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author proteore
date Fri, 12 Jul 2019 07:49:45 -0400
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+**Description**
+
+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 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
+
+Accession numbers with an hyphen ("-") that normally correspond to isoform are not considered as similar to its canonical form.
+
+.. class:: warningmark
+
+In copy/paste mode, the number of IDs considered in input is limited to 5000.
+
+-----
+
+**Parameters**
+
+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 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.
+
+-----
+
+**Data sources (release date)**
+
+This tool is using the following source file:
+
+- `HumanSRMAtlasPeptidesFinalAnnotated (2016-04) (Kusebauch et al., 2016, PMID: 27453469) <http://www.srmatlas.org/downloads/HumanSRMAtlasPeptidesFinalAnnotated.xlsx>`_.
+
+-----
+
+.. class:: infomark
+
+**Authors**
+
+David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
+
+Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
+
+This work has been partially funded through the French National Agency for Research (ANR) IFB project.
+
+Help: contact@proteore.org for any questions or concerns about this tool.
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