combined_protein.tsv with empty sample columns

[loganjohnson0]

Hello FragPipe Team,

I have been analyzing a dataset with the TMT-bridge default workflow. Samples labeled with TMT10plex and a 131C bridge channel with 10 TMT runs. My question might be Philosopher related, so my apologises if that is the case.

FragPipe runs without error, but I noticed that the creation of the combined_protein.tsv file generates with each sample placed in a new column, yet no information exists in the rows of these sample columns. The indistinguishable proteins column is also empty, with the indistinguishable proteins placed in the first column of the sample columns (images below as an example).

I am using an in-house generated contaminants file with contam_ labels in addition to a one-protein-per-gene UniProt Sus scrofa file and decoys added by FragPipe. I have some NCBI sequences appended, but they are annotated to prescribe to the requirements of Philosopher.

I have seen this in a few different datasets I've tried and wasn't sure if this was a feature or a bug. I'm generating an MSstats file with Philosopher and using that for my downstream analysis, and I haven't noticed an impact on any data. I am attaching my log file below and can share other files if it helps.

Thank you for the great software!

log_2025-01-25_13-48-47.txt

Version info:
FragPipe version 22.0
MSFragger version 4.1
IonQuant version 1.10.27
diaTracer version 1.1.5
Philosopher version 5.1.1

[fcyu]

The log file is not readable. Could you re-uploaded it again?

Thanks,

Fengchao

[loganjohnson0]

Sorry, I realized that right after I submitted the issue. I have edited my original comment and have it below.

log_2025-01-25_13-48-47.txt

[fcyu]

No worries. Yeah, it seems to be a bug in Philosopher. We actually don't use the combined_*.tsv tables much for the TMT data. The recommended tables are those in the tmt-report folder. And the bug should also not affect the MSstats files.

Best,

Fengchao

[loganjohnson0]

Ya, I usually just quickly look at the combined_*.tsv files, but I figured I'd report it anyway. Thanks!