Mercurial > repos > proteore > proteore_get_unique_peptide_srm_method

annotate README.rst @ 0:a61b50b16a16 draft

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author proteore
date Wed, 10 Jul 2019 10:19:48 -0400
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1 **Description**
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2
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3 This tool allows you to get SRM/MRM informations from Uniprot-AC IDs.
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4
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5 -----
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6
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7 **Input**
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8
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9 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.
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10 If your input is a multiple-column file, the mapped IDs column(s) will be added at the end of the input file.
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11
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12 .. class:: warningmark
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13
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14 Accession numbers with an hyphen ("-") that normally correspond to isoform are not considered as similar to its canonical form.
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15
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16 .. class:: warningmark
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17
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18 In copy/paste mode, the number of IDs considered in input is limited to 5000.
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19
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20 -----
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21
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22 **Parameters**
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23
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24 - **Enter IDS:** enter your Uniprot-AC from a file or a copy paste
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25 - **Release:** choose the release you want to use for retrieving protein sequences / features
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26 - **Protein sequence/Features:** choose proteins features you want to retrieve
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27
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28 -----
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29
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30 **Output**
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31
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32 A text file containing the selected protein features (in addition to the original column(s) provided).
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33 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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34
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35 -----
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36
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37 **Data sources (release date)**
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38
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39 This tool is using the following source file:
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40
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41 - `HumanSRMAtlasPeptidesFinalAnnotated (2016-04) <http://www.srmatlas.org/downloads/HumanSRMAtlasPeptidesFinalAnnotated.xlsx>`_.
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42
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43 -----
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44
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45 .. class:: infomark
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46
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47 **Authors**
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48
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49 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR
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50
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51 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR
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52
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53 This work has been partially funded through the French National Agency for Research (ANR) IFB project.
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54
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55 Help: contact@proteore.org for any questions or concerns about this tool.