--- a/README.rst	Wed Jul 10 10:26:50 2019 -0400
+++ b/README.rst	Thu Jul 11 03:30:41 2019 -0400
@@ -1,13 +1,19 @@
-        **Description**
+**Description**
 
-This tool allows you to get SRM/MRM informations from Uniprot-AC IDs.
+This tool allows to retrieve unique proteotypic peptide and related information (from SRMAtlas) 
+for building Selected Reaction Monitoring (SRM) method using a list of Uniprot accession number as input. 
+The SRMAtlas is a compendium of targeted proteomics assays resulting from high-quality measurements of natural 
+and synthetic peptides conducted on a triple quadrupole mass spectrometer, and is intended as a resource 
+for building selected/multiple reaction monitoring (SRM/MRM)-based proteomic methods.
 
 -----
 
 **Input**
 
-A list of IDs (entered in a copy/paste mode) or a single-column file, the tool will then return a file containing the wanted protein features. 
-If your input is a multiple-column file, the mapped IDs column(s) will be added at the end of the input file.
+A list of IDs (entered in a copy/paste mode) or a single-column file, the tool will then return a file containing 
+the selected information (peptide sequence/features). If your input is a multiple-column file, the column(s) 
+containing the selected information will be added at the end of the input file. Only Uniprot accession number (e.g. P31946) are allowed. 
+If your list of IDs is not in this form, please use the ID_Converter tool of ProteoRE.
 
 .. class:: warningmark
 
@@ -21,15 +27,18 @@
 
 **Parameters**
 
-- **Enter IDS:** enter your Uniprot-AC from a file or a copy paste
-- **Release:** choose the release you want to use for retrieving protein sequences / features 
-- **Protein sequence/Features:** choose proteins features you want to retrieve
+Release: choose the release you want to use for retrieving peptide sequences/features
+Peptide sequence/features: select peptide features you want to retrieve; Peptide sequence 
+(amino acid sequence of detected peptide, including any mass modifications); 
+SSRT (Sequence Specific Retention Time provides a hydrophobicity measure for each peptide using 
+the algorithm of Krohkin et al. SSRCalc); Length (peptide sequence length); MW (molecular weight); 
+PeptideAtlas Accession (PA_Acc).
 
 -----
 
 **Output**
 
-A text file containing the selected protein features (in addition to the original column(s) provided).
+A text file containing the selected peptide features (in addition to the original column(s) provided). 
 Please, note that a "NA" is returned when there is no match between a source ID and SRM/MRM source file.
 
 -----
@@ -38,7 +47,7 @@
 
 This tool is using the following source file:
 
-- `HumanSRMAtlasPeptidesFinalAnnotated (2016-04) <http://www.srmatlas.org/downloads/HumanSRMAtlasPeptidesFinalAnnotated.xlsx>`_.
+- `HumanSRMAtlasPeptidesFinalAnnotated (2016-04) (Kusebauch et al., 2016, PMID: 27453469) <http://www.srmatlas.org/downloads/HumanSRMAtlasPeptidesFinalAnnotated.xlsx>`_.
 
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