No peptides and spectral but identified as a protein

[LiTing99-cutie]

Dear philosopher team,

After i ran a LFQ-MBR workflow using fragpipe, and inspected the result: i found a wierd row in the protein.tsv:sp|P27870|VAV_MOUSE P27870 VAV_MOUSE Vav1 845 Mus musculus Proto-oncogene vav 1:Experimental evidence at protein level 0.71 0.3871 0.8196 0 0 0 0 000 0 0,
since this protein has no peptides and spectra, why does it still identified as a protein?

Besides, i input 6 samples for running at a time, i notices the protein number would also be different from that of running one at a time. Which strategy should i used?

My platform and the philosopher version:

• Linux
• Version: v 5.1.1

Log file is in the attachments
log_2024-11-18_12-39-25.txt

[fcyu]

After i ran a LFQ-MBR workflow using fragpipe, and inspected the result: i found a wierd row in the protein.tsv:sp|P27870|VAV_MOUSE P27870 VAV_MOUSE Vav1 845 Mus musculus Proto-oncogene vav 1:Experimental evidence at protein level 0.71 0.3871 0.8196 0 0 0 0 000 0 0,
since this protein has no peptides and spectra, why does it still identified as a protein?

Can you share the file you mentioned? My guess is that the protein is from MBR.

Besides, i input 6 samples for running at a time, i notices the protein number would also be different from that of running one at a time. Which strategy should i used?

FDR control are different. Run 6 samples one at a time basically perform FDR filtering 6 times, but running 6 samples together perform one global FDR once. You should run 6 samples together.

Best,

Fengchao

[LiTing99-cutie]

Of cource, i actually tested ionquant.mbr=0 and the row also existed, I uploaded the protein.txt in the attachment now.

Also when i used ionquant.mbr=0 and quantitation.run-label-free-quant=false, and the row turned into
sp|P27870|VAV_MOUSE P27870 VAV_MOUSE Vav1 845 Mus musculus Proto-oncogene vav 1:Experimental evidence at protein level 0.71 0.3871 0.8196 1 0 0 1 0 0 0 0 0, shows it has one total peptide and one spectral count. But when i grep VAV_MOUSE in the psm.tsv, ion.tsv and peptide.tsv, i got no result. It should be in the mapped protein colunm or something? I don't know why.

Also, i also noticed when all of the samples are inputted together, the razor peptide column of protein.tsv could be 0 sometimes. Is this normal? Without razor peptide but still identified as a protein?

protein.txt

[fcyu]

Thanks for sharing the file. It seems to be a bug.....

Best,

Fengchao