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compomics / peptide-shaker

Interpretation of proteomics identification results
http://compomics.github.io/projects/peptide-shaker.html
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PeptideShaker output in tabular format #507

Closed trishorts closed 1 year ago

trishorts commented 1 year ago

We have a FlashLFQ user that wants to know how to export peptide shaker output in tabular format so they can import the results into our software. Do you have a manual or wiki entry that might help them out?

https://github.com/smith-chem-wisc/FlashLFQ/issues/125

hbarsnes commented 1 year ago

There is a section in our tutorial material on how to export data from PeptideShaker in different formats. Please check out pages 35 to 39 of Chapter 1.4 - Browsing Identification Results.

trishorts commented 1 year ago

Thanks. I will pass the message onto our user and see if it resolves the issue.

hbarsnes commented 1 year ago

Great! The exports are also available via the command line: https://github.com/compomics/peptide-shaker/wiki/PeptideShakerCLI#b---reportcli

justmpm commented 1 year ago

Hi, I wasn't able to find a way to export a .tabular file from PeptideShaker, but I did find that both the Default PSM Report and the Extended PSM Report are compatible with FlashLFQ.

Cheers Mike

hbarsnes commented 1 year ago

Hi Mike,

Great that you were able to find a solution. All the text-based exports from PeptideShaker are indeed by default tab separated, and should therefore already be in the wanted format. Hence it is just a matter of including the columns you need.

Best regards, Harald