Questions tagged [peptide-shaker]

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How to do protein quantification with Peptideshaker output (TMT labeled, MS2)?

I have TMT tagged MS2 mass spec run processed with Peptideshaker. I saved the project in a peptideshaker format cpsx. Now, I would like to do the quantification ...
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How to export peptide-shaker data from commandline?

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,...