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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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No peptide IDs for specified spectra files were found #144

Open TheB1307 opened 1 month ago

TheB1307 commented 1 month ago

Hi everyone I am new to FlashFLQ and I try to use it to quantify my proteomics data. The identification was done with sage and MS2 Rescore. I tried to generate the generic table for FlashLFQ with the exact names and added all the mzML-files. The searching starts but in the window (under the "run FlashLFQ" box), there are following messages "Caution! PSM with could not be read. Monoisotopic mass not interpretable.". After a while the software stops and gives following error message "No peptide IDs for the specified spectra files were found! Check to make sure the spectra file names match between the ID file and the spectra files.". I checked again if I had all the needed raw files and also changed the path where the raw files are stored so everything is in one folder. But I still get this messages. Can somebody help me with this? If you need the files, let me now how to submit them so not everyone has access to them. Have a great day!

Alexander-Sol commented 1 month ago

Can you upload some of the files to Box or somewhere similar? I'll download them and take a look

TheB1307 commented 1 month ago

I have this: https://we.tl/t-AI5NyNFJbb There I uploaded a smaller table with just one sample type and one raw.file. Does it work? I was not able to manage it differently.. sorry

Alexander-Sol commented 1 month ago

I'm no longer able to download the file you shared. Would you mind sending it again?

TheB1307 commented 1 month ago

I was able to generate with MS2 Rescore a functional input file. I guess the problem was in doing it with R. Maybe I made a mistake. Anyways, thank you very much!

ArthurDeclercq commented 6 days ago

Hi all,

Just a quick addition to this for people encountering this issue as well, I had this is well with the error message Caution! PSM with could not be read. Monoisotopic mass not interpretable. In the end this turned out to be caused (in my case) by a wrong column name in the input file, not even having to do with the Monoisotopic Mass column (in my case it read Protein Accessions instead of Protein Accession). So this could help future issues people have. It would be very helpful if the error message could say the column name is wrong, if this is indeed the case in a future release. thank you!