improving docs

Author: ypriverol

docs/formats.rst

@@ -21,6 +21,21 @@ SDRF: experimental design
 
 The HUPO-PSI and ProteomeXchange recently developed the MAGE-TAB an standard file format for experimental design representation. Within the MAGE-TAB, the Sample and Data Relationship Format (SDRF) is a lightweight tab delimited format to represent the sample metadata and its relation with the data files (RAW or mzML files).
 
+.. image:: https://raw.githubusercontent.com/bigbio/proteomics-metadata-standard/master/sdrf-proteomics/images/sdrf-nutshell.png
+   :width: 900
+   :align: center
+
+|
+Multiple concepts from SDRF and **relevant and important** for the quantms pipeline:
+
+**Peptide Search Parameters**:
+
+- comment[cleavage agent details]: enzyme used in the experiment, including sites and positions.
+- comment[modification parameters]: post-translation modifications that will be consider within the peptide/protein search
+- comment[precursor mass tolerance], comment[fragment mass tolerance]: Precursor mass tolerance use for the peptide search. Both each engines Comet and MSGF+ use this parameter.
+
+
+
 Spectra Data
 ~~~~~~~~~~~~~~~~~~~~~~~~~~
 

docs/index.rst

@@ -29,6 +29,8 @@ Contents
    .. toctree::
    :maxdepth: 2
 
+|
+
 The following links should be follow to get support and help with the quantms maintainers:
 
 |Get help on Slack|   |Report Issue| |Get help on GitHub Forum|

docs/introduction.rst

@@ -8,6 +8,7 @@ Bottom-up proteomics is a common method to identify proteins and characterize th
    :width: 400
    :align: center
 
+|
 
 .. sidebar:: Pipelines and tools
    :subtitle: **It can make your life easier** if you want to explore individual tools:
@@ -30,7 +31,8 @@ Mass spectrometry quantitative data analysis can be divided in three main steps:
 - downstream data analysis and quality control
 
 .. image:: images/quantms.png
-   :width: 350
+   :width: 450
+   :align: center
 
 References
 --------------------------------