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I would like to export the data from Protein-Shaker proteomics analysis software and use it in downstream analysis. For example the overview data, numbers of validated peptides per protein, confidence, etc. Ideally I would like to generate this output from commandline without the gui and, if possible to plain txt or csv.

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You have to start PeptideShaker calling java with the -cp argument an input project file and provide a comma/space-separated list of integers for the reports you want to export:

java -cp PeptideShaker-1.16.37.jar eu.isas.peptideshaker.cmd.ReportCLI -in input.cpsx -reports "0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10"`

Here is the list of reports you can export:

-reports                   Comma separated list of types of report to export. 
                           0: Certificate of Analysis, 
                           1: Default Hierarchical Report, 
                           2: Default PSM Phosphorylation Report, 
                           3: Default PSM Report, 
                           4: Default PSM Report with non-validated matches, 
                           5: Default Peptide Phosphorylation Report, 
                           6: Default Peptide Report, 
                           7: Default Peptide Report with non-validated matches, 
                           8: Default Protein Phosphorylation Report, 
                           9: Default Protein Report, 
                           10: Default Protein Report with non-validated matches, 
                           11: Extended PSM Report, 
                           12-n: Your own custom reports.

I don't know whether you can also use the SearchGUI output zip to generate this files. The program accepts zip files as input, but I think that means PeptideShaker project that are exported to zip files, but not SearchGUI output zips. So, in the end you might need to run the GUI at least one time, unfortunately.

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