Mercurial > repos > proteore > proteore_get_unique_peptide_srm_method
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author | proteore |
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date | Fri, 12 Jul 2019 07:49:45 -0400 |
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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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8 |
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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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17 |
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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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21 |
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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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36 |
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37 ----- |
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38 |
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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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43 |
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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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49 |
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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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51 |
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52 ----- |
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54 .. class:: infomark |
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56 **Authors** |
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57 |
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58 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR |
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59 |
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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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61 |
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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. |