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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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Problem with file name excluding format extension #127

Open ClaSofMag opened 1 year ago

ClaSofMag commented 1 year ago

Hello,

I ran into an issue while FlashLFQ was at the 1st analysis step "Opening PSM file". It reported an error saying "The given key '12_NET_12' was not present in the dictionary. The error report could not be written: Could not load file or assembly 'Easy.Common, Version=4.3.0.0, Culture=neutral, PublicKeyToken=null'. The system cannot find the file specified."

I suppose that's because the Spectrum file is called 12_NET_12.3.raw, so it is excluding everything after the first dot.

I'm using the identification file from PeptideShaker (default PSM Report.txt) and .raw spectra files.

Thanks for the help

trishorts commented 1 year ago

It should be robust to that but I will have to double check. Is there any way that you could share the psm file and at least one raw file so that I can reproduce the error? Then I will fix it. Thanks.

ClaSofMag commented 1 year ago

Sure, thank you. Here:

Default PSM Report.txt Link for raw file: https://ualg365-my.sharepoint.com/:i:/g/personal/csraposo_ualg_pt/EWnRq3CgWF9Gtd9qIW-4GPEBXN2H6Vqp27YOGfMwa7gwow?e=1r0PAh

trishorts commented 1 year ago

FlashLFQ can handle some instances of multiple .s but your presents a funny case. In the peptide shaker output it thinks the .3 is the file extension. The easiest solution is to add .raw to all the text in the column labeled "Spectrum File". Will you give that a try please? I did the relabeling on the file you sent to me. maybe you could try it?

trishorts commented 1 year ago

Default.PSM.Report_raw.txt

ClaSofMag commented 1 year ago

That worked perfectly! Thank you for your help