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** | |
2 | |
3 This tool allows to retrieve unique proteotypic peptide and related information (from SRMAtlas) | |
4 for building Selected Reaction Monitoring (SRM) method using a list of Uniprot accession number as input. | |
5 The SRMAtlas is a compendium of targeted proteomics assays resulting from high-quality measurements of natural | |
6 and synthetic peptides conducted on a triple quadrupole mass spectrometer, and is intended as a resource | |
7 for building selected/multiple reaction monitoring (SRM/MRM)-based proteomic methods. | |
8 | |
9 ----- | |
10 | |
11 **Input** | |
12 | |
13 A list of IDs (entered in a copy/paste mode) or a single-column file, the tool will then return a file containing | |
14 the selected information (peptide sequence/features). If your input is a multiple-column file, the column(s) | |
15 containing the selected information will be added at the end of the input file. Only Uniprot accession number (e.g. P31946) are allowed. | |
16 If your list of IDs is not in this form, please use the ID_Converter tool of ProteoRE. | |
17 | |
18 .. class:: warningmark | |
19 | |
20 Accession numbers with an hyphen ("-") that normally correspond to isoform are not considered as similar to its canonical form. | |
21 | |
22 .. class:: warningmark | |
23 | |
24 In copy/paste mode, the number of IDs considered in input is limited to 5000. | |
25 | |
26 ----- | |
27 | |
28 **Parameters** | |
29 | |
30 Release: choose the release you want to use for retrieving peptide sequences/features | |
31 Peptide sequence/features: select peptide features you want to retrieve; Peptide sequence | |
32 (amino acid sequence of detected peptide, including any mass modifications); | |
33 SSRT (Sequence Specific Retention Time provides a hydrophobicity measure for each peptide using | |
34 the algorithm of Krohkin et al. SSRCalc); Length (peptide sequence length); MW (molecular weight); | |
35 PeptideAtlas Accession (PA_Acc). | |
36 | |
37 ----- | |
38 | |
39 **Output** | |
40 | |
41 A text file containing the selected peptide features (in addition to the original column(s) provided). | |
42 Please, note that a "NA" is returned when there is no match between a source ID and SRM/MRM source file. | |
43 | |
44 ----- | |
45 | |
46 **Data sources (release date)** | |
47 | |
48 This tool is using the following source file: | |
49 | |
50 - `HumanSRMAtlasPeptidesFinalAnnotated (2016-04) (Kusebauch et al., 2016, PMID: 27453469) <http://www.srmatlas.org/downloads/HumanSRMAtlasPeptidesFinalAnnotated.xlsx>`_. | |
51 | |
52 ----- | |
53 | |
54 .. class:: infomark | |
55 | |
56 **Authors** | |
57 | |
58 David Christiany, Florence Combes, Yves Vandenbrouck CEA, INSERM, CNRS, Grenoble-Alpes University, BIG Institute, FR | |
59 | |
60 Sandra Dérozier, Olivier Rué, Christophe Caron, Valentin Loux INRA, Paris-Saclay University, MAIAGE Unit, Migale Bioinformatics platform, FR | |
61 | |
62 This work has been partially funded through the French National Agency for Research (ANR) IFB project. | |
63 | |
64 Help: contact@proteore.org for any questions or concerns about this tool. |