OpenMS
2.6.0
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Converter to input for MSstats
This util consumes an ID-mapped consensusXML file and OpenMS experimental design in TSV format to create a CSV file which can subsequently be used as input for the R package MSstats [1].
[1] M. Choi et al. MSstats: an R package for statistical analysis for quantitative mass spectrometry-based proteomic experiments. Bioinformatics (2014), 30 (17): 2524-2526
The command line parameters of this tool are:
MSstatsConverter -- Converter to input for MSstats Full documentation: http://www.openms.de/documentation/UTILS_MSstatsConverter.html Version: 2.6.0 Sep 30 2020, 12:54:34, Revision: c26f752 To cite OpenMS: Rost HL, Sachsenberg T, Aiche S, Bielow C et al.. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nat Meth. 2016; 13, 9: 741-748. doi:10.1038/nmeth.3959. Usage: MSstatsConverter <options> Options (mandatory options marked with '*'): -in <in>* Input consensusXML with peptide intensities (valid formats: 'consensusXML') -in_design <in_design>* Experimental Design file (valid formats: 'tsv') -method <method> Method used in the experiment(label free [LFQ], isobaric labe ling [ISO])) (default: 'LFQ' valid: 'LFQ', 'ISO') -msstats_bioreplicate <msstats_bioreplicate> Which column in the condition table should be used for MSstat s 'BioReplicate' (default: 'MSstats_BioReplicate') -msstats_condition <msstats_condition> Which column in the condition table should be used for MSstat s 'Condition' (default: 'MSstats_Condition') -msstats_mixture msstats_mixture Which column in the condition table should be used for MSstat s 'Mixture' (default: 'MSstats_Mixture') -labeled_reference_peptides If set, IsotopeLabelType is 'H', else 'L' -out <out>* Input CSV file for MSstats. (valid formats: 'csv') Common UTIL options: -ini <file> Use the given TOPP INI file -threads <n> Sets the number of threads allowed to be used by the TOPP tool (default: '1') -write_ini <file> Writes the default configuration file --help Shows options --helphelp Shows all options (including advanced)
INI file documentation of this tool: