OpenMS
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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/doxygen/release/3.3.0/html/TOPP_MSstatsConverter.html Version: 3.3.0 Dec 21 2024, 15:25:20, Revision: 35c5e65 To cite OpenMS: + Pfeuffer, J., Bielow, C., Wein, S. et al.. OpenMS 3 enables reproducible analysis of large-scale mass spec trometry data. Nat Methods (2024). doi:10.1038/s41592-024-02197-7. 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 TOPP 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: