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author proteore
date Mon, 10 May 2021 13:48:56 +0000
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1 **Description**
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3 This tool allows to retrieve unique proteotypic peptide and related information (from SRMAtlas)
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4 for building Selected Reaction Monitoring (SRM) method using a list of Uniprot accession number as input.
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5 The SRMAtlas is a compendium of targeted proteomics assays resulting from high-quality measurements of natural
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6 and synthetic peptides conducted on a triple quadrupole mass spectrometer, and is intended as a resource
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7 for building selected/multiple reaction monitoring (SRM/MRM)-based proteomic methods.
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9 -----
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11 **Input**
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13 A list of IDs (entered in a copy/paste mode) or a single-column file, the tool will then return a file containing
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14 the selected information (peptide sequence/features). If your input is a multiple-column file, the column(s)
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15 containing the selected information will be added at the end of the input file. Only Uniprot accession number (e.g. P31946) are allowed.
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16 If your list of IDs is not in this form, please use the ID_Converter tool of ProteoRE.
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18 .. class:: warningmark
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20 Accession numbers with an hyphen ("-") that normally correspond to isoform are not considered as similar to its canonical form.
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22 .. class:: warningmark
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24 In copy/paste mode, the number of IDs considered in input is limited to 5000.
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26 -----
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28 **Parameters**
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30 Release: choose the release you want to use for retrieving peptide sequences/features
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31 Peptide sequence/features: select peptide features you want to retrieve; Peptide sequence
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32 (amino acid sequence of detected peptide, including any mass modifications);
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33 SSRT (Sequence Specific Retention Time provides a hydrophobicity measure for each peptide using
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34 the algorithm of Krohkin et al. SSRCalc); Length (peptide sequence length); MW (molecular weight);
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35 PeptideAtlas Accession (PA_Acc).
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37 -----
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39 **Output**
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41 A text file containing the selected peptide features (in addition to the original column(s) provided).
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42 Please, note that a "NA" is returned when there is no match between a source ID and SRM/MRM source file.
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44 -----
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46 **Data sources (release date)**
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48 This tool is using the following source file:
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50 - `HumanSRMAtlasPeptidesFinalAnnotated (2016-04) (Kusebauch et al., 2016, PMID: 27453469) <http://www.srmatlas.org/downloads/HumanSRMAtlasPeptidesFinalAnnotated.xlsx>`_.
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52 -----
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54 .. class:: infomark
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56 **Authors**
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58 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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60 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
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62 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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64 Help: contact@proteore.org for any questions or concerns about this tool.