The new release, version 3.0, has focused on improving the multidimensional data processing and molecular annotation capabilities. By enhancing the foundation core modules, this update aims to provide a more reliable and stable solution for chromatographic-based mass spectrometry data processing. Along with bug fixes, we have also improved the documentation of the primary classes and added advanced algorithms for noise threshold, peak picking, and more.

Changelog

[3.0.0] - 2023-10-29

Added

Introduced a SpectraParserInterface abstact base class object that all mass spectra parsers should adhere to.
Added the LCMSMassFeature class to the chroma_peak/factory/ChromaPeakClasses.py module.
Added a MZMLSpectraParser (child of SpectraParserInterface) to ingest .mzml files and instantiate MassSpectraBase and LCMSBase objects.
Added print, copy, and check equality methods for all encapsulated parameter classes.
Added parameters to the LiquidChromatographySettings class to declare which parts of the LCMSBase object to export.
Implemented functionality for GCMS workflow to use MetabRef database.
Added calculations for persistent homology to mass_spectra/calc/lc_calc module as PHCalculations class
Added inheritance of new PHCalculations class to mass_spectra/factory/lc_class LCMSBase class.
Added test that incorporates input, instantiating LCMSBase, and peak picking to tests.
Added HDF5 export and import capability for LCMSBase objects.
Added MetabRefInterface class and subclasses MetabRefGCInterface and MetabRefLCInterface.
Added LCMSMassFeatures class to chroma_peak/factory module for storing information about LCMS mass features.
Added calcuations for LCMSMassFeatures class (LCMSMassFeatureCalculation) to chroma_peak/calc module including peak shape metrics
Added LCMSSpectralSearch class to enable spectral searching against a reference database for LCMSMassFeatures within the LCMSBase class.
Added SpectrumSearchResults class to store the spectral search results.
Added LipidomicsExport class and lipidomics workflow test.
Added functionality for (optional) deconvolution of ms1 spectra for LCMSMassFeatures, including import, export, and plotting capabilities.
Added verbose processing parameter to the encapsulated parameters for the MSParameters, LCMSParameters, and GCMSParameters classes.
Added stoichiometry calculations for aromaticity index and nominal oxidation state to MolecularFormulaCalc module and ability to add these to output reporting dataframes.

Changed

Heavily edited ImportMassSpectraThermoMSFileReader to instantiate MassSpectraBase and LCMSBase objects.
- Removed the inheritance of LC_Calculations (now inherited by MassSpectraBase objects).
- Moved some functionality from ImportMassSpectraThermoMSFileReader to support code for better logical separation.
Heavily edited the LCMSBase class object within the mass_spectra/factory module.
Incorporated some functionality of the DataDependentLCMS class into the LCMSBase class.
Restructured the LCMSParameters class and altered all functions that call the mass spectrum-related parameters from this class.
- This restructuring re-uses the MSParameters class within the LCMSParameters class (indexed by ms1 and ms2 by default). This adds the flexibility to attach different MSParameters instances to the ms1 and ms2 spectra within an LCMSBase object.
Renamed two modules (LC_Class and LC_Calc) to snake_case to adhere by PEP8 formating.
Improved functionality for exporting LCMSBase objects to HDF5.
Changed many print statements to warnings.

Fixed

Fixed small bug in signal processing when dealing with the end of the EIC.

Removed

Removed win_only spectra parsers.
Removed the DataDependentLCMS class as its functionality has been incorporated into the LCMSBase class.
Removed the DataDependentPeak class within the chroma_peak/factory/ChromaPeakClasses.py module and incorporated functionality as needed into the LCMSMassFeature class.
Removed old (deprecated) version of mass spectra HDF5 importer and exporter from tests.
Removed the min_op_filter, min_hc_filter, min_oc_filter, max_oc_filter attributes from the MolecularLookupDictSettings class.

Full Changelog: v2.0.0...v3.0.0

The new release, version 2.0.0, has been designed to address multiple bugs and issues that were affecting the fundamental functionalities of signal processing and molecular formula assignment. The primary purpose of this update is to provide a more reliable and stable solution for mass spectrometry data processing by enhancing the foundation core modules. Along with bug fixes, we have also improved the documentation of the primary classes and added advanced algorithms for noise threshold, peak picking, and more.

What's Changed

Fix for a bug causing an index error in mass_spectrum\calc\PeakPicking.py by @Kzra in #2
Bump urllib3 from 1.25.4 to 1.25.8 by @dependabot in #1
Added options for nominal kendrick mass calculation by @Kzra in #3
Stable by @corilo in #4
Bump urllib3 from 1.25.8 to 1.26.5 by @dependabot in #5
Lcms by @deweycw in #11
Adjust thermo reader to comply with pythonnet 3.0 changes by @jmrd98 in #14
Update core_ms tutorial by @GeorgiosDolias in #16
Update rawFileReader.py by @jmrd98 in #15