Format error in combined_protein.tsv when MS1 quant is disabled

[hollenstein]

Dear developers,

I've stumbled upon a small, but rather inconvenient bug when FragPipe is used without MS1 quant enabled. It appears that the combined_protein.tsv contains more cells in the entry rows than in the header row. I.e. one additional tab at the end of each row, starting from row 2. This causes an issue when reading the tsv file with e.g. Python or R. Of course there are ways to deal with this situation, however, I think it would be better to fix the file then having to create a workaround.

I've attached a combined_protein.tsv file and the log: log_and_combined_protein.zip

Would be great if you could look into this issue. Once again, thanks for your help.

Version info:
FragPipe version 20.0
MSFragger version 3.8
IonQuant version 1.9.8
Philosopher version 5.0.0

[fcyu]

Thanks for the bug reporting. Without MS1 Quant (IonQuant), the combined_protein.tsv is generated by Philosopher.

@AimeeD90 can you take a look?

Thanks,

Fengchao