Mercurial > repos > proteore > proteore_get_unique_peptide_srm_method
diff README.rst @ 0:a2b06836de90 draft
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author | proteore |
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date | Fri, 12 Jul 2019 07:49:45 -0400 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/README.rst Fri Jul 12 07:49:45 2019 -0400 @@ -0,0 +1,64 @@ +**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. \ No newline at end of file