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smith-chem-wisc / FlashLFQ

Ultra-fast label-free quantification algorithm for mass-spectrometry proteomics
GNU Lesser General Public License v3.0
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Question about using with PeptideShaker #125

Open justmpm opened 1 year ago

justmpm commented 1 year ago

Hi, In the instructions, it says you can load a .tabular file from PeptideShaker, but I don't see a way for PeptideShaker to export in the .tabular format. Do you know which export filters I need to use to get a .tabular output, or which output I can use with FlashLFQ?

Thanks! Mike

trishorts commented 1 year ago

i don't have a ready answer. i posted an issue on the peptide shaker github https://github.com/compomics/peptide-shaker/issues/507

trishorts commented 1 year ago

this comment by the peptide shaker team: 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.

justmpm commented 1 year ago

Hi, There is no way that I can find, even using the tutorial, to export a .tabular. However, I did find that both Export->Identification Features->Default PSM Report is compatible with FlashLFQ. So is Export->Identification Features->Extended PSM Report. The native .txt file exported by PeptideShaker is fine, no need to change the file name to end with .tabular.

Thanks for your help! Cheers Mike