single_value}, + {MS_median_MS2_precursor_charge_in_identified_spectra, MS_single_value}, + {MS_contaminant_protein_abundance_fraction, MS_single_value}, + {MS_precursor_ppm_deviation_mean, MS_single_value}, + {MS_precursor_ppm_deviation_sigma, MS_single_value}, + {MS_table_of_missed_cleavage_counts, MS_table}, + {MS_identified_MS2_quarter_RT_fraction, MS_n_tuple}, {UNIMOD_Acetyl, UNIMOD_unimod_root_node}, {UNIMOD_Amidated, UNIMOD_unimod_root_node}, {UNIMOD_Biotin, UNIMOD_unimod_root_node}, @@ -10328,6 +10545,17 @@ CVIDPair relationsIsA_[] = {UNIMOD_Di_L_Gln_N___propargyl_L_Gln_desthiobiotin, UNIMOD_unimod_root_node}, {UNIMOD_L_Gln, UNIMOD_unimod_root_node}, {UNIMOD_Glyceroyl, UNIMOD_unimod_root_node}, + {UNIMOD_N6pAMP, UNIMOD_unimod_root_node}, + {UNIMOD_DABCYL_C2_maleimide, UNIMOD_unimod_root_node}, + {UNIMOD_NBF, UNIMOD_unimod_root_node}, + {UNIMOD_DCP, UNIMOD_unimod_root_node}, + {UNIMOD_Ethynyl, UNIMOD_unimod_root_node}, + {UNIMOD_QQTGG, UNIMOD_unimod_root_node}, + {UNIMOD_Pyro_QQTGG, UNIMOD_unimod_root_node}, + {UNIMOD_NQTGG, UNIMOD_unimod_root_node}, + {UNIMOD_DVFQQQTGG, UNIMOD_unimod_root_node}, + {UNIMOD_iST_NHS_specific_cysteine_modification, UNIMOD_unimod_root_node}, + {UNIMOD_Label_13C_2_15N_1_, UNIMOD_unimod_root_node}, {UO_length_unit, UO_unit}, {UO_mass_unit, UO_unit}, {UO_time_unit, UO_unit}, @@ -10863,6 +11091,7 @@ CVIDPair relationsPartOf_[] = {MS_native_spectrum_identifier_format__combined_spectra, MS_source_data_file}, {MS_identification_parameter, MS_spectrum_interpretation}, {MS_crosslinking_result_details, MS_spectrum_interpretation}, + {MS_measured_element, MS_binary_data_array}, {MS_adduct_ion_attribute, MS_adduct_ion}, {MS_external_reference_data, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies}, {MS_named_element, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies}, @@ -10903,6 +11132,8 @@ CVIDPair relationsPartOf_[] = {MS_spectrum_match, MS_spectrum_interpretation}, {MS_spectral_similarity, MS_spectrum_spectrum_match}, {MS_proteomics, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies}, + {MS_specification_document_extension_version, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies}, + {MS_mzIdentML_extension_version, MS_mzIdentML_format}, {MS_PSI_MS_CV_Quality_Control_Vocabulary, MS_Proteomics_Standards_Initiative_Mass_Spectrometry_Vocabularies}, {MS_QC_metric, MS_PSI_MS_CV_Quality_Control_Vocabulary}, {MS_QC_metric_value_type, MS_PSI_MS_CV_Quality_Control_Vocabulary}, @@ -11022,11 +11253,14 @@ OtherRelationPair relationsOther_[] = {MS_flow_rate_array, "has_units", UO_microliters_per_minute}, {MS_pressure_array, "has_units", UO_pascal}, {MS_temperature_array, "has_units", UO_kelvin}, + {MS_temperature_array, "has_units", UO_degree_Celsius}, {MS_elution_time, "has_units", UO_second}, {MS_elution_time, "has_units", UO_minute}, {MS_isolation_window_target_m_z, "has_units", MS_m_z}, {MS_isolation_window_lower_offset, "has_units", MS_m_z}, {MS_isolation_window_upper_offset, "has_units", MS_m_z}, + {MS_precision, "has_units", MS_m_z}, + {MS_precision, "has_units", UO_parts_per_million}, {MS_matrix_solution_concentration, "has_units", UO_gram_per_liter}, {MS_wavelength_OBSOLETE, "has_units", UO_nanometer}, {MS_focus_diameter_x, "has_units", UO_micrometer}, @@ -11319,6 +11553,7 @@ OtherRelationPair relationsOther_[] = {MS_other_attribute_value, "has_value_type", MS_list_of_integers}, {MS_other_attribute_value, "has_value_type", MS_list_of_floats}, {MS_Luciphor_deltaScore, "has_regexp", MS_regular_expression_for_modification_localization_scoring}, + {MS_contributing_replicate_spectrum_keys, "has_value_type", MS_list_of_integers}, {MS_number_of_identified_protein_groups, "has_metric_category", MS_ID_based_metric}, {MS_number_of_identified_protein_groups, "has_units", UO_count_unit}, {MS_number_of_identified_proteoforms, "has_metric_category", MS_ID_based_metric}, @@ -11328,18 +11563,22 @@ OtherRelationPair relationsOther_[] = {MS_residue_pair_passes_threshold, "has_regexp", MS_regular_expression_for_whether_interaction_score_derived_from_crosslinking_passes_threshold}, {MS_protein_protein_interaction_passes_threshold, "has_regexp", MS_regular_expression_for_whether_interaction_score_derived_from_crosslinking_passes_threshold}, {MS_residue_pair_ref, "has_regexp", MS_regular_expression_for_residue_pair_ref}, + {MS_SelexION_compensation_voltage, "has_units", UO_volt}, + {MS_specification_document_extension_version, "has_regexp", MS_semantic_version_regexp}, + {MS_crosslinker_cleavage_characteristics, "has_regexp", MS_crosslinker_cleavage_regular_expression}, + {MS_SelexION_separation_voltage, "has_units", UO_volt}, + {MS_Scout_score, "has_order", MS_Scout}, + {MS_electron_beam_energy, "has_units", UO_electronvolt}, {MS_XIC50_fraction, "has_metric_category", MS_ID_free_metric}, {MS_XIC50_fraction, "has_metric_category", MS_single_run_based_metric}, {MS_XIC50_fraction, "has_value_concept", UO_fraction}, {MS_XIC_FWHM_quantiles, "has_metric_category", MS_ID_free_metric}, {MS_XIC_FWHM_quantiles, "has_metric_category", MS_single_run_based_metric}, {MS_XIC_FWHM_quantiles, "has_metric_category", MS_XIC_metric}, - {MS_XIC_FWHM_quantiles, "has_units", UO_second}, {MS_XIC_FWHM_quantiles, "has_value_concept", MS_full_width_at_half_maximum}, {MS_XIC_Height_quartile_ratios, "has_metric_category", MS_ID_free_metric}, {MS_XIC_Height_quartile_ratios, "has_metric_category", MS_single_run_based_metric}, {MS_XIC_Height_quartile_ratios, "has_metric_category", MS_XIC_metric}, - {MS_XIC_Height_quartile_ratios, "has_value_concept", UO_fraction}, {MS_chromatography_duration, "has_metric_category", MS_ID_free_metric}, {MS_chromatography_duration, "has_metric_category", MS_single_run_based_metric}, {MS_chromatography_duration, "has_metric_category", MS_retention_time_metric}, @@ -11379,7 +11618,6 @@ OtherRelationPair relationsOther_[] = {MS_MS1_density_quantiles, "has_metric_category", MS_ID_free_metric}, {MS_MS1_density_quantiles, "has_metric_category", MS_single_run_based_metric}, {MS_MS1_density_quantiles, "has_metric_category", MS_MS1_metric}, - {MS_MS1_density_quantiles, "has_units", UO_count_unit}, {MS_MS1_density_quantiles, "has_value_concept", NCIT_Density}, {MS_MS2_density_quantiles, "has_metric_category", MS_ID_free_metric}, {MS_MS2_density_quantiles, "has_metric_category", MS_single_run_based_metric}, @@ -11576,17 +11814,21 @@ OtherRelationPair relationsOther_[] = {MS_MS2_peak_density_distribution_low_outliers, "has_metric_category", MS_MS2_metric}, {MS_MS2_peak_density_distribution_high_outliers, "has_metric_category", MS_ID_free_metric}, {MS_MS2_peak_density_distribution_high_outliers, "has_metric_category", MS_MS2_metric}, - {MS_precursor_intensity_distribution_quantiles, "has_metric_category", MS_ID_free_metric}, - {MS_precursor_intensity_distribution_quantiles, "has_metric_category", MS_MS2_metric}, - {MS_precursor_intensity_distribution_quantiles, "has_units", MS_intensity_unit}, - {MS_precursor_intensity_distribution_mean, "has_metric_category", MS_ID_free_metric}, - {MS_precursor_intensity_distribution_mean, "has_units", MS_intensity_unit}, - {MS_precursor_intensity_distribution_sigma, "has_metric_category", MS_ID_free_metric}, - {MS_precursor_intensity_distribution_sigma, "has_units", MS_intensity_unit}, - {MS_precursor_intensity_distribution_low_outliers, "has_metric_category", MS_ID_free_metric}, - {MS_precursor_intensity_distribution_low_outliers, "has_units", MS_intensity_unit}, - {MS_precursor_intensity_distribution_high_outliers, "has_metric_category", MS_ID_free_metric}, - {MS_precursor_intensity_distribution_high_outliers, "has_units", MS_intensity_unit}, + {MS_MS2_precursor_intensity_distribution, "has_metric_category", MS_ID_free_metric}, + {MS_MS2_precursor_intensity_distribution, "has_metric_category", MS_MS2_metric}, + {MS_MS2_precursor_intensity_distribution, "has_units", MS_intensity_unit}, + {MS_MS2_precursor_intensity_distribution_mean, "has_metric_category", MS_ID_free_metric}, + {MS_MS2_precursor_intensity_distribution_mean, "has_metric_category", MS_MS2_metric}, + {MS_MS2_precursor_intensity_distribution_mean, "has_units", MS_intensity_unit}, + {MS_MS2_precursor_intensity_distribution_sigma, "has_metric_category", MS_ID_free_metric}, + {MS_MS2_precursor_intensity_distribution_sigma, "has_metric_category", MS_MS2_metric}, + {MS_MS2_precursor_intensity_distribution_sigma, "has_units", MS_intensity_unit}, + {MS_MS2_precursor_intensity_distribution_low_outliers, "has_metric_category", MS_ID_free_metric}, + {MS_MS2_precursor_intensity_distribution_low_outliers, "has_metric_category", MS_MS2_metric}, + {MS_MS2_precursor_intensity_distribution_low_outliers, "has_units", MS_intensity_unit}, + {MS_MS2_precursor_intensity_distribution_high_outliers, "has_metric_category", MS_ID_free_metric}, + {MS_MS2_precursor_intensity_distribution_high_outliers, "has_metric_category", MS_MS2_metric}, + {MS_MS2_precursor_intensity_distribution_high_outliers, "has_units", MS_intensity_unit}, {MS_MS1_signal_to_noise_ratio_quantiles, "has_metric_category", MS_ID_free_metric}, {MS_MS1_signal_to_noise_ratio_quantiles, "has_metric_category", MS_MS1_metric}, {MS_MS1_signal_to_noise_ratio_mean, "has_metric_category", MS_ID_free_metric}, @@ -11635,6 +11877,107 @@ OtherRelationPair relationsOther_[] = {MS_MS2_ion_collection_time_high_outliers, "has_metric_category", MS_ID_free_metric}, {MS_MS2_ion_collection_time_high_outliers, "has_metric_category", MS_MS2_metric}, {MS_MS2_ion_collection_time_high_outliers, "has_units", UO_millisecond}, + {MS_iRT_calibration_formula, "has_metric_category", MS_ID_based_metric}, + {MS_iRT_calibration_formula, "has_metric_category", MS_retention_time_metric}, + {MS_iRT_calibration_adjusted_r_squared, "has_metric_category", MS_ID_based_metric}, + {MS_iRT_calibration_adjusted_r_squared, "has_metric_category", MS_retention_time_metric}, + {MS_MS2_precursor_median_m_z_of_identified_quantification_data_points, "has_metric_category", MS_ID_based_metric}, + {MS_MS2_precursor_median_m_z_of_identified_quantification_data_points, "has_metric_category", MS_ion_source_metric}, + {MS_MS2_precursor_median_m_z_of_identified_quantification_data_points, "has_metric_category", MS_MS2_metric}, + {MS_MS2_precursor_median_m_z_of_identified_quantification_data_points, "has_units", MS_m_z}, + {MS_interquartile_RT_period_for_identified_quantification_data_points, "has_metric_category", MS_ID_based_metric}, + {MS_interquartile_RT_period_for_identified_quantification_data_points, "has_metric_category", MS_chromatogram_metric}, + {MS_interquartile_RT_period_for_identified_quantification_data_points, "has_units", UO_second}, + {MS_rate_of_the_interquartile_RT_period_for_identified_quantification_data_points, "has_metric_category", MS_ID_based_metric}, + {MS_rate_of_the_interquartile_RT_period_for_identified_quantification_data_points, "has_metric_category", MS_chromatogram_metric}, + {MS_rate_of_the_interquartile_RT_period_for_identified_quantification_data_points, "has_units", UO_hertz}, + {MS_area_under_TIC, "has_metric_category", MS_ID_free_metric}, + {MS_area_under_TIC, "has_metric_category", MS_chromatogram_metric}, + {MS_area_under_TIC_RT_quantiles, "has_metric_category", MS_ID_free_metric}, + {MS_area_under_TIC_RT_quantiles, "has_metric_category", MS_chromatogram_metric}, + {MS_extent_of_identified_MS2_precursor_intensity, "has_metric_category", MS_ID_based_metric}, + {MS_extent_of_identified_MS2_precursor_intensity, "has_metric_category", MS_MS2_metric}, + {MS_median_of_TIC_values_in_the_RT_range_in_which_the_middle_half_of_quantification_data_points_are_identified, "has_metric_category", MS_ID_based_metric}, + {MS_median_of_TIC_values_in_the_shortest_RT_range_in_which_half_of_the_quantification_data_points_are_identified, "has_metric_category", MS_ID_based_metric}, + {MS_MS2_precursor_intensity_range, "has_metric_category", MS_ID_free_metric}, + {MS_MS2_precursor_intensity_range, "has_metric_category", MS_MS2_metric}, + {MS_identified_MS2_precursor_intensity_distribution, "has_metric_category", MS_ID_based_metric}, + {MS_identified_MS2_precursor_intensity_distribution, "has_metric_category", MS_MS2_metric}, + {MS_identified_MS2_precursor_intensity_distribution, "has_units", MS_intensity_unit}, + {MS_unidentified_MS2_precursor_intensity_distribution, "has_metric_category", MS_ID_based_metric}, + {MS_unidentified_MS2_precursor_intensity_distribution, "has_metric_category", MS_MS2_metric}, + {MS_unidentified_MS2_precursor_intensity_distribution, "has_units", MS_intensity_unit}, + {MS_identified_MS2_precursor_intensity_distribution_mean, "has_metric_category", MS_ID_based_metric}, + {MS_identified_MS2_precursor_intensity_distribution_mean, "has_metric_category", MS_MS2_metric}, + {MS_identified_MS2_precursor_intensity_distribution_mean, "has_units", MS_intensity_unit}, + {MS_unidentified_MS2_precursor_intensity_distribution_mean, "has_metric_category", MS_ID_based_metric}, + {MS_unidentified_MS2_precursor_intensity_distribution_mean, "has_metric_category", MS_MS2_metric}, + {MS_unidentified_MS2_precursor_intensity_distribution_mean, "has_units", MS_intensity_unit}, + {MS_identified_MS2_precursor_intensity_distribution_sigma, "has_metric_category", MS_ID_based_metric}, + {MS_identified_MS2_precursor_intensity_distribution_sigma, "has_metric_category", MS_MS2_metric}, + {MS_identified_MS2_precursor_intensity_distribution_sigma, "has_units", MS_intensity_unit}, + {MS_unidentified_MS2_precursor_intensity_distribution_sigma, "has_metric_category", MS_ID_based_metric}, + {MS_unidentified_MS2_precursor_intensity_distribution_sigma, "has_metric_category", MS_MS2_metric}, + {MS_unidentified_MS2_precursor_intensity_distribution_sigma, "has_units", MS_intensity_unit}, + {MS_ratio_of_1__over_2__of_all_MS2_known_precursor_charges, "has_metric_category", MS_ID_free_metric}, + {MS_ratio_of_1__over_2__of_all_MS2_known_precursor_charges, "has_metric_category", MS_single_run_based_metric}, + {MS_ratio_of_1__over_2__of_all_MS2_known_precursor_charges, "has_metric_category", MS_ion_source_metric}, + {MS_ratio_of_1__over_2__of_all_MS2_known_precursor_charges, "has_metric_category", MS_MS2_metric}, + {MS_ratio_of_1__over_2__of_identified_MS2_known_precursor_charges, "has_metric_category", MS_ID_based_metric}, + {MS_ratio_of_1__over_2__of_identified_MS2_known_precursor_charges, "has_metric_category", MS_single_run_based_metric}, + {MS_ratio_of_1__over_2__of_identified_MS2_known_precursor_charges, "has_metric_category", MS_ion_source_metric}, + {MS_ratio_of_1__over_2__of_identified_MS2_known_precursor_charges, "has_metric_category", MS_MS2_metric}, + {MS_ratio_of_3__over_2__of_all_MS2_known_precursor_charges, "has_metric_category", MS_ID_free_metric}, + {MS_ratio_of_3__over_2__of_all_MS2_known_precursor_charges, "has_metric_category", MS_single_run_based_metric}, + {MS_ratio_of_3__over_2__of_all_MS2_known_precursor_charges, "has_metric_category", MS_ion_source_metric}, + {MS_ratio_of_3__over_2__of_all_MS2_known_precursor_charges, "has_metric_category", MS_MS2_metric}, + {MS_ratio_of_3__over_2__of_identified_MS2_known_precursor_charges, "has_metric_category", MS_ID_based_metric}, + {MS_ratio_of_3__over_2__of_identified_MS2_known_precursor_charges, "has_metric_category", MS_single_run_based_metric}, + {MS_ratio_of_3__over_2__of_identified_MS2_known_precursor_charges, "has_metric_category", MS_ion_source_metric}, + {MS_ratio_of_3__over_2__of_identified_MS2_known_precursor_charges, "has_metric_category", MS_MS2_metric}, + {MS_ratio_of_4__over_2__of_all_MS2_known_precursor_charges, "has_metric_category", MS_ID_free_metric}, + {MS_ratio_of_4__over_2__of_all_MS2_known_precursor_charges, "has_metric_category", MS_single_run_based_metric}, + {MS_ratio_of_4__over_2__of_all_MS2_known_precursor_charges, "has_metric_category", MS_ion_source_metric}, + {MS_ratio_of_4__over_2__of_all_MS2_known_precursor_charges, "has_metric_category", MS_MS2_metric}, + {MS_ratio_of_4__over_2__of_identified_MS2_known_precursor_charges, "has_metric_category", MS_ID_based_metric}, + {MS_ratio_of_4__over_2__of_identified_MS2_known_precursor_charges, "has_metric_category", MS_single_run_based_metric}, + {MS_ratio_of_4__over_2__of_identified_MS2_known_precursor_charges, "has_metric_category", MS_ion_source_metric}, + {MS_ratio_of_4__over_2__of_identified_MS2_known_precursor_charges, "has_metric_category", MS_MS2_metric}, + {MS_mean_MS2_precursor_charge_in_all_spectra, "has_metric_category", MS_ID_free_metric}, + {MS_mean_MS2_precursor_charge_in_all_spectra, "has_metric_category", MS_single_run_based_metric}, + {MS_mean_MS2_precursor_charge_in_all_spectra, "has_metric_category", MS_ion_source_metric}, + {MS_mean_MS2_precursor_charge_in_all_spectra, "has_metric_category", MS_MS2_metric}, + {MS_mean_MS2_precursor_charge_in_identified_spectra, "has_metric_category", MS_ID_based_metric}, + {MS_mean_MS2_precursor_charge_in_identified_spectra, "has_metric_category", MS_single_run_based_metric}, + {MS_mean_MS2_precursor_charge_in_identified_spectra, "has_metric_category", MS_ion_source_metric}, + {MS_mean_MS2_precursor_charge_in_identified_spectra, "has_metric_category", MS_MS2_metric}, + {MS_median_MS2_precursor_charge_in_all_spectra, "has_metric_category", MS_ID_free_metric}, + {MS_median_MS2_precursor_charge_in_all_spectra, "has_metric_category", MS_single_run_based_metric}, + {MS_median_MS2_precursor_charge_in_all_spectra, "has_metric_category", MS_ion_source_metric}, + {MS_median_MS2_precursor_charge_in_all_spectra, "has_metric_category", MS_MS2_metric}, + {MS_median_MS2_precursor_charge_in_identified_spectra, "has_metric_category", MS_ID_based_metric}, + {MS_median_MS2_precursor_charge_in_identified_spectra, "has_metric_category", MS_single_run_based_metric}, + {MS_median_MS2_precursor_charge_in_identified_spectra, "has_metric_category", MS_ion_source_metric}, + {MS_median_MS2_precursor_charge_in_identified_spectra, "has_metric_category", MS_MS2_metric}, + {MS_contaminant_protein_abundance_fraction, "has_domain", MS_value_between_0_and_1_inclusive}, + {MS_contaminant_protein_abundance_fraction, "has_metric_category", MS_ID_based_metric}, + {MS_contaminant_protein_abundance_fraction, "has_order", MS_lower_score_better}, + {MS_precursor_ppm_deviation_mean, "has_metric_category", MS_ID_based_metric}, + {MS_precursor_ppm_deviation_mean, "has_metric_category", MS_MS1_metric}, + {MS_precursor_ppm_deviation_mean, "has_units", UO_parts_per_million}, + {MS_precursor_ppm_deviation_mean, "has_value_concept", MS_accuracy}, + {MS_precursor_ppm_deviation_sigma, "has_metric_category", MS_ID_based_metric}, + {MS_precursor_ppm_deviation_sigma, "has_metric_category", MS_MS1_metric}, + {MS_precursor_ppm_deviation_sigma, "has_units", UO_parts_per_million}, + {MS_precursor_ppm_deviation_sigma, "has_value_concept", MS_precision}, + {MS_table_of_missed_cleavage_counts, "has_column", MS_number_of_missed_cleavages}, + {MS_table_of_missed_cleavage_counts, "has_column", NCIT_Number_of_Occurrences}, + {MS_table_of_missed_cleavage_counts, "has_metric_category", MS_ID_based_metric}, + {MS_identified_MS2_quarter_RT_fraction, "has_metric_category", MS_single_run_based_metric}, + {MS_identified_MS2_quarter_RT_fraction, "has_metric_category", MS_ID_based_metric}, + {MS_identified_MS2_quarter_RT_fraction, "has_metric_category", MS_MS2_metric}, + {MS_identified_MS2_quarter_RT_fraction, "has_metric_category", MS_retention_time_metric}, + {MS_identified_MS2_quarter_RT_fraction, "has_units", UO_fraction}, }; // relationsOther_ @@ -11848,6 +12191,7 @@ CVIDStringPair relationsExactSynonym_[] = {MS_volt_second_per_square_centimeter, "Vs/cm^2"}, {MS_library_spectrum_name, "spectrum name"}, {MS_universal_spectrum_identifier, "USI"}, + {MS_mzPAF_peptide_ion_annotation_format, "peptide ion annotation format"}, {MS_crosslinked_peptide_ion_annotation_format, "cross-linked peptide ion annotation format"}, {MS_PTX_QC, "PTXQC"}, {MS_QuaMeter_IDFree, "QuaMeter"}, @@ -11862,6 +12206,10 @@ CVIDStringPair relationsExactSynonym_[] = {MS_peptide_spectrum_match, "PSM"}, {MS_spectrum_spectrum_match, "SSM"}, {MS_spectral_dot_product, "cosine similarity"}, + {MS_looplink_spectrum_identification_item, "loop-link spectrum identification item"}, + {MS_ChemClipse, "chemclipse"}, + {MS_OpenChrom, "openchrom"}, + {MS_asymmetric_track_lossless_time_of_flight_analyzer, "Astral"}, {MS_XIC50_fraction, "XIC-WideFrac"}, {MS_number_of_MS1_spectra, "MS1-Count"}, {MS_number_of_MS2_spectra, "MS2-Count"}, @@ -24572,6 +24920,14 @@ PropertyValuePair propertyValue_[] = {UNIMOD_Biotin_tyramide, "spec_1_hidden", "1"}, {UNIMOD_Biotin_tyramide, "spec_1_position", "Anywhere"}, {UNIMOD_Biotin_tyramide, "spec_1_site", "Y"}, + {UNIMOD_Biotin_tyramide, "spec_2_classification", "Chemical derivative"}, + {UNIMOD_Biotin_tyramide, "spec_2_hidden", "1"}, + {UNIMOD_Biotin_tyramide, "spec_2_position", "Anywhere"}, + {UNIMOD_Biotin_tyramide, "spec_2_site", "C"}, + {UNIMOD_Biotin_tyramide, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Biotin_tyramide, "spec_3_hidden", "1"}, + {UNIMOD_Biotin_tyramide, "spec_3_position", "Anywhere"}, + {UNIMOD_Biotin_tyramide, "spec_3_site", "W"}, {UNIMOD_Tris, "approved", "0"}, {UNIMOD_Tris, "delta_composition", "H(10) C(4) N O(2)"}, {UNIMOD_Tris, "spec_1_classification", "Artefact"}, @@ -24828,6 +25184,18 @@ PropertyValuePair propertyValue_[] = {UNIMOD_Xlink_BuUrBu_111_, "spec_2_hidden", "1"}, {UNIMOD_Xlink_BuUrBu_111_, "spec_2_position", "Protein N-term"}, {UNIMOD_Xlink_BuUrBu_111_, "spec_2_site", "N-term"}, + {UNIMOD_Xlink_BuUrBu_111_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_111_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_111_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_111_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_111_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_111_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_111_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_111_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_111_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_111_, "spec_3_site", "S"}, + {UNIMOD_Xlink_BuUrBu_111_, "spec_3_site", "T"}, + {UNIMOD_Xlink_BuUrBu_111_, "spec_3_site", "Y"}, {UNIMOD_Xlink_BuUrBu_85_, "approved", "0"}, {UNIMOD_Xlink_BuUrBu_85_, "delta_composition", "H(7) C(4) N O"}, {UNIMOD_Xlink_BuUrBu_85_, "spec_1_classification", "Chemical derivative"}, @@ -24838,6 +25206,18 @@ PropertyValuePair propertyValue_[] = {UNIMOD_Xlink_BuUrBu_85_, "spec_2_hidden", "1"}, {UNIMOD_Xlink_BuUrBu_85_, "spec_2_position", "Protein N-term"}, {UNIMOD_Xlink_BuUrBu_85_, "spec_2_site", "N-term"}, + {UNIMOD_Xlink_BuUrBu_85_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_85_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_85_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_85_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_85_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_85_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_85_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_85_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_85_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_85_, "spec_3_site", "S"}, + {UNIMOD_Xlink_BuUrBu_85_, "spec_3_site", "T"}, + {UNIMOD_Xlink_BuUrBu_85_, "spec_3_site", "Y"}, {UNIMOD_Xlink_BuUrBu_213_, "approved", "0"}, {UNIMOD_Xlink_BuUrBu_213_, "delta_composition", "H(15) C(9) N(3) O(3)"}, {UNIMOD_Xlink_BuUrBu_213_, "spec_1_classification", "Chemical derivative"}, @@ -24848,6 +25228,18 @@ PropertyValuePair propertyValue_[] = {UNIMOD_Xlink_BuUrBu_213_, "spec_2_hidden", "1"}, {UNIMOD_Xlink_BuUrBu_213_, "spec_2_position", "Protein N-term"}, {UNIMOD_Xlink_BuUrBu_213_, "spec_2_site", "N-term"}, + {UNIMOD_Xlink_BuUrBu_213_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_213_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_213_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_213_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_213_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_213_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_213_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_213_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_213_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_213_, "spec_3_site", "S"}, + {UNIMOD_Xlink_BuUrBu_213_, "spec_3_site", "T"}, + {UNIMOD_Xlink_BuUrBu_213_, "spec_3_site", "Y"}, {UNIMOD_Xlink_BuUrBu_214_, "approved", "0"}, {UNIMOD_Xlink_BuUrBu_214_, "delta_composition", "H(14) C(9) N(2) O(4)"}, {UNIMOD_Xlink_BuUrBu_214_, "spec_1_classification", "Chemical derivative"}, @@ -24858,6 +25250,18 @@ PropertyValuePair propertyValue_[] = {UNIMOD_Xlink_BuUrBu_214_, "spec_2_hidden", "1"}, {UNIMOD_Xlink_BuUrBu_214_, "spec_2_position", "Protein N-term"}, {UNIMOD_Xlink_BuUrBu_214_, "spec_2_site", "N-term"}, + {UNIMOD_Xlink_BuUrBu_214_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_214_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_214_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_214_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_214_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_214_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_214_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_214_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_214_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_214_, "spec_3_site", "S"}, + {UNIMOD_Xlink_BuUrBu_214_, "spec_3_site", "T"}, + {UNIMOD_Xlink_BuUrBu_214_, "spec_3_site", "Y"}, {UNIMOD_Xlink_BuUrBu_317_, "approved", "0"}, {UNIMOD_Xlink_BuUrBu_317_, "delta_composition", "H(23) C(13) N(3) O(6)"}, {UNIMOD_Xlink_BuUrBu_317_, "spec_1_classification", "Chemical derivative"}, @@ -24868,6 +25272,18 @@ PropertyValuePair propertyValue_[] = {UNIMOD_Xlink_BuUrBu_317_, "spec_2_hidden", "1"}, {UNIMOD_Xlink_BuUrBu_317_, "spec_2_position", "Protein N-term"}, {UNIMOD_Xlink_BuUrBu_317_, "spec_2_site", "N-term"}, + {UNIMOD_Xlink_BuUrBu_317_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_317_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_317_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_317_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_317_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_317_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_317_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_317_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_317_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_317_, "spec_3_site", "S"}, + {UNIMOD_Xlink_BuUrBu_317_, "spec_3_site", "T"}, + {UNIMOD_Xlink_BuUrBu_317_, "spec_3_site", "Y"}, {UNIMOD_Xlink_DSSO_158_, "approved", "0"}, {UNIMOD_Xlink_DSSO_158_, "delta_composition", "H(6) C(6) O(3) S"}, {UNIMOD_Xlink_DSSO_158_, "spec_1_classification", "Chemical derivative"}, @@ -24908,6 +25324,18 @@ PropertyValuePair propertyValue_[] = {UNIMOD_Xlink_BuUrBu_196_, "spec_2_hidden", "1"}, {UNIMOD_Xlink_BuUrBu_196_, "spec_2_position", "Protein N-term"}, {UNIMOD_Xlink_BuUrBu_196_, "spec_2_site", "N-term"}, + {UNIMOD_Xlink_BuUrBu_196_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_196_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_196_, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_Xlink_BuUrBu_196_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_196_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_196_, "spec_3_hidden", "1"}, + {UNIMOD_Xlink_BuUrBu_196_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_196_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_196_, "spec_3_position", "Anywhere"}, + {UNIMOD_Xlink_BuUrBu_196_, "spec_3_site", "S"}, + {UNIMOD_Xlink_BuUrBu_196_, "spec_3_site", "T"}, + {UNIMOD_Xlink_BuUrBu_196_, "spec_3_site", "Y"}, {UNIMOD_Xlink_DTBP_172_, "approved", "0"}, {UNIMOD_Xlink_DTBP_172_, "delta_composition", "H(8) C(6) N(2) S(2)"}, {UNIMOD_Xlink_DTBP_172_, "spec_1_classification", "Chemical derivative"}, @@ -26209,15 +26637,11 @@ PropertyValuePair propertyValue_[] = {UNIMOD_DBIA, "spec_1_position", "Anywhere"}, {UNIMOD_DBIA, "spec_1_site", "C"}, {UNIMOD_Mono_N___propargyl_L_Gln_desthiobiotin, "approved", "0"}, - {UNIMOD_Mono_N___propargyl_L_Gln_desthiobiotin, "delta_composition", "H(44) C(26) N(8) O(7)"}, + {UNIMOD_Mono_N___propargyl_L_Gln_desthiobiotin, "delta_composition", "H(44) C(26) N(8) O(8)"}, {UNIMOD_Mono_N___propargyl_L_Gln_desthiobiotin, "spec_1_classification", "Chemical derivative"}, {UNIMOD_Mono_N___propargyl_L_Gln_desthiobiotin, "spec_1_hidden", "1"}, {UNIMOD_Mono_N___propargyl_L_Gln_desthiobiotin, "spec_1_position", "Anywhere"}, - {UNIMOD_Mono_N___propargyl_L_Gln_desthiobiotin, "spec_1_site", "D"}, - {UNIMOD_Mono_N___propargyl_L_Gln_desthiobiotin, "spec_2_classification", "Chemical derivative"}, - {UNIMOD_Mono_N___propargyl_L_Gln_desthiobiotin, "spec_2_hidden", "1"}, - {UNIMOD_Mono_N___propargyl_L_Gln_desthiobiotin, "spec_2_position", "Anywhere"}, - {UNIMOD_Mono_N___propargyl_L_Gln_desthiobiotin, "spec_2_site", "E"}, + {UNIMOD_Mono_N___propargyl_L_Gln_desthiobiotin, "spec_1_site", "C"}, {UNIMOD_Di_L_Glu_N___propargyl_L_Gln_desthiobiotin, "approved", "0"}, {UNIMOD_Di_L_Glu_N___propargyl_L_Gln_desthiobiotin, "delta_composition", "H(51) C(31) N(9) O(10)"}, {UNIMOD_Di_L_Glu_N___propargyl_L_Gln_desthiobiotin, "spec_1_classification", "Chemical derivative"}, @@ -26258,6 +26682,92 @@ PropertyValuePair propertyValue_[] = {UNIMOD_Glyceroyl, "spec_2_hidden", "1"}, {UNIMOD_Glyceroyl, "spec_2_position", "Protein N-term"}, {UNIMOD_Glyceroyl, "spec_2_site", "N-term"}, + {UNIMOD_N6pAMP, "approved", "0"}, + {UNIMOD_N6pAMP, "delta_composition", "H(14) C(13) N(5) O(6) P"}, + {UNIMOD_N6pAMP, "spec_1_classification", "Chemical derivative"}, + {UNIMOD_N6pAMP, "spec_1_hidden", "1"}, + {UNIMOD_N6pAMP, "spec_1_position", "Anywhere"}, + {UNIMOD_N6pAMP, "spec_1_site", "S"}, + {UNIMOD_N6pAMP, "spec_2_classification", "Chemical derivative"}, + {UNIMOD_N6pAMP, "spec_2_hidden", "1"}, + {UNIMOD_N6pAMP, "spec_2_position", "Anywhere"}, + {UNIMOD_N6pAMP, "spec_2_site", "T"}, + {UNIMOD_N6pAMP, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_N6pAMP, "spec_3_hidden", "1"}, + {UNIMOD_N6pAMP, "spec_3_position", "Anywhere"}, + {UNIMOD_N6pAMP, "spec_3_site", "Y"}, + {UNIMOD_DABCYL_C2_maleimide, "approved", "0"}, + {UNIMOD_DABCYL_C2_maleimide, "delta_composition", "H(21) C(21) N(5) O(3)"}, + {UNIMOD_DABCYL_C2_maleimide, "spec_1_classification", "Chemical derivative"}, + {UNIMOD_DABCYL_C2_maleimide, "spec_1_hidden", "1"}, + {UNIMOD_DABCYL_C2_maleimide, "spec_1_position", "Anywhere"}, + {UNIMOD_DABCYL_C2_maleimide, "spec_1_site", "C"}, + {UNIMOD_DABCYL_C2_maleimide, "spec_2_classification", "Chemical derivative"}, + {UNIMOD_DABCYL_C2_maleimide, "spec_2_hidden", "1"}, + {UNIMOD_DABCYL_C2_maleimide, "spec_2_position", "Anywhere"}, + {UNIMOD_DABCYL_C2_maleimide, "spec_2_site", "K"}, + {UNIMOD_NBF, "approved", "0"}, + {UNIMOD_NBF, "delta_composition", "H C(6) N(3) O(3)"}, + {UNIMOD_NBF, "spec_1_classification", "Chemical derivative"}, + {UNIMOD_NBF, "spec_1_hidden", "1"}, + {UNIMOD_NBF, "spec_1_position", "Anywhere"}, + {UNIMOD_NBF, "spec_1_site", "C"}, + {UNIMOD_NBF, "spec_2_classification", "Chemical derivative"}, + {UNIMOD_NBF, "spec_2_hidden", "1"}, + {UNIMOD_NBF, "spec_2_position", "Anywhere"}, + {UNIMOD_NBF, "spec_2_site", "K"}, + {UNIMOD_NBF, "spec_3_classification", "Chemical derivative"}, + {UNIMOD_NBF, "spec_3_hidden", "1"}, + {UNIMOD_NBF, "spec_3_position", "Anywhere"}, + {UNIMOD_NBF, "spec_3_site", "R"}, + {UNIMOD_DCP, "approved", "0"}, + {UNIMOD_DCP, "delta_composition", "H(12) C(9) O(3)"}, + {UNIMOD_DCP, "spec_1_classification", "Chemical derivative"}, + {UNIMOD_DCP, "spec_1_hidden", "1"}, + {UNIMOD_DCP, "spec_1_position", "Anywhere"}, + {UNIMOD_DCP, "spec_1_site", "C"}, + {UNIMOD_Ethynyl, "approved", "0"}, + {UNIMOD_Ethynyl, "delta_composition", "C(2)"}, + {UNIMOD_Ethynyl, "spec_1_classification", "Chemical derivative"}, + {UNIMOD_Ethynyl, "spec_1_hidden", "1"}, + {UNIMOD_Ethynyl, "spec_1_position", "Anywhere"}, + {UNIMOD_Ethynyl, "spec_1_site", "C"}, + {UNIMOD_QQTGG, "approved", "0"}, + {UNIMOD_QQTGG, "delta_composition", "H(29) C(18) N(7) O(8)"}, + {UNIMOD_QQTGG, "spec_1_classification", "Other"}, + {UNIMOD_QQTGG, "spec_1_hidden", "1"}, + {UNIMOD_QQTGG, "spec_1_position", "Anywhere"}, + {UNIMOD_QQTGG, "spec_1_site", "K"}, + {UNIMOD_Pyro_QQTGG, "approved", "0"}, + {UNIMOD_Pyro_QQTGG, "delta_composition", "H(26) C(18) N(6) O(8)"}, + {UNIMOD_Pyro_QQTGG, "spec_1_classification", "Other"}, + {UNIMOD_Pyro_QQTGG, "spec_1_hidden", "1"}, + {UNIMOD_Pyro_QQTGG, "spec_1_position", "Anywhere"}, + {UNIMOD_Pyro_QQTGG, "spec_1_site", "K"}, + {UNIMOD_NQTGG, "approved", "0"}, + {UNIMOD_NQTGG, "delta_composition", "H(27) C(17) N(7) O(8)"}, + {UNIMOD_NQTGG, "spec_1_classification", "Other"}, + {UNIMOD_NQTGG, "spec_1_hidden", "1"}, + {UNIMOD_NQTGG, "spec_1_position", "Anywhere"}, + {UNIMOD_NQTGG, "spec_1_site", "K"}, + {UNIMOD_DVFQQQTGG, "approved", "0"}, + {UNIMOD_DVFQQQTGG, "delta_composition", "H(60) C(41) N(12) O(15)"}, + {UNIMOD_DVFQQQTGG, "spec_1_classification", "Other"}, + {UNIMOD_DVFQQQTGG, "spec_1_hidden", "1"}, + {UNIMOD_DVFQQQTGG, "spec_1_position", "Anywhere"}, + {UNIMOD_DVFQQQTGG, "spec_1_site", "K"}, + {UNIMOD_iST_NHS_specific_cysteine_modification, "approved", "0"}, + {UNIMOD_iST_NHS_specific_cysteine_modification, "delta_composition", "H(11) C(6) N O"}, + {UNIMOD_iST_NHS_specific_cysteine_modification, "spec_1_classification", "Chemical derivative"}, + {UNIMOD_iST_NHS_specific_cysteine_modification, "spec_1_hidden", "1"}, + {UNIMOD_iST_NHS_specific_cysteine_modification, "spec_1_position", "Anywhere"}, + {UNIMOD_iST_NHS_specific_cysteine_modification, "spec_1_site", "C"}, + {UNIMOD_Label_13C_2_15N_1_, "approved", "0"}, + {UNIMOD_Label_13C_2_15N_1_, "delta_composition", "C(-2) 13C(2) N(-1) 15N"}, + {UNIMOD_Label_13C_2_15N_1_, "spec_1_classification", "Isotopic label"}, + {UNIMOD_Label_13C_2_15N_1_, "spec_1_hidden", "1"}, + {UNIMOD_Label_13C_2_15N_1_, "spec_1_position", "Anywhere"}, + {UNIMOD_Label_13C_2_15N_1_, "spec_1_site", "G"}, }; // propertyValue_ @@ -26309,16 +26819,16 @@ class CVTermData : public boost::singleton cvMap_["PEFF"].URI = cvMap_["MS"].URI; cvMap_["MS"].id = "MS"; - cvMap_["MS"].version = "4.1.117"; + cvMap_["MS"].version = "4.1.163"; cvMap_["NCIT"].id = "NCIT"; - cvMap_["NCIT"].version = "4.1.117"; + cvMap_["NCIT"].version = "4.1.163"; cvMap_["PEFF"].id = "PEFF"; - cvMap_["PEFF"].version = "4.1.117"; + cvMap_["PEFF"].version = "4.1.163"; cvMap_["UNIMOD"].id = "UNIMOD"; - cvMap_["UNIMOD"].version = "2022-10-20"; + cvMap_["UNIMOD"].version = "2024-02-29"; cvMap_["UO"].id = "UO"; cvMap_["UO"].version = "09:04:2014"; diff --git a/src/pwiz/data/common/cv.hpp b/src/pwiz/data/common/cv.hpp index 5b0d40de5..284a328c9 100644 --- a/src/pwiz/data/common/cv.hpp +++ b/src/pwiz/data/common/cv.hpp @@ -41,12 +41,10 @@ // [psi-ms.obo] #define _PSI_MS_OBO_ // format-version: 1.2 -// data-version: 4.1.117 -// date: 17:03:2023 11:30 -// saved-by: Matt Chambers +// data-version: 4.1.163 +// date: 19:07:2024 07:15 +// saved-by: Joshua Klein // auto-generated-by: OBO-Edit 2.3.1 -// import: http://purl.obolibrary.org/obo/pato.obo -// import: http://purl.obolibrary.org/obo/stato.owl // default-namespace: MS // namespace-id-rule: * MS:$sequence(7,0,9999999)$ // namespace-id-rule: * PEFF:$sequence(7,0,9999999)$ @@ -79,7 +77,7 @@ // [unimod.obo] #define _UNIMOD_OBO_ // format-version: 1.4 -// date: 20:10:2022 14:06 +// date: 29:02:2024 10:49 // // [unit.obo] #define _UNIT_OBO_ @@ -307,6 +305,9 @@ enum PWIZ_API_DECL CVID /// Duration: The period of time during which something continues. NCIT_Duration = 100325330, + /// Number: A numeral or string of numerals expressing value, quantity, or identification. + NCIT_Number = 100325337, + /// Action: A thing done. NCIT_Action = 100325404, @@ -430,7 +431,7 @@ enum PWIZ_API_DECL CVID /// customization: Free text description of a single customization made to the instrument; for several modifications, use several entries. MS_customization = 1000032, - /// deisotoping: The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution. + /// deisotoping: The removal of isotope peaks to represent the ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution. MS_deisotoping = 1000033, /// charge deconvolution: The determination of the mass of an ion based on the mass spectral peaks that represent multiple-charge ions. @@ -1645,7 +1646,7 @@ enum PWIZ_API_DECL CVID /// MS/MS in Space: A tandem mass spectrometry method in which product ion spectra are recorded in m/z analyzers separated in space. Specific m/z separation functions are designed such that in one section of the instrument ions are selected, dissociated in an intermediate region, and the product ions are then transmitted to another analyser for m/z separation and data acquisition. MS_MS_MS_in_Space_OBSOLETE = 1000335, - /// neutral loss: The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID: 21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type). + /// neutral loss: The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID:21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type). MS_neutral_loss = 1000336, /// nth generation product ion: Serial product ions from dissociation of selected precursor ions where n refers to the number of stages of dissociation. The term granddaughter ion is deprecated. @@ -1822,6 +1823,9 @@ enum PWIZ_API_DECL CVID /// laser desorption ionization: The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material. MS_laser_desorption_ionization = 1000393, + /// no sequence database: No reference sequence database was used in the search process to determine the identified peptide sequence, for example as with de novo sequencing. + MS_no_sequence_database = 1000394, + /// liquid secondary ionization: The ionization of any species by the interaction of a focused beam of ions with a sample that is dissolved in a solvent matrix. See also fast atom bombardment and secondary ionization. MS_liquid_secondary_ionization = 1000395, @@ -2719,6 +2723,9 @@ enum PWIZ_API_DECL CVID /// 4000 Series Explorer Software: SCIEX or Applied Biosystems software for data acquisition and analysis. MS_4000_Series_Explorer_Software = 1000659, + /// Xevo MRT MS: Waters Corporation Xevo MRT Mass Spectrometer. + MS_Xevo_MRT_MS = 1000660, + /// GPS Explorer: SCIEX or Applied Biosystems software for data acquisition and analysis. MS_GPS_Explorer = 1000661, @@ -3256,6 +3263,9 @@ enum PWIZ_API_DECL CVID /// isolation window upper offset: The extent of the isolation window in m/z above the isolation window target m/z. The lower and upper offsets may be asymmetric about the target m/z. MS_isolation_window_upper_offset = 1000829, + /// precision: Precision is the degree of how close repeated measurements are to each other. This can, for example, be expressed using the standard deviation. + MS_precision = 1000830, + /// sample preparation: Properties of the preparation steps which took place before the measurement was performed. MS_sample_preparation = 1000831, @@ -3373,8 +3383,8 @@ enum PWIZ_API_DECL CVID /// structural formula: A chemical formula showing the number of atoms of each element in a molecule, their spatial arrangement, and their linkage to each other. MS_structural_formula = 1000867, - /// SMILES formula: The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string. - MS_SMILES_formula = 1000868, + /// SMILES string: The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string. + MS_SMILES_string = 1000868, /// collision gas pressure: The gas pressure of the collision gas used for collisional excitation. MS_collision_gas_pressure = 1000869, @@ -8713,6 +8723,12 @@ enum PWIZ_API_DECL CVID /// FLASHDeconv: Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics. MS_FLASHDeconv = 1002714, + /// temperature chromatogram: Representation of temperature versus time. + MS_temperature_chromatogram = 1002715, + + /// measured element: The component or dimension of an object being measured, for example the temperature of an instrument component over time. + MS_measured_element = 1002716, + /// Pegasus BT: LECO bench-top GC time-of-flight mass spectrometer. MS_Pegasus_BT = 1002719, @@ -9868,8 +9884,11 @@ enum PWIZ_API_DECL CVID /// ion annotation format: Annotation format used for annotating individual spectrum ion peaks. MS_ion_annotation_format = 1003103, - /// peptide ion annotation format: Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions. - MS_peptide_ion_annotation_format = 1003104, + /// mzPAF peptide ion annotation format: Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions. + MS_mzPAF_peptide_ion_annotation_format = 1003104, + + /// peptide ion annotation format (mzPAF peptide ion annotation format): Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions. + MS_peptide_ion_annotation_format = MS_mzPAF_peptide_ion_annotation_format, /// crosslinked peptide ion annotation format: Annotation format designed specifically for crosslinked peptide ion peaks. MS_crosslinked_peptide_ion_annotation_format = 1003105, @@ -10576,8 +10595,11 @@ enum PWIZ_API_DECL CVID /// number of identified proteoforms: The number of proteoforms that pass the threshold to be considered identified with sufficient confidence. MS_number_of_identified_proteoforms = 1003328, - /// loop-link spectrum identification item: Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a loop-link. - MS_loop_link_spectrum_identification_item = 1003329, + /// looplink spectrum identification item: Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a looplink. + MS_looplink_spectrum_identification_item = 1003329, + + /// loop-link spectrum identification item (looplink spectrum identification item): Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a looplink. + MS_loop_link_spectrum_identification_item = MS_looplink_spectrum_identification_item, /// noncovalently associated peptides search: Noncovalently associated peptides search performed. Noncovalently associated peptides are two different peptides which were not crosslinked but stayed associated with each other throughout the workflow, due to noncovalent interactions. MS_noncovalently_associated_peptides_search = 1003330, @@ -10588,7 +10610,7 @@ enum PWIZ_API_DECL CVID /// identification based on multiple spectra: Provides an identifier to encode identifications based on multiple spectra. MS_identification_based_on_multiple_spectra = 1003332, - /// regular expression for encoding identifications based on multiple spectra.: ^(?[0-9]+)(?::(?P|C))$ + /// regular expression for encoding identifications based on multiple spectra.: ^(?[0-9]+)(?::(?P|C))?$ MS_regular_expression_for_encoding_identifications_based_on_multiple_spectra_ = 1003333, /// parent term for PSM-level scores for identifications based on multiple spectra: Parent term for PSM-level scores for identifications based on multiple spectra. @@ -10660,6 +10682,180 @@ enum PWIZ_API_DECL CVID /// Orbitrap Ascend: Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers. MS_Orbitrap_Ascend = 1003356, + /// ANN-SoLo: ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up open modification searching by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate and the shifted dot product score to sensitively match modified spectra to their unmodified counterpart. + MS_ANN_SoLo = 1003357, + + /// XCorr rank: The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the XCorr score. + MS_XCorr_rank = 1003358, + + /// exact p-value: A p-value for the XCorr score, calculated using dynamic programming. + MS_exact_p_value = 1003359, + + /// refactored XCorr: A modified version of the XCorr score that is made amenable to dynamic programming calculation of p-values by changing a max operation to a sum. + MS_refactored_XCorr = 1003360, + + /// res-ev score: The residue-evidence (res-ev) score measures the quality of a match between a peptide and observed spectrum using a method similar to XCorr, but considering all pairs of observed peaks. + MS_res_ev_score = 1003361, + + /// res-ev rank: The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the res-ev score. + MS_res_ev_rank = 1003362, + + /// res-ev p-value: The residue-evidence p-value is computed from the residue-evidence score using a dynamic programming procedure. + MS_res_ev_p_value = 1003363, + + /// combined p-value: A p-value that is computed by taking the product of the exact p-value and the res-ev p-value and then adjusting for dependencies between them. + MS_combined_p_value = 1003364, + + /// combined p-value rank: The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the combined p-value. + MS_combined_p_value_rank = 1003365, + + /// tailor score: A calibrated version of the XCorr score, computed by dividing the XCorr by the 99th percentile of the distribution of all scores for a particular spectrum. + MS_tailor_score = 1003366, + + /// monoisotopic mass deisotoping: The removal of isotope peaks to represent each ion as one data point corresponding to the ion's monoisotopic mass. It is done in conjunction with the charge state deconvolution. + MS_monoisotopic_mass_deisotoping = 1003367, + + /// most abundant mass deisotoping: The removal of isotope peaks to represent each ion as one data point corresponding to the ion's most abundant isotopic mass. It is done in conjunction with the charge state deconvolution. + MS_most_abundant_mass_deisotoping = 1003368, + + /// average mass deisotoping: The removal of isotope peaks to represent each ion as one data point corresponding to the ion's average mass. It is done in conjunction with the charge state deconvolution. + MS_average_mass_deisotoping = 1003369, + + /// reduction to summed singly charged peak list: The summing of peaks corresponding to the same mass at multiple charge states and presented as singly charged m/z. + MS_reduction_to_summed_singly_charged_peak_list = 1003370, + + /// SelexION compensation voltage: The voltage applied in the SelexION device to allow certain ions to transmit through to the mass spectrometer. + MS_SelexION_compensation_voltage = 1003371, + + /// specification document extension version: The versioning of a an extension to a specification document that the current file requires to be read correctly. The version should encode the name of the extension, and some ordinal expression of its revision, preferably in semantic versioning notation. Signals that readers that do not know this extension should return an appropriately informative error if they do not think they can or should try to interpret the file. + MS_specification_document_extension_version = 1003372, + + /// mzIdentML extension version: The versioning of an mzIdentML extension document. + MS_mzIdentML_extension_version = 1003373, + + /// Open Chromatography Binary OCB format: ChemClipse/OpenChrom file format. + MS_Open_Chromatography_Binary_OCB_format = 1003374, + + /// Conversion to OCB: Conversion of a file format to Open Chromatography Binary OCB file format. + MS_Conversion_to_OCB = 1003375, + + /// ChemClipse: ChemClipse is part of the Eclipse Science project. Primarily developed by Lablicate GmbH. + MS_ChemClipse = 1003376, + + /// chemclipse (ChemClipse): ChemClipse is part of the Eclipse Science project. Primarily developed by Lablicate GmbH. + MS_chemclipse = MS_ChemClipse, + + /// OpenChrom: OpenChrom is an Open Source software for data processing and analysis. Based upon Eclipse ChemClipse. + MS_OpenChrom = 1003377, + + /// openchrom (OpenChrom): OpenChrom is an Open Source software for data processing and analysis. Based upon Eclipse ChemClipse. + MS_openchrom = MS_OpenChrom, + + /// Orbitrap Astral: Thermo Scientific Orbitrap Astral mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral analyzer. + MS_Orbitrap_Astral = 1003378, + + /// asymmetric track lossless time-of-flight analyzer: A TOF-like mass analyzer with asymmetric ion mirrors to direct ions into transversal asymmetric oscillations and ion foil shapes and maintains ion packet for transmission and resolution. + MS_asymmetric_track_lossless_time_of_flight_analyzer = 1003379, + + /// Astral (asymmetric track lossless time-of-flight analyzer): A TOF-like mass analyzer with asymmetric ion mirrors to direct ions into transversal asymmetric oscillations and ion foil shapes and maintains ion packet for transmission and resolution. + MS_Astral = MS_asymmetric_track_lossless_time_of_flight_analyzer, + + /// Xevo G3 QTof: Waters Corporation Xevo G3 QTof quadrupole time-of-flight mass spectrometer. + MS_Xevo_G3_QTof = 1003380, + + /// ACQUITY RDa Detector: Waters Corporation RDa time-of-flight mass detector. + MS_ACQUITY_RDa_Detector = 1003381, + + /// waters_connect: Waters Corporation waters_connect software for liquid chromatography and mass spectrometry acquisition and processing. + MS_waters_connect = 1003382, + + /// timsTOF Ultra: Bruker Daltonics' timsTOF Ultra. + MS_timsTOF_Ultra = 1003383, + + /// semantic version regexp: v?(\d+)\.(\d+)\.(\d+)(?:-(\S+))? + MS_semantic_version_regexp = 1003384, + + /// mzIdentML crosslinking extension document version: The versioning of the crosslinking mzIdentML extension document. + MS_mzIdentML_crosslinking_extension_document_version = 1003385, + + /// Spectra: Bioconductor package Spectra for mass spectrometry data representation and processing. + MS_Spectra = 1003386, + + /// MetaboAnnotation: Bioconductor package MetaboAnnotation for annotation of untargeted metabolomics data. + MS_MetaboAnnotation = 1003387, + + /// CompoundDb: Bioconductor package CompoundDb for creation, usage and maintenance of public or library-specific annotation databases and spectra libraries. + MS_CompoundDb = 1003388, + + /// mzTab-M: Expanded tabular result format for metabolomics experiments reporting quantitative summary data, MS features and identification evidence. + MS_mzTab_M = 1003389, + + /// crosslinker cleavage characteristics: Signifies that the crosslinker is cleavable and on cleavage can leave a given stub. The pattern specifies three slots ::. + MS_crosslinker_cleavage_characteristics = 1003390, + + /// crosslinker cleavage regular expression: ^(?[A-Za-z]):(?[+-]?[0-9]+(\.[0-9]+)?([eE][+-]?[0-9]+(\.[0-9]+)?)?):(?[A-Za-z]+)$ + MS_crosslinker_cleavage_regular_expression = 1003391, + + /// search modification id: A unique identifier within an in mzIdentML document denoting a search modification rule. The same modification may be present multiple times with different id values to reflect different specificities or neutral losses. + MS_search_modification_id = 1003392, + + /// search modification id ref: A reference to a `search modification id` in the current mzIdentML document that defines the properties of this modification instance. + MS_search_modification_id_ref = 1003393, + + /// SelexION separation voltage: RF voltage applied in the SelexION device to separate ions in trajectory based on the difference in their mobility between the high field and low field portions of the applied RF. + MS_SelexION_separation_voltage = 1003394, + + /// Q Exactive GC Orbitrap: Q Exactive GC Orbitrap GC-MS/MS hybrid quadrupole Orbitrap mass spectrometer. + MS_Q_Exactive_GC_Orbitrap = 1003395, + + /// 8890 GC/MS: Agilent 8890 Gas Chromatograph System. + MS_8890_GC_MS = 1003396, + + /// timsTOF fleX MALDI-2: Bruker Daltonics' timsTOF fleX MALDI-2. + MS_timsTOF_fleX_MALDI_2 = 1003397, + + /// deconvoluted data: The data contained in this file have been processed to remove, collapse, or label one or more dimensions of the original dataset, such as charge deconvolution or ion mobility deconvolution. To determine the type of deconvolution done, the reader should consult the appropriate section of the file, such as the data processing methods in an mzML file. + MS_deconvoluted_data = 1003398, + + /// quality control software: Software that creates or manipulates QC-related data. + MS_quality_control_software = 1003399, + + /// rmzqc: An R package for reading, validating, and writing mzQC files. + MS_rmzqc = 1003400, + + /// jmzqc: A Java package for reading, validating, and writing mzQC files. + MS_jmzqc = 1003401, + + /// pymzqc: A Python package for reading, validating, and writing mzQC files. + MS_pymzqc = 1003402, + + /// InChI: IUPAC International Chemical Identifier. + MS_InChI = 1003403, + + /// timsTOF HT: Bruker Daltonics' timsTOF HT. + MS_timsTOF_HT = 1003404, + + /// mzRecal: MS1 recalibration using identified peptides as internal calibrants. + MS_mzRecal = 1003405, + + /// spectrum clustering software: Software designed to group multiple mass spectra by high similarity, generally with the goal of grouping replicate spectra derived from the same analyte. + MS_spectrum_clustering_software = 1003406, + + /// Scout: Identifying crosslinked peptides in complex protein mixtures + MS_Scout = 1003407, + + /// Scout score: Scout identification search engine score + MS_Scout_score = 1003408, + + /// Stellar: Thermo Scientific Stellar mass spectrometer contains a quadrupole mass filter, a collision cell, and a quadrupole linear ion trap mass analyzer. + MS_Stellar = 1003409, + + /// electron beam energy: The kinetic energy of the electron beam used in dissociation methods induced by a free electron beam, such as electron-capture dissociation (ECD), electron-detachment dissociation (EDD), and electron-activated dissociation (EAD). + MS_electron_beam_energy = 1003410, + + /// Number of Occurrences: The number of times something happened. + NCIT_Number_of_Occurrences = 103150827, + /// PSI-MS CV Quality Control Vocabulary: PSI Quality Control controlled vocabulary term. MS_PSI_MS_CV_Quality_Control_Vocabulary = 4000000, @@ -10909,10 +11105,10 @@ enum PWIZ_API_DECL CVID /// slowest frequency for MS level 2 collection: The slowest acquisition speed with which product MS scans were collected. Scan acquisition frequency can be used to gauge the suitability of used instrument settings for the sample content used. MS_slowest_frequency_for_MS_level_2_collection = 4000096, - /// MS1 signal jump (10x) count: The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans. An unusual high count of signal jumps or falls can indicate ESI stability issues. + /// MS1 signal jump (10x) count: The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans. MS_MS1_signal_jump__10x__count = 4000097, - /// MS1 signal fall (10x) count: The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans. An unusual high count of signal jumps or falls can indicate ESI stability issues. + /// MS1 signal fall (10x) count: The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans. MS_MS1_signal_fall__10x__count = 4000098, /// number of empty MS1 scans: Number of MS1 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks). @@ -10966,20 +11162,20 @@ enum PWIZ_API_DECL CVID /// MS2 peak density distribution high outliers: From the distribution of peak densities in MS2, the list of outliers above a in-file defined threshold MS_MS2_peak_density_distribution_high_outliers = 4000115, - /// precursor intensity distribution quantiles: From the distribution of precursor intensities, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 - MS_precursor_intensity_distribution_quantiles = 4000116, + /// MS2 precursor intensity distribution: From the distribution of MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. + MS_MS2_precursor_intensity_distribution = 4000116, - /// precursor intensity distribution mean: From the distribution of precursor intensities, the mean - MS_precursor_intensity_distribution_mean = 4000117, + /// MS2 precursor intensity distribution mean: From the distribution of MS2 precursor intensities, the mean + MS_MS2_precursor_intensity_distribution_mean = 4000117, - /// precursor intensity distribution sigma: From the distribution of precursor intensities, the sigma value - MS_precursor_intensity_distribution_sigma = 4000118, + /// MS2 precursor intensity distribution sigma: From the distribution of MS2 precursor intensities, the sigma value + MS_MS2_precursor_intensity_distribution_sigma = 4000118, - /// precursor intensity distribution low outliers: From the distribution of precursor intensities, the list of outliers below a in-file defined threshold - MS_precursor_intensity_distribution_low_outliers = 4000119, + /// MS2 precursor intensity distribution low outliers: From the distribution of precursor intensities, the list of outliers below a in-file defined threshold + MS_MS2_precursor_intensity_distribution_low_outliers = 4000119, - /// precursor intensity distribution high outliers: From the distribution of precursor intensities, the list of outliers above a in-file defined threshold - MS_precursor_intensity_distribution_high_outliers = 4000120, + /// MS2 precursor intensity distribution high outliers: From the distribution of precursor intensities, the list of outliers above a in-file defined threshold + MS_MS2_precursor_intensity_distribution_high_outliers = 4000120, /// MS1 signal-to-noise ratio quantiles: From the distribution of signal-to-noise ratio in MS1, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3 MS_MS1_signal_to_noise_ratio_quantiles = 4000121, @@ -11044,27 +11240,126 @@ enum PWIZ_API_DECL CVID /// outlier threshold criterion: The definition of the outlier criteria applied. MS_outlier_threshold_criterion = 4000141, - /// Tukey's fence: Defines outliers with Tukey's fence as <(Q1-x*IQR) for low outliers and >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5 + /// Tukey's fence: Defines outliers with Tukey's fence as <(Q1-x*IQR) for low outliers and >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5. MS_Tukey_s_fence = 4000142, - /// Tukey's fence high outliers: Defines high outliers with Tukey's fence as >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5 + /// Tukey's fence high outliers: Defines high outliers with Tukey's fence as >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5. MS_Tukey_s_fence_high_outliers = 4000143, - /// Tukey's fence low outliers: Defines low outliers with Tukey's fence as <(Q1-x*IQR) for low outliers, where x is defined by the term's value. The default is x=1.5 + /// Tukey's fence low outliers: Defines low outliers with Tukey's fence as <(Q1-x*IQR) for low outliers, where x is defined by the term's value. The default is x=1.5. MS_Tukey_s_fence_low_outliers = 4000144, - /// Z-score threshold: Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3 + /// Z-score threshold: Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3. MS_Z_score_threshold = 4000145, - /// Z-score threshold high outliers: Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3 + /// Z-score threshold high outliers: Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3. MS_Z_score_threshold_high_outliers = 4000146, - /// Z-score threshold low outliers: Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3 + /// Z-score threshold low outliers: Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3. MS_Z_score_threshold_low_outliers = 4000147, - /// algorithmical threshold: Defines outliers algorithmically, where a single value threshold might not be applicable or p.r.n. multivariate decision making is applied. The value of the term should name the algorithmical method used + /// algorithmical threshold: Defines outliers algorithmically, where a single value threshold might not be applicable or p.r.n. multivariate decision making is applied. The value of the term should name the algorithmical method used. MS_algorithmical_threshold = 4000148, + /// iRT calibration formula: A polynomial formula to calibrate retention time based on iRT reference peptides. The order of the values corresponds to polynomial terms. I.e. a linear equation is represented by a two-tuple consisting of (slope, intercept). More general, the position in the n_tuple indicates the power of `x`: position `n → x^0`, position `n - 1 → x^1`, position `n - 2 → x^2`, etc. + MS_iRT_calibration_formula = 4000149, + + /// iRT calibration adjusted r-squared: The goodness of fit statistic between observed retention times and iRT calibrated retention times. + MS_iRT_calibration_adjusted_r_squared = 4000150, + + /// MsQuality: MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data. + MS_MsQuality = 4000151, + + /// MS2 precursor median m/z of identified quantification data points: Median m/z value for MS2 precursors of all quantification data points after user-defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_MS2_precursor_median_m_z_of_identified_quantification_data_points = 4000152, + + /// interquartile RT period for identified quantification data points: The interquartile retention time period, in seconds, for all quantification data points after user-defined acceptance criteria are applied over the complete run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_interquartile_RT_period_for_identified_quantification_data_points = 4000153, + + /// rate of the interquartile RT period for identified quantification data points: The rate of identified quantification data points for the interquartile retention time period, in identified quantification data points per second. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_rate_of_the_interquartile_RT_period_for_identified_quantification_data_points = 4000154, + + /// area under TIC: The area under the total ion chromatogram. + MS_area_under_TIC = 4000155, + + /// area under TIC RT quantiles: The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple. + MS_area_under_TIC_RT_quantiles = 4000156, + + /// extent of identified MS2 precursor intensity: Ratio of 95th over 5th percentile of MS2 precursor intensity for all quantification data points after user-defined acceptance criteria are applied. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_extent_of_identified_MS2_precursor_intensity = 4000157, + + /// median of TIC values in the RT range in which the middle half of quantification data points are identified: Median of TIC values in the RT range in which half of quantification data points are identified (RT values of Q1 to Q3 of identifications). These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_median_of_TIC_values_in_the_RT_range_in_which_the_middle_half_of_quantification_data_points_are_identified = 4000158, + + /// median of TIC values in the shortest RT range in which half of the quantification data points are identified: Median of TIC values in the shortest RT range in which half of the quantification data points are identified. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_median_of_TIC_values_in_the_shortest_RT_range_in_which_half_of_the_quantification_data_points_are_identified = 4000159, + + /// MS2 precursor intensity range: Minimum and maximum MS2 precursor intensity recorded. + MS_MS2_precursor_intensity_range = 4000160, + + /// identified MS2 precursor intensity distribution: From the distribution of identified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_identified_MS2_precursor_intensity_distribution = 4000161, + + /// unidentified MS2 precursor intensity distribution: From the distribution of unidentified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_unidentified_MS2_precursor_intensity_distribution = 4000162, + + /// identified MS2 precursor intensity distribution mean: From the distribution of identified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_identified_MS2_precursor_intensity_distribution_mean = 4000163, + + /// unidentified MS2 precursor intensity distribution mean: From the distribution of unidentified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_unidentified_MS2_precursor_intensity_distribution_mean = 4000164, + + /// identified MS2 precursor intensity distribution sigma: From the distribution of identified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_identified_MS2_precursor_intensity_distribution_sigma = 4000165, + + /// unidentified MS2 precursor intensity distribution sigma: From the distribution of unidentified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_unidentified_MS2_precursor_intensity_distribution_sigma = 4000166, + + /// ratio of 1+ over 2+ of all MS2 known precursor charges: The ratio of 1+ over 2+ MS2 precursor charge count of all spectra. + MS_ratio_of_1__over_2__of_all_MS2_known_precursor_charges = 4000167, + + /// ratio of 1+ over 2+ of identified MS2 known precursor charges: The ratio of 1+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_ratio_of_1__over_2__of_identified_MS2_known_precursor_charges = 4000168, + + /// ratio of 3+ over 2+ of all MS2 known precursor charges: The ratio of 3+ over 2+ MS2 precursor charge count of all spectra. + MS_ratio_of_3__over_2__of_all_MS2_known_precursor_charges = 4000169, + + /// ratio of 3+ over 2+ of identified MS2 known precursor charges: The ratio of 3+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_ratio_of_3__over_2__of_identified_MS2_known_precursor_charges = 4000170, + + /// ratio of 4+ over 2+ of all MS2 known precursor charges: The ratio of 4+ over 2+ MS2 precursor charge count of all spectra. + MS_ratio_of_4__over_2__of_all_MS2_known_precursor_charges = 4000171, + + /// ratio of 4+ over 2+ of identified MS2 known precursor charges: The ratio of 4+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_ratio_of_4__over_2__of_identified_MS2_known_precursor_charges = 4000172, + + /// mean MS2 precursor charge in all spectra: Mean MS2 precursor charge in all spectra + MS_mean_MS2_precursor_charge_in_all_spectra = 4000173, + + /// mean MS2 precursor charge in identified spectra: Mean MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_mean_MS2_precursor_charge_in_identified_spectra = 4000174, + + /// median MS2 precursor charge in all spectra: Median MS2 precursor charge in all spectra + MS_median_MS2_precursor_charge_in_all_spectra = 4000175, + + /// median MS2 precursor charge in identified spectra: Median MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability. + MS_median_MS2_precursor_charge_in_identified_spectra = 4000176, + + /// contaminant protein abundance fraction: The fraction of total protein abundance in a mass spectrometry run or a group of runs which can be attributed to a user-defined list of contaminant proteins (e.g. using the cRAP contaminant database). + MS_contaminant_protein_abundance_fraction = 4000177, + + /// precursor ppm deviation mean: The mean of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied + MS_precursor_ppm_deviation_mean = 4000178, + + /// precursor ppm deviation sigma: The standard deviation of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied + MS_precursor_ppm_deviation_sigma = 4000179, + + /// table of missed cleavage counts: The number of identified peptides with corresponding number of missed cleavages after user-defined acceptance criteria are applied. The number of missed cleavages per peptide is given in the 'number of missed cleavages' column, the respective count of such peptides identified in the 'Number of Occurrences' column. The highest 'missed cleavages' row is to be interpreted as that number of missed cleavages or higher. + MS_table_of_missed_cleavage_counts = 4000180, + + /// identified MS2 quarter RT fraction: The interval used for acquisition of the first, second, third, and fourth quarter of all identified MS2 events divided by retention time duration. + MS_identified_MS2_quarter_RT_fraction = 4000181, + /// unimod root node: The root node of the unimod modifications ontology. UNIMOD_unimod_root_node = 300000000, @@ -15607,6 +15902,39 @@ enum PWIZ_API_DECL CVID /// Glyceroyl: Glyceroylation. UNIMOD_Glyceroyl = 300002072, + /// N6pAMP: Plain N6-Propargyl-AMP modified proteins without any clicked enrichment tag. + UNIMOD_N6pAMP = 300002073, + + /// DABCYL-C2-maleimide: DABCYL-C2-maleimide Thiol-reactive dye for fluorescence labelling of proteins. + UNIMOD_DABCYL_C2_maleimide = 300002074, + + /// NBF: Thiol blocking reagent. + UNIMOD_NBF = 300002079, + + /// DCP: Dimedone-Based Chemical Probes. + UNIMOD_DCP = 300002080, + + /// Ethynyl: Ethynlation of cysteine residues. + UNIMOD_Ethynyl = 300002081, + + /// QQTGG: SUMOylation leaving QQTGG. + UNIMOD_QQTGG = 300002082, + + /// Pyro-QQTGG: SUMOylation leaving Pyro-QQTGG. + UNIMOD_Pyro_QQTGG = 300002083, + + /// NQTGG: SUMOylation leaving NQTGG. + UNIMOD_NQTGG = 300002084, + + /// DVFQQQTGG: SUMOylation by Endogenous SUMO2/3 following Lys C and Asp-N serial digestion. + UNIMOD_DVFQQQTGG = 300002085, + + /// iST-NHS specific cysteine modification: Preomics iST-NHS Kit specific cysteine modification. + UNIMOD_iST_NHS_specific_cysteine_modification = 300002086, + + /// Label:13C(2)15N(1): 13C(2) 15N(1) Silac label. + UNIMOD_Label_13C_2_15N_1_ = 300002088, + /// unit: A unit of measurement is a standardized quantity of a physical quality. UO_unit = 400000000, diff --git a/src/pwiz/data/common/psi-ms.obo b/src/pwiz/data/common/psi-ms.obo index 34d4db4d2..3b372e969 100644 --- a/src/pwiz/data/common/psi-ms.obo +++ b/src/pwiz/data/common/psi-ms.obo @@ -1,10 +1,8 @@ format-version: 1.2 -data-version: 4.1.117 -date: 17:03:2023 11:30 -saved-by: Matt Chambers +data-version: 4.1.163 +date: 19:07:2024 07:15 +saved-by: Joshua Klein auto-generated-by: OBO-Edit 2.3.1 -import: http://purl.obolibrary.org/obo/pato.obo -import: http://purl.obolibrary.org/obo/stato.owl default-namespace: MS namespace-id-rule: * MS:$sequence(7,0,9999999)$ namespace-id-rule: * PEFF:$sequence(7,0,9999999)$ @@ -45,6 +43,7 @@ name: has_units [Typedef] id: part_of name: part_of +xref: BFO:0000050 is_transitive: true [Typedef] @@ -184,6 +183,19 @@ name: Principal Component def: "One of the axes representing the projection of varience resulting from principal component analysis." [] {http://purl.obolibrary.org/obo/NCIT_C60694="NCI"} is_a: NCIT:C19044 ! Statistical Technique +[Term] +id: NCIT:C25337 +name: Number +def: "A numeral or string of numerals expressing value, quantity, or identification." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +is_a: NCIT:C20189 ! Property or Attribute + +[Term] +id: NCIT:C150827 +name: Number of Occurrences +def: "The number of times something happened." [] {http://purl.obolibrary.org/obo/NCIT_P378="NCI"} +synonym: "Number of Occurrences" EXACT [] {http://purl.obolibrary.org/obo/NCIT_P383="PT", http://purl.obolibrary.org/obo/NCIT_P384="NCI"} +is_a: NCIT:C25337 ! Number + [Term] id: MS:0000000 name: Proteomics Standards Initiative Mass Spectrometry Vocabularies @@ -424,7 +436,7 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter [Term] id: MS:1000033 name: deisotoping -def: "The removal of isotope peaks to represent the fragment ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution." [PSI:MS] +def: "The removal of isotope peaks to represent the ion as one data point and is commonly done to reduce complexity. It is done in conjunction with the charge state deconvolution." [PSI:MS] is_a: MS:1000543 ! data processing action [Term] @@ -2504,7 +2516,7 @@ is_obsolete: true [Term] id: MS:1000336 name: neutral loss -def: "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID: 21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type)." [PSI:MS] +def: "The loss of an uncharged species during a rearrangement process. The value slot holds the molecular formula in Hill notation of the neutral loss molecule, see PMID:21182243. This term must be used in conjunction with a child of the term MS:1002307 (fragmentation ion type)." [PSI:MS] is_a: MS:1001055 ! modification parameters relationship: has_value_type xsd:string ! The allowed value-type for this CV term @@ -2892,6 +2904,12 @@ name: laser desorption ionization def: "The formation of gas-phase ions by the interaction of a pulsed laser with a solid or liquid material." [PSI:MS] is_a: MS:1000247 ! desorption ionization +[Term] +id: MS:1000394 +name: no sequence database +def: "No reference sequence database was used in the search process to determine the identified peptide sequence, for example as with de novo sequencing." [PSI:PI] +is_a: MS:1001347 ! database file format + [Term] id: MS:1000395 name: liquid secondary ionization @@ -4689,6 +4707,12 @@ is_a: MS:1001455 ! acquisition software is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software +[Term] +id: MS:1000660 +name: Xevo MRT MS +def: "Waters Corporation Xevo MRT Mass Spectrometer." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + [Term] id: MS:1000661 name: GPS Explorer @@ -5827,6 +5851,7 @@ xref: binary-data-type:MS\:1000521 "32-bit float" xref: binary-data-type:MS\:1000523 "64-bit float" is_a: MS:1000513 ! binary data array relationship: has_units UO:0000012 ! kelvin +relationship: has_units UO:0000027 ! degree Celsius [Term] id: MS:1000823 @@ -5879,6 +5904,16 @@ is_a: MS:1000792 ! isolation window attribute relationship: has_units MS:1000040 ! m/z relationship: has_value_type xsd:float ! The allowed value-type for this CV term +[Term] +id: MS:1000830 +name: precision +def: "Precision is the degree of how close repeated measurements are to each other. This can, for example, be expressed using the standard deviation." [PSI:MS] +comment: See MS:1000014 for the related term of accuracy. +is_a: MS:1000480 ! mass analyzer attribute +relationship: has_units MS:1000040 ! m/z +relationship: has_units UO:0000169 ! parts per million +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + [Term] id: MS:1000831 name: sample preparation @@ -6132,9 +6167,9 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter [Term] id: MS:1000868 -name: SMILES formula +name: SMILES string def: "The simplified molecular input line entry specification or SMILES is a specification for unambiguously describing the structure of a chemical compound using a short ASCII string." [EDAM:2301] -is_a: MS:1000864 ! chemical formula +is_a: MS:1000867 ! structural formula relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] @@ -9521,6 +9556,7 @@ name: SpectraST def: "Open-source software for mass spectral library creation and searching, developed at the Institute for Systems Biology and the Hong Kong University of Science and Technology. Part of the Trans-Proteomic Pipeline." [PSI:PI] is_a: MS:1001456 ! analysis software is_a: MS:1003207 ! library creation software +is_a: MS:1003406 ! spectrum clustering software [Term] id: MS:1001478 @@ -10184,6 +10220,7 @@ name: FAIMS compensation voltage def: "The DC potential applied to the asymmetric waveform in FAIMS that compensates for the difference between high and low field mobility of an ion." [PSI:MS] synonym: "FAIMS CV" EXACT [] is_a: MS:1002892 ! ion mobility attribute +is_a: MS:1000455 ! ion selection attribute is_a: MS:1003254 ! peak attribute relationship: has_units UO:0000218 ! volt relationship: has_value_type xsd:double ! The allowed value-type for this CV term @@ -17868,6 +17905,19 @@ def: "Ultrafast, High-Quality Feature Deconvolution for Top-Down Proteomics." [D is_a: MS:1001456 ! analysis software is_a: MS:1001457 ! data processing software +[Term] +id: MS:1002715 +name: temperature chromatogram +def: "Representation of temperature versus time." [PSI:MS] +is_a: MS:1000626 ! chromatogram type + +[Term] +id: MS:1002716 +name: measured element +def: "The component or dimension of an object being measured, for example the temperature of an instrument component over time." [PSI:MS] +relationship: part_of MS:1000513 ! binary data array +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + [Term] id: MS:1002719 name: Pegasus BT @@ -19418,6 +19468,7 @@ id: MS:1002954 name: collisional cross sectional area def: "Structural molecular descriptor for the effective interaction area between the ion and neutral gas measured in ion mobility mass spectrometry." [PSI:PI] is_a: MS:1000861 ! molecular entity property +is_a: MS:1000455 ! ion selection attribute relationship: has_units UO:0000324 ! square angstrom relationship: has_value_type xsd:double ! The allowed value-type for this CV term @@ -19991,12 +20042,14 @@ id: MS:1003043 name: number of residues def: "Number of amino acid residues in a peptide, commonly referred to as the peptide length." [PSI:PI] is_a: MS:1000887 ! peptide attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003044 name: number of missed cleavages def: "Number of amino acid residue bonds that should have been cleaved by the cleavage agent used, but were not." [PSI:PI] is_a: MS:1000887 ! peptide attribute +relationship: has_value_type xsd:integer ! The allowed value-type for this CV term [Term] id: MS:1003045 @@ -20390,9 +20443,10 @@ is_a: MS:1003078 ! interpreted spectrum attribute [Term] id: MS:1003104 -name: peptide ion annotation format +name: mzPAF peptide ion annotation format def: "Annotation format designed primarily for peptides, with allowances for generic chemical formulas and other miscellaneous named ions." [PSI:MS] is_a: MS:1003103 ! ion annotation format +synonym: "peptide ion annotation format" EXACT [] [Term] id: MS:1003105 @@ -21216,6 +21270,7 @@ id: MS:1003221 name: data-dependent acquisition def: "Mass spectrometer data acquisition method wherein MSn spectra are triggered based on the m/z of precursor ions detected in the same run." [PSI:MS] is_a: MS:1003214 ! mass spectrometry acquisition method aspect +is_a: MS:1003213 ! mass spectrometry acquisition method synonym: "DDA" EXACT [] [Term] @@ -21530,6 +21585,7 @@ id: MS:1003270 name: proforma peptidoform ion notation def: "A string describing the peptidoform ion using the PSI ProForma notation, which should include the charge state, and optionally the adduct type." [PSI:PI] is_a: MS:1003256 ! peptidoform ion attribute +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003271 @@ -21720,12 +21776,14 @@ id: MS:1003298 name: contributing replicate spectrum keys def: "A list of cross references to contributing replicate spectra in the same library, in the form of library spectrum keys." [PSI:PI] relationship: part_of MS:1003297 ! contributing replicate spectrum +relationship: has_value_type MS:1002712 ! The allowed value-type for this CV term [Term] id: MS:1003299 name: contributing replicate spectrum USI def: "A list of cross references to contributing replicate spectra, in the form of PSI Universal Spectrum Identifiers." [PSI:PI] relationship: part_of MS:1003297 ! contributing replicate spectrum +relationship: has_value_type xsd:string ! The allowed value-type for this CV term [Term] id: MS:1003300 @@ -21751,7 +21809,7 @@ synonym: "SSM" EXACT [] id: MS:1003303 name: spectral similarity def: "A measure of how similar two spectra are, based on the features of the spectra (the locations and intensities of peaks) alone." [PSI:PI] -is_a: MS:1002694 ! single identification attribute +is_a: MS:1002694 ! single identification result attribute relationship: part_of MS:1003302 ! spectrum-spectrum match [Term] @@ -21929,8 +21987,9 @@ relationship: has_units UO:0000189 ! count unit [Term] id: MS:1003329 -name: loop-link spectrum identification item -def: "Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a loop-link." [PSI:MS] +name: looplink spectrum identification item +def: "Identification of an internally linked peptide (a peptide that contains both ends of a crosslink), also known as a looplink." [PSI:MS] +synonym: "loop-link spectrum identification item" EXACT [] is_a: MS:1002508 ! crosslinking attribute [Term] @@ -21958,7 +22017,7 @@ relationship: has_value_type xsd:string ! The allowed value-type for this CV ter [Term] id: MS:1003333 name: regular expression for encoding identifications based on multiple spectra. -def: "^(?[0-9]+)(?::(?P|C))$" [PSI:MS] +def: "^(?[0-9]+)(?::(?P|C))?$" [PSI:MS] is_a: MS:1002479 ! regular expression [Term] @@ -21989,7 +22048,7 @@ name: crosslinked PSM-level global FDR def: "Estimation of the global false discovery rate of crosslinked peptide spectrum matches." [PSI:MS] is_a: MS:1002701 ! PSM-level result list statistic is_a: MS:1002483 ! PSM-level statistical threshold -is_a: MS:1002664 ! interaction score derived from crosslinking +is_a: MS:1002664 ! interaction score derived from crosslinking relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] @@ -21998,7 +22057,7 @@ name: peptide-pair sequence-level global FDR def: "Estimation of the global false discovery rate for distinct peptide-pairs (id est multiple PSMs have been collapsed to one entry). Applicable in the case of crosslinked peptides or noncovalently associated peptides." [PSI:MS] is_a: MS:1002703 ! peptide sequence-level result list statistic is_a: MS:1002484 ! peptide-level statistical threshold -is_a: MS:1002664 ! interaction score derived from crosslinking +is_a: MS:1002664 ! interaction score derived from crosslinking relationship: has_value_type xsd:double ! The allowed value-type for this CV term [Term] @@ -22118,6 +22177,359 @@ name: Orbitrap Ascend def: "Thermo Scientific Orbitrap Ascend mass spectrometer with Tribrid architecture consisting of quadrupole mass filter, linear ion trap and Orbitrap mass analyzers." [PSI:PI] is_a: MS:1000494 ! Thermo Scientific instrument model +[Term] +id: MS:1003357 +name: ANN-SoLo +def: "ANN-SoLo (Approximate Nearest Neighbor Spectral Library) is a spectral library search engine for fast and accurate open modification searching. ANN-SoLo uses approximate nearest neighbor indexing to speed up open modification searching by selecting only a limited number of the most relevant library spectra to compare to an unknown query spectrum. This is combined with a cascade search strategy to maximize the number of identified unmodified and modified spectra while strictly controlling the false discovery rate and the shifted dot product score to sensitively match modified spectra to their unmodified counterpart." [doi:10.1021/acs.jproteome.8b00359, doi:10.1021/acs.jproteome.9b00291] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003358 +name: XCorr rank +def: "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the XCorr score." [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003359 +name: exact p-value +def: "A p-value for the XCorr score, calculated using dynamic programming." [PMID:24895379] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003360 +name: refactored XCorr +def: "A modified version of the XCorr score that is made amenable to dynamic programming calculation of p-values by changing a max operation to a sum." [PMID:30221945] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003361 +name: res-ev score +def: "The residue-evidence (res-ev) score measures the quality of a match between a peptide and observed spectrum using a method similar to XCorr, but considering all pairs of observed peaks." [PMID:30221945] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003362 +name: res-ev rank +def: "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the res-ev score." [PMID:30221945] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003363 +name: res-ev p-value +def: "The residue-evidence p-value is computed from the residue-evidence score using a dynamic programming procedure." [PMID:30221945] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003364 +name: combined p-value +def: "A p-value that is computed by taking the product of the exact p-value and the res-ev p-value and then adjusting for dependencies between them." [PMID:30221945] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003365 +name: combined p-value rank +def: "The rank of this PSM relative to all other PSMs involving this spectrum, when sorting by the combined p-value." [PMID:30221945] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003366 +name: tailor score +def: "A calibrated version of the XCorr score, computed by dividing the XCorr by the 99th percentile of the distribution of all scores for a particular spectrum." [PMID:32175744] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + +[Term] +id: MS:1003367 +name: monoisotopic mass deisotoping +def: "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's monoisotopic mass. It is done in conjunction with the charge state deconvolution." [PSI:MS] +is_a: MS:1000033 ! deisotoping + +[Term] +id: MS:1003368 +name: most abundant mass deisotoping +def: "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's most abundant isotopic mass. It is done in conjunction with the charge state deconvolution." [PSI:MS] +is_a: MS:1000033 ! deisotoping + +[Term] +id: MS:1003369 +name: average mass deisotoping +def: "The removal of isotope peaks to represent each ion as one data point corresponding to the ion's average mass. It is done in conjunction with the charge state deconvolution." [PSI:MS] +is_a: MS:1000033 ! deisotoping + +[Term] +id: MS:1003370 +name: reduction to summed singly charged peak list +def: "The summing of peaks corresponding to the same mass at multiple charge states and presented as singly charged m/z." [PSI:MS] +is_a: MS:1000543 ! data processing action + +[Term] +id: MS:1003371 +name: SelexION compensation voltage +def: "The voltage applied in the SelexION device to allow certain ions to transmit through to the mass spectrometer." [PSI:MS] +is_a: MS:1002892 ! ion mobility attribute +is_a: MS:1000455 ! ion selection attribute +is_a: MS:1003254 ! peak attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003372 +name: specification document extension version +def: "The versioning of a an extension to a specification document that the current file requires to be read correctly. The version should encode the name of the extension, and some ordinal expression of its revision, preferably in semantic versioning notation. Signals that readers that do not know this extension should return an appropriately informative error if they do not think they can or should try to interpret the file." [PSI:MS] +relationship: part_of MS:0000000 ! Proteomics Standards Initiative Mass Spectrometry Vocabularies +relationship: has_regexp MS:1003384 ! semantic version regexp + +[Term] +id: MS:1003373 +name: mzIdentML extension version +def: "The versioning of an mzIdentML extension document." [PSI:PI] +is_a: MS:1003372 ! specification document extension version +relationship: part_of MS:1002073 ! mzIdentML format + +[Term] +id: MS:1003374 +name: Open Chromatography Binary OCB format +def: "ChemClipse/OpenChrom file format." [PSI:MS] +is_a: MS:1000560 ! mass spectrometer file format + +[Term] +id: MS:1003375 +name: Conversion to OCB +def: "Conversion of a file format to Open Chromatography Binary OCB file format." [PSI:MS] +is_a: MS:1000530 ! file format conversion + +[Term] +id: MS:1003376 +name: ChemClipse +def: "ChemClipse is part of the Eclipse Science project. Primarily developed by Lablicate GmbH." [https://projects.eclipse.org/projects/science.chemclipse] +synonym: "chemclipse" EXACT [] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003377 +name: OpenChrom +def: "OpenChrom is an Open Source software for data processing and analysis. Based upon Eclipse ChemClipse." [PMID:20673335, DOI:10.1186/1471-2105-11-405, https://www.openchrom.net/] +synonym: "openchrom" EXACT [] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003378 +name: Orbitrap Astral +def: "Thermo Scientific Orbitrap Astral mass spectrometer contains three mass analyzers: a quadrupole analyzer, an Orbitrap analyzer, and the Astral analyzer." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003379 +name: asymmetric track lossless time-of-flight analyzer +def: "A TOF-like mass analyzer with asymmetric ion mirrors to direct ions into transversal asymmetric oscillations and ion foil shapes and maintains ion packet for transmission and resolution." [PSI:MS] +synonym: "Astral" EXACT [] +is_a: MS:1000084 ! time-of-flight + +[Term] +id: MS:1003380 +name: Xevo G3 QTof +def: "Waters Corporation Xevo G3 QTof quadrupole time-of-flight mass spectrometer." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1003381 +name: ACQUITY RDa Detector +def: "Waters Corporation RDa time-of-flight mass detector." [PSI:MS] +is_a: MS:1000126 ! Waters instrument model + +[Term] +id: MS:1003382 +name: waters_connect +def: "Waters Corporation waters_connect software for liquid chromatography and mass spectrometry acquisition and processing." [PSI:MS] +is_a: MS:1000694 ! Waters software +is_a: MS:1001455 ! acquisition software +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003383 +name: timsTOF Ultra +def: "Bruker Daltonics' timsTOF Ultra." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003384 +name: semantic version regexp +def: "v?(\d+)\.(\d+)\.(\d+)(?:-(\S+))?" [PSI:PI] +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1003385 +name: mzIdentML crosslinking extension document version +def: "The versioning of the crosslinking mzIdentML extension document." [PSI:PI] +is_a: MS:1003373 ! mzIdentML extension version +relationship: has_value_type xsd:string + +[Term] +id: MS:1003386 +name: Spectra +def: "Bioconductor package Spectra for mass spectrometry data representation and processing." [PSI:MS, https://doi.org/doi:10.18129/B9.bioc.Spectra] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003387 +name: MetaboAnnotation +def: "Bioconductor package MetaboAnnotation for annotation of untargeted metabolomics data." [PSI:MS, https://doi.org/doi:10.18129/B9.bioc.MetaboAnnotation, https://doi.org/10.3390/metabo12020173, PMID:35208247] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003388 +name: CompoundDb +def: "Bioconductor package CompoundDb for creation, usage and maintenance of public or library-specific annotation databases and spectra libraries." [PSI:MS, https://doi.org/doi:10.18129/B9.bioc.CompoundDb, https://doi.org/10.3390/metabo12020173, PMID:35208247] +is_a: MS:1001456 ! analysis software +is_a: MS:1001457 ! data processing software +is_a: MS:1003207 ! library creation software + +[Term] +id: MS:1003389 +name: mzTab-M +def: "Expanded tabular result format for metabolomics experiments reporting quantitative summary data, MS features and identification evidence." [PMID:30688441, PMID:31525911, https://www.psidev.info/mztab] +is_a: MS:1000914 ! tab delimited text format + +[Term] +id: MS:1003390 +name: crosslinker cleavage characteristics +def: "Signifies that the crosslinker is cleavable and on cleavage can leave a given stub. The pattern specifies three slots ::." [PSI:PI] +is_a: MS:1001471 ! peptide modification details +relationship: has_regexp MS:1003391 ! crosslinker cleavage regular expression +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003391 +name: crosslinker cleavage regular expression +def: "^(?[A-Za-z]):(?[+-]?[0-9]+(\.[0-9]+)?([eE][+-]?[0-9]+(\.[0-9]+)?)?):(?[A-Za-z]+)$" [PSI:PI] +is_a: MS:1002479 ! regular expression + +[Term] +id: MS:1003392 +name: search modification id +def: "A unique identifier within an in mzIdentML document denoting a search modification rule. The same modification may be present multiple times with different id values to reflect different specificities or neutral losses." [PSI:PI] +is_a: MS:1001471 ! peptide modification details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003393 +name: search modification id ref +def: "A reference to a `search modification id` in the current mzIdentML document that defines the properties of this modification instance." [PSI:PI] +is_a: MS:1001471 ! peptide modification details +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003394 +name: SelexION separation voltage +def: "RF voltage applied in the SelexION device to separate ions in trajectory based on the difference in their mobility between the high field and low field portions of the applied RF." [PSI:MS] +is_a: MS:1002892 ! ion mobility attribute +is_a: MS:1000455 ! ion selection attribute +is_a: MS:1003254 ! peak attribute +relationship: has_units UO:0000218 ! volt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:1003395 +name: Q Exactive GC Orbitrap +def: "Q Exactive GC Orbitrap GC-MS/MS hybrid quadrupole Orbitrap mass spectrometer." [PSI:MS] +is_a: MS:1000483 ! Thermo Fisher Scientific instrument model + +[Term] +id: MS:1003396 +name: 8890 GC/MS +def: "Agilent 8890 Gas Chromatograph System." [PSI:MS] +is_a: MS:1000490 ! Agilent instrument model + +[Term] +id: MS:1003397 +name: timsTOF fleX MALDI-2 +def: "Bruker Daltonics' timsTOF fleX MALDI-2." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003398 +name: deconvoluted data +def: "The data contained in this file have been processed to remove, collapse, or label one or more dimensions of the original dataset, such as charge deconvolution or ion mobility deconvolution. To determine the type of deconvolution done, the reader should consult the appropriate section of the file, such as the data processing methods in an mzML file." [PSI:MS] +is_a: MS:1000524 ! data file content + +[Term] +id: MS:1003399 +name: quality control software +def: "Software that creates or manipulates QC-related data." [PSI:MS] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003400 +name: rmzqc +def: "An R package for reading, validating, and writing mzQC files." [https://github.com/MS-Quality-hub/rmzqc] +is_a: MS:1003399 ! quality control software + +[Term] +id: MS:1003401 +name: jmzqc +def: "A Java package for reading, validating, and writing mzQC files." [https://github.com/MS-Quality-hub/jmzqc] +is_a: MS:1003399 ! quality control software + +[Term] +id: MS:1003402 +name: pymzqc +def: "A Python package for reading, validating, and writing mzQC files." [https://github.com/MS-Quality-hub/pymzqc] +is_a: MS:1003399 ! quality control software + +[Term] +id: MS:1003403 +name: InChI +def: "IUPAC International Chemical Identifier." [PMID:26136848] +is_a: MS:1001405 ! spectrum identification result details +is_a: MS:1000867 ! structural formula +relationship: has_value_type xsd:string ! The allowed value-type for this CV term + +[Term] +id: MS:1003404 +name: timsTOF HT +def: "Bruker Daltonics' timsTOF HT." [PSI:MS] +is_a: MS:1003123 ! Bruker Daltonics timsTOF series + +[Term] +id: MS:1003405 +name: mzRecal +def: "MS1 recalibration using identified peptides as internal calibrants." [DOI:10.1093/bioinformatics/btab056, PMID:33538780, https://github.com/524D/mzrecal] +is_a: MS:1001457 ! data processing software + +[Term] +id: MS:1003406 +name: spectrum clustering software +def: "Software designed to group multiple mass spectra by high similarity, generally with the goal of grouping replicate spectra derived from the same analyte." [PSI:MS] +is_a: MS:1000531 ! software + +[Term] +id: MS:1003409 +name: Stellar +def: "Thermo Scientific Stellar mass spectrometer contains a quadrupole mass filter, a collision cell, and a quadrupole linear ion trap mass analyzer." [PSI:MS] +is_a: MS:1000494 ! Thermo Scientific instrument model + +[Term] +id: MS:1003410 +name: electron beam energy +def: "The kinetic energy of the electron beam used in dissociation methods induced by a free electron beam, such as electron-capture dissociation (ECD), electron-detachment dissociation (EDD), and electron-activated dissociation (EAD)." [PSI:MS] +is_a: MS:1000510 ! precursor activation attribute +relationship: has_units UO:0000266 ! electronvolt +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + + [Term] id: MS:4000000 name: PSI-MS CV Quality Control Vocabulary @@ -22289,8 +22701,6 @@ relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000018 ! XIC metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_value_concept MS:1000086 ! full width at half-maximum -relationship: has_value_concept STATO:0000291 ! quantile -relationship: has_units UO:0000010 ! second [Term] id: MS:4000052 @@ -22304,13 +22714,12 @@ relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000018 ! XIC metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term -relationship: has_value_concept STATO:0000105 ! log signal intensity ratio -relationship: has_value_concept UO:0000191 ! fraction [Term] id: MS:4000053 name: chromatography duration def: "The retention time duration of the chromatography in seconds." [PSI:MS] +comment: Longer duration may indicate a better chromatographic separation of compounds which depends, however, also on the sampling/scan rate of the MS instrument. synonym: "RT-Duration" RELATED [PMID:24494671] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric @@ -22324,6 +22733,7 @@ relationship: has_units UO:0000010 ! second id: MS:4000054 name: TIC quarters RT fraction def: "The interval when the respective quarter of the TIC accumulates divided by retention time duration." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. The metric provides information on the sample (compound) flow along the chromatographic run, potentially revealing poor chromatographic performance, such as the absence of a signal for a significant portion of the run. synonym: "RT-TIC-Q1" RELATED [PMID:24494671] synonym: "RT-TIC-Q2" RELATED [PMID:24494671] synonym: "RT-TIC-Q3" RELATED [PMID:24494671] @@ -22340,6 +22750,7 @@ relationship: has_units UO:0000191 ! fraction id: MS:4000055 name: MS1 quarter RT fraction def: "The interval used for acquisition of the first, second, third, and fourth quarter of all MS1 events divided by retention time duration." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS1 scans, the values are expected to be in a similar range across samples of the same type. synonym: "RT-MS-Q1" RELATED [PMID:24494671] synonym: "RT-MS-Q2" RELATED [PMID:24494671] synonym: "RT-MS-Q3" RELATED [PMID:24494671] @@ -22356,6 +22767,7 @@ relationship: has_units UO:0000191 ! fraction id: MS:4000056 name: MS2 quarter RT fraction def: "The interval used for acquisition of the first, second, third, and fourth quarter of all MS2 events divided by retention time duration." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation. synonym: "RT-MSMS-Q1" RELATED [PMID:24494671] synonym: "RT-MSMS-Q2" RELATED [PMID:24494671] synonym: "RT-MSMS-Q3" RELATED [PMID:24494671] @@ -22372,6 +22784,7 @@ relationship: has_units UO:0000191 ! fraction id: MS:4000057 name: MS1 TIC-change quartile ratios def: "The log ratios of successive TIC-change quartiles. The TIC changes are the list of MS1 total ion current (TIC) value changes from one to the next scan, produced when each MS1 TIC is subtracted from the preceding MS1 TIC. The metric's value triplet represents the log ratio of the TIC-change Q2 to Q1, Q3 to Q2, TIC-change-max to Q3" [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation.This metric evaluates the stability (similarity) of MS1 TIC values from scan to scan along the LC run. High log ratios representing very large intensity differences between pairs of scans might be due to electrospray instability or presence of a chemical contaminant. synonym: "MS1-TIC-Change-Q2" RELATED [PMID:24494671] synonym: "MS1-TIC-Change-Q3" RELATED [PMID:24494671] synonym: "MS1-TIC-Change-Q4" RELATED [PMID:24494671] @@ -22381,12 +22794,12 @@ relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000017 ! chromatogram metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term -relationship: has_value_concept STATO:0000105 ! log signal intensity ratio [Term] id: MS:4000058 name: MS1 TIC quartile ratios def: "The log ratios of successive TIC quartiles. The metric's value triplet represents the log ratios of TIC-Q2 to TIC-Q1, TIC-Q3 to TIC-Q2, TIC-max to TIC-Q3." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. The ratios provide information on the distribution of the TIC values for one LC-MS run. Within an experiment, with the same LC setup, values should be comparable between samples. synonym: "MS1-TIC-Q2" RELATED [PMID:24494671] synonym: "MS1-TIC-Q3" RELATED [PMID:24494671] synonym: "MS1-TIC-Q4" RELATED [PMID:24494671] @@ -22396,12 +22809,12 @@ relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000017 ! chromatogram metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term -relationship: has_value_concept STATO:0000105 ! log signal intensity ratio [Term] id: MS:4000059 name: number of MS1 spectra def: "The number of MS1 events in the run." [PSI:MS] +comment: An unusual low number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. synonym: "MS1-Count" EXACT [PMID:24494671] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric @@ -22414,6 +22827,7 @@ relationship: has_units UO:0000189 ! count unit id: MS:4000060 name: number of MS2 spectra def: "The number of MS2 events in the run." [PSI:MS] +comment: An unusual low number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. synonym: "MS2-Count" EXACT [PMID:24494671] is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric @@ -22436,8 +22850,6 @@ relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000021 ! MS1 metric relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_concept NCIT:C45781 ! Density -relationship: has_value_concept STATO:0000291 ! quantile -relationship: has_units UO:0000189 ! count unit [Term] id: MS:4000062 @@ -22453,13 +22865,13 @@ relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_type xsd:int ! The allowed value-type for this CV term relationship: has_value_concept NCIT:C45781 ! Density -relationship: has_value_concept STATO:0000291 ! quantile relationship: has_units UO:0000189 ! count unit [Term] id: MS:4000063 name: MS2 known precursor charges fractions def: "The fraction of MS/MS precursors of the corresponding charge. The fractions [0,1] are given in the 'Fraction' column, corresponding charges in the 'Charge state' column. The highest charge state is to be interpreted as that charge state or higher." [PSI:MS] +comment: the MS2-PrecZ metrics can be directly read from the table respective table rows, the ratios of IS-3 metrics must be derived from the respective table rows, IS-3A as ratio of +1 over +2, IS-3B as ratio of +3 over +2, IS-3C as +4 over +2. synonym: "MS2-PrecZ-1" NARROW [PMID:24494671] synonym: "MS2-PrecZ-2" NARROW [PMID:24494671] synonym: "MS2-PrecZ-3" NARROW [PMID:24494671] @@ -22469,7 +22881,6 @@ synonym: "MS2-PrecZ-more" NARROW [PMID:24494671] synonym: "IS-3A" RELATED [PMID:19837981] synonym: "IS-3B" RELATED [PMID:19837981] synonym: "IS-3C" RELATED [PMID:19837981] -comment: the MS2-PrecZ metrics can be directly read from the table respective table rows, the ratios of IS-3 metrics must be derived from the respective table rows, IS-3A as ratio of +1 over +2, IS-3B as ratio of +3 over +2, IS-3C as +4 over +2. is_a: MS:4000005 ! table relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric @@ -22547,23 +22958,23 @@ relationship: has_relation MS:1000285 ! total ion current id: MS:4000069 name: m/z acquisition range def: "Upper and lower limit of m/z precursor values at which MSn spectra are recorded." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition. Based on the used MS instrument configuration, the values should be similar. Variations between measurements may arise when employing acquisition in DDA mode. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000019 ! MS metric relationship: has_units MS:1000040 ! m/z -relationship: has_value_concept STATO:0000035 ! range [Term] id: MS:4000070 name: retention time acquisition range def: "Upper and lower limit of retention time at which spectra are recorded." [PSI:MS] +comment: An unusual low range may indicate incomplete sampling and/or a premature or failed LC run. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_metric_category MS:4000016 ! retention time metric relationship: has_units UO:0000010 ! second -relationship: has_value_concept STATO:0000035 ! range [Term] id: MS:4000071 @@ -22580,6 +22991,7 @@ relationship: has_units UO:0000189 ! count unit id: MS:4000072 name: observed mass accuracy def: "Observed mass accuracy in ppm, calculated by 1E6 x (observed m/z - theoretical m/z)/theoretical m/z of a selected and identified ion in a mass spectrum." [PSI:MS] +is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000014 ! single spectrum based metric relationship: has_metric_category MS:4000008 ! ID based metric relationship: has_metric_category MS:4000022 ! MS2 metric @@ -22825,7 +23237,8 @@ relationship: has_metric_category MS:4000022 ! MS2 metric [Term] id: MS:4000097 name: MS1 signal jump (10x) count -def: "The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans. An unusual high count of signal jumps or falls can indicate ESI stability issues." [PSI:MS] +def: "The number of times where MS1 TIC increased more than 10-fold between adjacent MS1 scans." [PSI:MS] +comment: An unusual high count of signal jumps or falls may indicate ESI stability issues. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric @@ -22836,7 +23249,8 @@ synonym: "IS-1A" RELATED [] [Term] id: MS:4000098 name: MS1 signal fall (10x) count -def: "The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans. An unusual high count of signal jumps or falls can indicate ESI stability issues." [PSI:MS] +def: "The number of times where MS1 TIC decreased more than 10-fold between adjacent MS1 scans." [PSI:MS] +comment: An unusual high count of signal jumps or falls may indicate ESI stability issues. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric @@ -22848,6 +23262,7 @@ synonym: "IS-1B" RELATED [] id: MS:4000099 name: number of empty MS1 scans def: "Number of MS1 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS] +comment: An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric @@ -22859,6 +23274,7 @@ relationship: has_value_type xsd:integer ! The allowed value-type for this CV te id: MS:4000100 name: number of empty MS2 scans def: "Number of MS2 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS] +comment: An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric @@ -22870,6 +23286,7 @@ relationship: has_value_type xsd:integer ! The allowed value-type for this CV te id: MS:4000101 name: number of empty MS3 scans def: "Number of MS3 scans where the scans' peaks intensity sums to 0 (i.e. no peaks or only 0-intensity peaks)." [PSI:MS] +comment: An unusual high number may indicate incomplete sampling/scan rate of the MS instrument, low sample volume and/or failed injection of a sample. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric @@ -22914,7 +23331,7 @@ relationship: has_column MS:1000285 ! total ion current id: MS:4000105 name: ion injection parameters def: "Tabular representation of the parameters around ion selection like the amount of time spent filling an ion trapping device for each scan acquisition." [PSI:MS] -is_a: MS:4000005 ! table name: scan window upper limit +is_a: MS:4000005 ! table relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000012 ! single run based metric relationship: has_column MS:1000767 ! native spectrum identifier format @@ -22956,7 +23373,6 @@ comment: The distribution of peak densities in MS1 can provide insight into the is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -22967,7 +23383,6 @@ comment: The distribution of peak densities in MS1 can provide insight into the is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -22978,7 +23393,6 @@ comment: The distribution of peak densities in MS1 can provide insight into the is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -22989,7 +23403,6 @@ comment: The distribution of peak densities in MS1 can provide insight into the is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23000,7 +23413,6 @@ comment: The distribution of peak densities in MS2 can provide insight into the is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23011,7 +23423,6 @@ comment: The distribution of peak densities in MS2 can provide insight into the is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23022,7 +23433,6 @@ comment: The distribution of peak densities in MS2 can provide insight into the is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23033,62 +23443,60 @@ comment: The distribution of peak densities in MS2 can provide insight into the is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] id: MS:4000116 -name: precursor intensity distribution quantiles -def: "From the distribution of precursor intensities, the quantiles. I.e. a value triplet represents the quartiles Q1, Q2, Q3" [PSI:MS] +name: MS2 precursor intensity distribution +def: "From the distribution of MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3." [PSI:MS] comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000291 ! quantile relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000117 -name: precursor intensity distribution mean -def: "From the distribution of precursor intensities, the mean" [PSI:MS] +name: MS2 precursor intensity distribution mean +def: "From the distribution of MS2 precursor intensities, the mean" [PSI:MS] comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric -relationship: has_value_concept STATO:0000401 ! sample mean +relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000118 -name: precursor intensity distribution sigma -def: "From the distribution of precursor intensities, the sigma value" [PSI:MS] +name: MS2 precursor intensity distribution sigma +def: "From the distribution of MS2 precursor intensities, the sigma value" [PSI:MS] comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric -relationship: has_value_concept STATO:0000237 ! standard deviation +relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000119 -name: precursor intensity distribution low outliers +name: MS2 precursor intensity distribution low outliers def: "From the distribution of precursor intensities, the list of outliers below a in-file defined threshold" [PSI:MS] comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric -relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit [Term] id: MS:4000120 -name: precursor intensity distribution high outliers +name: MS2 precursor intensity distribution high outliers def: "From the distribution of precursor intensities, the list of outliers above a in-file defined threshold" [PSI:MS] comment: The intensity distribution of the precursors informs about the dynamic range of the acquisition. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric -relationship: has_value_concept STATO:0000036 ! outlier +relationship: has_metric_category MS:4000022 ! MS2 metric relationship: has_value_type xsd:float ! The allowed value-type for this CV term relationship: has_units MS:1000043 ! intensity unit @@ -23100,7 +23508,6 @@ comment: The Signal-to-noise ratio in MS1 distribution can provide insight to th is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000291 ! quantile relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23111,7 +23518,6 @@ comment: The signal-to-noise ratio in MS1 distribution can provide insight into is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23122,7 +23528,6 @@ comment: The Signal-to-noise ratio in MS1 distribution can provide insight into is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23133,7 +23538,6 @@ comment: The Signal-to-noise ratio in MS1 distribution can provide insight into is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23144,7 +23548,6 @@ comment: The Signal-to-noise ratio in MS1 distribution can provide insight into is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23155,7 +23558,6 @@ comment: A high signal-to-noise ratio in MS2 distribution can explain a high rat is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000291 ! quantile relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23166,7 +23568,6 @@ comment: A high signal-to-noise ratio in MS2 distribution can explain a high rat is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23177,7 +23578,6 @@ comment: A high signal-to-noise ratio in MS2 distribution can explain a high rat is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23188,7 +23588,6 @@ comment: A high signal-to-noise ratio in MS2 distribution can explain a high rat is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23199,7 +23598,6 @@ comment: A high signal-to-noise ratio in MS2 distribution can explain a high rat is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000036 ! outlier relationship: has_value_type xsd:float ! The allowed value-type for this CV term [Term] @@ -23209,7 +23607,6 @@ def: "From the distribution of ion injection times (MS:1000927) for MS1, the qua comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000291 ! quantile relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term @@ -23221,7 +23618,6 @@ comment: Injection time distribution can be used to gauge the suitability of use is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term @@ -23233,7 +23629,6 @@ comment: Injection time distribution can be used to gauge the suitability of use is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term @@ -23245,7 +23640,6 @@ comment: Injection time distribution can be used to gauge the suitability of use is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000036 ! outlier relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term @@ -23257,7 +23651,6 @@ comment: Injection time distribution can be used to gauge the suitability of use is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000021 ! MS1 metric -relationship: has_value_concept STATO:0000036 ! outlier relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term @@ -23268,7 +23661,6 @@ def: "From the distribution of ion injection times (MS:1000927) for MS2, the qua comment: Injection time distribution can be used to gauge the suitability of used instrument settings for the sample content used. is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric -relationship: has_value_concept STATO:0000291 ! quantile relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term @@ -23280,7 +23672,6 @@ comment: Injection time distribution can be used to gauge the suitability of use is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000401 ! sample mean relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term @@ -23292,7 +23683,6 @@ comment: Injection time distribution can be used to gauge the suitability of use is_a: MS:4000003 ! single value relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000237 ! standard deviation relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term @@ -23304,7 +23694,6 @@ comment: Injection time distribution can be used to gauge the suitability of use is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000036 ! outlier relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term @@ -23316,7 +23705,6 @@ comment: Injection time distribution can be used to gauge the suitability of use is_a: MS:4000004 ! n-tuple relationship: has_metric_category MS:4000009 ! ID free metric relationship: has_metric_category MS:4000022 ! MS2 metric -relationship: has_value_concept STATO:0000036 ! outlier relationship: has_units UO:0000028 ! millisecond relationship: has_value_type xsd:float ! The allowed value-type for this CV term @@ -23324,49 +23712,463 @@ relationship: has_value_type xsd:float ! The allowed value-type for this CV term id: MS:4000141 name: outlier threshold criterion def: "The definition of the outlier criteria applied." [PSI:MS] +is_a: MS:4000080 ! QC non-metric term [Term] id: MS:4000142 name: Tukey's fence -def: "Defines outliers with Tukey's fence as <(Q1-x*IQR) for low outliers and >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5" [PSI:MS] +def: "Defines outliers with Tukey's fence as <(Q1-x*IQR) for low outliers and >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion [Term] id: MS:4000143 name: Tukey's fence high outliers -def: "Defines high outliers with Tukey's fence as >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5" [PSI:MS] +def: "Defines high outliers with Tukey's fence as >(Q3+x*IQR) for high outliers, where x is defined by the term's value. The default is x=1.5." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion [Term] id: MS:4000144 name: Tukey's fence low outliers -def: "Defines low outliers with Tukey's fence as <(Q1-x*IQR) for low outliers, where x is defined by the term's value. The default is x=1.5" [PSI:MS] +def: "Defines low outliers with Tukey's fence as <(Q1-x*IQR) for low outliers, where x is defined by the term's value. The default is x=1.5." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion [Term] id: MS:4000145 name: Z-score threshold -def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3" [PSI:MS] +def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion [Term] id: MS:4000146 name: Z-score threshold high outliers -def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3" [PSI:MS] +def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion [Term] id: MS:4000147 name: Z-score threshold low outliers -def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3" [PSI:MS] +def: "Defines outliers with a Z-score threshold as <(-x) for low outliers and >(+x) for high outliers, where x is defined by the term's value. The default is x=3." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion [Term] id: MS:4000148 name: algorithmical threshold -def: "Defines outliers algorithmically, where a single value threshold might not be applicable or p.r.n. multivariate decision making is applied. The value of the term should name the algorithmical method used" [PSI:MS] +def: "Defines outliers algorithmically, where a single value threshold might not be applicable or p.r.n. multivariate decision making is applied. The value of the term should name the algorithmical method used." [PSI:MS] is_a: MS:4000141 ! outlier threshold criterion +[Term] +id: MS:4000149 +name: iRT calibration formula +def: "A polynomial formula to calibrate retention time based on iRT reference peptides. The order of the values corresponds to polynomial terms. I.e. a linear equation is represented by a two-tuple consisting of (slope, intercept). More general, the position in the n_tuple indicates the power of `x`: position `n → x^0`, position `n - 1 → x^1`, position `n - 2 → x^2`, etc." [PSI:MS] +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000150 +name: iRT calibration adjusted r-squared +def: "The goodness of fit statistic between observed retention times and iRT calibrated retention times." [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000151 +name: MsQuality +def: "MsQuality – an interoperable open-source package for the calculation of standardized quality metrics of mass spectrometry data." [DOI:10.1101/2023.05.12.540477, https://github.com/tnaake/MsQuality/] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:4000152 +name: MS2 precursor median m/z of identified quantification data points +def: "Median m/z value for MS2 precursors of all quantification data points after user-defined acceptance criteria are applied. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The m/z distribution informs about the dynamic range of the acquisition. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_units MS:1000040 ! m/z + +[Term] +id: MS:4000153 +name: interquartile RT period for identified quantification data points +def: "The interquartile retention time period, in seconds, for all quantification data points after user-defined acceptance criteria are applied over the complete run. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: Longer duration may indicate a better chromatographic separation of compounds which depends, however, also on the sampling/scan rate of the MS instrument. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000017 ! chromatogram metric +relationship: has_units UO:0000010 ! second +synonym: "C-2A" RELATED [PMID:19837981] + +[Term] +id: MS:4000154 +name: rate of the interquartile RT period for identified quantification data points +def: "The rate of identified quantification data points for the interquartile retention time period, in identified quantification data points per second. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: Higher rates may indicate a more efficient sampling and identification. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000017 ! chromatogram metric +relationship: has_units UO:0000106 ! hertz +synonym: "C-2B" RELATED [PMID:19837981] + +[Term] +id: MS:4000155 +name: area under TIC +def: "The area under the total ion chromatogram." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition. Differences between samples of an experiment may indicate differences in the dynamic range and/or in the sample content. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free +relationship: has_metric_category MS:4000017 ! chromatogram metric + +[Term] +id: MS:4000156 +name: area under TIC RT quantiles +def: "The area under the total ion chromatogram of the retention time quantiles. Number of quantiles are given by the n-tuple." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. Differences between samples of an experiment may indicate differences in chromatographic performance, differences in the dynamic range and/or in the sample content. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free +relationship: has_metric_category MS:4000017 ! chromatogram metric + +[Term] +id: MS:4000157 +name: extent of identified MS2 precursor intensity +def: "Ratio of 95th over 5th percentile of MS2 precursor intensity for all quantification data points after user-defined acceptance criteria are applied. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "MS1-3A" RELATED [PMID:19837981] + +[Term] +id: MS:4000158 +name: median of TIC values in the RT range in which the middle half of quantification data points are identified +def: "Median of TIC values in the RT range in which half of quantification data points are identified (RT values of Q1 to Q3 of identifications). These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric + +[Term] +id: MS:4000159 +name: median of TIC values in the shortest RT range in which half of the quantification data points are identified +def: "Median of TIC values in the shortest RT range in which half of the quantification data points are identified. These data points may be for example XIC profiles, isotopic pattern areas, or reporter ions (see MS:1001805). The used type should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition along the chromatographic separation. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +synonym: "MS1-2B" RELATED [PMID:19837981] + +[Term] +id: MS:4000160 +name: MS2 precursor intensity range +def: "Minimum and maximum MS2 precursor intensity recorded." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000009 ! ID free +relationship: has_metric_category MS:4000022 ! MS2 metric + +[Term] +id: MS:4000161 +name: identified MS2 precursor intensity distribution +def: "From the distribution of identified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000162 +name: unidentified MS2 precursor intensity distribution +def: "From the distribution of unidentified MS2 precursor intensities, the quantiles. E.g. a value triplet represents the quartiles Q1, Q2, Q3. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000163 +name: identified MS2 precursor intensity distribution mean +def: "From the distribution of identified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000164 +name: unidentified MS2 precursor intensity distribution mean +def: "From the distribution of unidentified MS2 precursor intensities, the mean. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000165 +name: identified MS2 precursor intensity distribution sigma +def: "From the distribution of identified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000166 +name: unidentified MS2 precursor intensity distribution sigma +def: "From the distribution of unidentified MS2 precursor intensities, the sigma value. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: The metric informs about the dynamic range of the acquisition in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units MS:1000043 ! intensity unit + +[Term] +id: MS:4000167 +name: ratio of 1+ over 2+ of all MS2 known precursor charges +def: "The ratio of 1+ over 2+ MS2 precursor charge count of all spectra." [PSI:MS] +comment: High ratios of 1+/2+ MS2 precursor charge count may indicate inefficient ionization. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "IS-3A" RELATED [PMID:19837981] +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] + +[Term] +id: MS:4000168 +name: ratio of 1+ over 2+ of identified MS2 known precursor charges +def: "The ratio of 1+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: High ratios of 1+/2+ MS2 precursor charge count may indicate inefficient ionization in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "IS-3A" RELATED [PMID:19837981] +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] + +[Term] +id: MS:4000169 +name: ratio of 3+ over 2+ of all MS2 known precursor charges +def: "The ratio of 3+ over 2+ MS2 precursor charge count of all spectra." [PSI:MS] +comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "IS-3B" RELATED [PMID:19837981] +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] + +[Term] +id: MS:4000170 +name: ratio of 3+ over 2+ of identified MS2 known precursor charges +def: "The ratio of 3+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "IS-3B" RELATED [PMID:19837981] +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] + +[Term] +id: MS:4000171 +name: ratio of 4+ over 2+ of all MS2 known precursor charges +def: "The ratio of 4+ over 2+ MS2 precursor charge count of all spectra." [PSI:MS] +comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "IS-3C" RELATED [PMID:19837981] +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] + +[Term] +id: MS:4000172 +name: ratio of 4+ over 2+ of identified MS2 known precursor charges +def: "The ratio of 4+ over 2+ MS2 precursor charge count of identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: Higher ratios of 3+/2+ MS2 precursor charge count may indicate e.g. preference for longer peptides in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "IS-3C" RELATED [PMID:19837981] +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] + +[Term] +id: MS:4000173 +name: mean MS2 precursor charge in all spectra +def: "Mean MS2 precursor charge in all spectra" [PSI:MS] +comment: Higher charges may indicate inefficient ionization or e.g. preference for longer peptides. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-5" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-more" RELATED [PMID:24494671] + +[Term] +id: MS:4000174 +name: mean MS2 precursor charge in identified spectra +def: "Mean MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: Higher charges may indicate inefficient ionization or e.g. preference for longer peptides in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-5" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-more" RELATED [PMID:24494671] + +[Term] +id: MS:4000175 +name: median MS2 precursor charge in all spectra +def: "Median MS2 precursor charge in all spectra" [PSI:MS] +comment: Higher charges may indicate inefficient ionization and/or e.g. preference for longer peptides. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000009 ! ID free metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-5" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-more" RELATED [PMID:24494671] + +[Term] +id: MS:4000176 +name: median MS2 precursor charge in identified spectra +def: "Median MS2 precursor charge in identified spectra. The used type of identification should be noted in the metadata or analysis methods section of the recording file for the respective run. In case of multiple acceptance criteria (FDR) available in proteomics, PSM-level FDR should be used for better comparability." [PSI:MS] +comment: Higher charges may indicate inefficient ionization and/or e.g. preference for longer peptides in relation to identifiability. +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000020 ! ion source metric +relationship: has_metric_category MS:4000022 ! MS2 metric +synonym: "MS2 known precursor charges fractions" RELATED [] +synonym: "MS2-PrecZ-1" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-2" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-3" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-4" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-5" RELATED [PMID:24494671] +synonym: "MS2-PrecZ-more" RELATED [PMID:24494671] + +[Term] +id: MS:4000177 +name: contaminant protein abundance fraction +def: "The fraction of total protein abundance in a mass spectrometry run or a group of runs which can be attributed to a user-defined list of contaminant proteins (e.g. using the cRAP contaminant database)." [PSI:MS] +comment: "High values may indicate a sample handling issue, and/or insufficient sample concentration." +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV +relationship: has_domain MS:1002305 ! value between 0 and 1 inclusive +relationship: has_order MS:1002109 ! lower score better +synonym: "PG: Contaminants" NARROW [] + +[Term] +id: MS:4000178 +name: precursor ppm deviation mean +def: "The mean of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied" [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept MS:1000014 ! accuracy +relationship: has_units UO:0000169 ! parts per million +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000179 +name: precursor ppm deviation sigma +def: "The standard deviation of the distribution of observed precursor mass accuracies (MS:4000072) [in ppm] of identified MS2 spectra after user-defined acceptance criteria (FDR) are applied" [PSI:MS] +is_a: MS:4000003 ! single value +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000021 ! MS1 metric +relationship: has_value_concept MS:1000830 ! precision +relationship: has_units UO:0000169 ! parts per million +relationship: has_value_type xsd:float ! The allowed value-type for this CV term + +[Term] +id: MS:4000180 +name: table of missed cleavage counts +def: "The number of identified peptides with corresponding number of missed cleavages after user-defined acceptance criteria are applied. The number of missed cleavages per peptide is given in the 'number of missed cleavages' column, the respective count of such peptides identified in the 'Number of Occurrences' column. The highest 'missed cleavages' row is to be interpreted as that number of missed cleavages or higher." [PSI:MS] +is_a: MS:4000005 ! table +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_column MS:1003044 ! number of missed cleavages +relationship: has_column NCIT:C150827 ! Number of Occurrences + +[Term] +id: MS:4000181 +name: identified MS2 quarter RT fraction +def: "The interval used for acquisition of the first, second, third, and fourth quarter of all identified MS2 events divided by retention time duration." [PSI:MS] +comment: The metric informs about the dynamic range of the MS2 identification process along the chromatographic separation. For MS2 scans, the comparability of the values depends on the acquisition mode and settings to select ions for fragmentation. +is_a: MS:4000004 ! n-tuple +relationship: has_metric_category MS:4000012 ! single run based metric +relationship: has_metric_category MS:4000008 ! ID based metric +relationship: has_metric_category MS:4000022 ! MS2 metric +relationship: has_metric_category MS:4000016 ! retention time metric +relationship: has_value_type xsd:float ! The allowed value-type for this CV term +relationship: has_units UO:0000191 ! fraction +synonym: "RT-MSMS-Q1" RELATED [PMID:24494671] +synonym: "RT-MSMS-Q2" RELATED [PMID:24494671] +synonym: "RT-MSMS-Q3" RELATED [PMID:24494671] +synonym: "RT-MSMS-Q4" RELATED [PMID:24494671] + +[Term] +id: MS:1003407 +name: Scout +def: "Identifying crosslinked peptides in complex protein mixtures" [PSI:MS] +is_a: MS:1001456 ! analysis software + +[Term] +id: MS:1003408 +name: Scout score +def: "Scout identification search engine score" [PSI:MS] +is_a: MS:1001143 ! PSM-level search engine specific statistic +relationship: has_order MS:1003407 ! higher score better +relationship: has_value_type xsd:double ! The allowed value-type for this CV term + [Term] id: PEFF:0000001 name: PEFF CV term @@ -23801,7 +24603,6 @@ namespace: unit.ontology def: "A unit which is a standard measure of the distance between two points." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000000 -relationship: is_unit_of PATO:0001708 created_by: george gkoutos [Term] @@ -23811,8 +24612,6 @@ namespace: unit.ontology def: "A unit which is a standard measure of the amount of matter/energy of a physical object." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000000 -relationship: is_unit_of PATO:0000125 -relationship: is_unit_of PATO:0000128 created_by: george gkoutos [Term] @@ -23824,8 +24623,6 @@ def: "A unit which is a standard measure of the dimension in which events occur subset: unit_group_slim synonym: "time derived unit" EXACT [] is_a: UO:0000000 -relationship: is_unit_of PATO:0000165 -relationship: is_unit_of PATO:0001309 created_by: george gkoutos [Term] @@ -23837,7 +24634,6 @@ def: "A unit which is a standard measure of the average kinetic energy of the pa subset: unit_group_slim synonym: "temperature derived unit" EXACT [] is_a: UO:0000000 -relationship: is_unit_of PATO:0000146 created_by: george gkoutos [Term] @@ -23953,7 +24749,6 @@ namespace: unit.ontology def: "A unit which is a standard measure of the amount of a 2-dimensional flat surface." [UOC:GVG] subset: unit_group_slim is_a: UO:0000000 -relationship: is_unit_of PATO:0001709 created_by: george gkoutos [Term] @@ -23964,7 +24759,6 @@ def: "A density unit which is a standard measure of the mass of a substance in a subset: unit_group_slim synonym: "mass per unit volume" EXACT [] is_a: UO:0000182 -relationship: is_unit_of PATO:0001353 created_by: george gkoutos [Term] @@ -23974,7 +24768,6 @@ namespace: unit.ontology def: "A unit which is a standard measure of the amount of space occupied by any substance, whether solid, liquid, or gas." [NIST:NIST] subset: unit_group_slim is_a: UO:0000000 -relationship: is_unit_of PATO:0001710 created_by: george gkoutos [Term] @@ -23995,7 +24788,6 @@ namespace: unit.ontology def: "A unit which is a standard measure of the number of repetitive actions in a particular time." [NIST:NIST] subset: unit_group_slim is_a: UO:0000000 -relationship: is_unit_of PATO:0000044 created_by: george gkoutos [Term] @@ -24016,7 +24808,6 @@ namespace: unit.ontology def: "A unit which is a standard measure of the force applied to a given area." [NIST:NIST] subset: unit_group_slim is_a: UO:0000000 -relationship: is_unit_of PATO:0001025 created_by: george gkoutos [Term] @@ -24036,8 +24827,6 @@ namespace: unit.ontology def: "A unit which is a standard measure of the work done by a certain force (gravitational, electric, magnetic, force of inertia, etc)." [NIST:NIST] subset: unit_group_slim is_a: UO:0000000 -relationship: is_unit_of PATO:0001021 -relationship: is_unit_of PATO:0001026 created_by: george gkoutos [Term] @@ -24057,7 +24846,6 @@ namespace: unit.ontology def: "A unit which is a standard measure of the figure or space formed by the junction of two lines or planes." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000000 -relationship: is_unit_of PATO:0000133 created_by: george gkoutos [Term] @@ -24117,7 +24905,6 @@ namespace: unit.ontology def: "A unit which is a standard measure of the influence exerted by some mass." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000000 -relationship: is_unit_of PATO:0001019 created_by: george gkoutos [Term] @@ -24183,7 +24970,6 @@ namespace: unit.ontology def: "A unit which is a standard measure of the work done per unit charge as a charge is moved between two points in an electric field." [Wikipedia:Wikipedia] subset: unit_group_slim is_a: UO:0000000 -relationship: is_unit_of PATO:0001464 created_by: george gkoutos [Term] @@ -24303,7 +25089,6 @@ subset: unit_slim synonym: "microlitres per minute" EXACT [] synonym: "uL/min" EXACT [] is_a: UO:0000270 -relationship: is_unit_of PATO:0001574 created_by: george gkoutos [Term] @@ -24315,3 +25100,5 @@ synonym: "A^[2]" RELATED [] is_a: UO:0000047 created_by: gkoutos creation_date: 2013-06-27T05:06:40Z + +