PeptideShaker output in tabular format

[trishorts]

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?

smith-chem-wisc/FlashLFQ#125

[hbarsnes]

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]

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

[hbarsnes]

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

[justmpm]

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]

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