Was the "contam_" flagging of contaminants removed?

[ruwoltMax]

Hi FragPipe Team,

I was wondering whether the flagging of contaminants with "contam_sp" was removed at some point. I usually generate my database by entering the .fasta and then adding decoys and contaminants through the GUI in FragPipe v23.1. I revisited my generated .fas files from July 2024 when "contam_" was still there. This was a different FragPipe version of course. After that, the flagging was gone in all future databases. Is it due to a setting in my GUI? Contaminants are successfully added but not flagged. I'd appreciate any comment on this!

Thank you!

[fcyu]

There is a checkbox in the "FDR filter and report" panel of the "validation" tab to enable/disable the contaminants removal.

Best,

Fengchao

[ruwoltMax]

Hi Fengchao,

Thanks for your fast reply! I know that there is this checkbox. In my case, it is unchecked so that contaminants still appear in my output (see below). But the identifications do not carry the "contam_" flag. Already in the .fas that FragPipe generates, the contaminants are not flagged with "contam_" anymore although I use a target only database as an input for FragPipe and then click "add decoys and contaminants".

Protein ID Entry Name Gene Length Is Decoy Is Contaminant Organism Protein Description
P02769 ALBU_BOVIN ALB 607 false false Bos taurus Albumin
P00366 DHE3_BOVIN GLUD1 558 false false Bos taurus Glutamate dehydrogenase 1, mitochondrial
P00761 TRYP_PIG 231 false false Sus scrofa Trypsin

This issue happens on all three of our workstations that have FragPipe installed and across multiple FragPipe versions. Any idea what could be the reason that in my case contaminants are not flagged?

Thanks for the support, highly appreciated!
Max.

[fcyu]

Already in the .fas that FragPipe generates, the contaminants are not flagged with "contam_" anymore although I use a target only database as an input for FragPipe and then click "add decoys and contaminants".

Philosopher (the one in FragPipe generating databases) can only append the contam_ prefix when downloading the database. Adding decoys and contaminants for existing databases won’t have the prefix. This bug/feature has need there since day one. If I remember it correctly, it is still unchanged.

Best,

Fengchao

[ruwoltMax]

Oh, I see now. Indeed, when downloading through Philosopher, I get the prefix. Thank you for the clarification! Would be great to also get the prefix when using a custom database.

Thank you Fengchao!

[fcyu]

Would be great to also get the prefix when using a custom database.

@AimeeD90 Is that something that can be easily fixed in Philosopher?

Thanks,

Fengchao

[AimeeD90]

@ruwoltMax Hi, the issue has been fixed, Philosopher can now add contaminants to a custom database, please download at https://www.dropbox.com/scl/fo/wi9u900jdw08vhkh5zqe0/APvIfPw1koglO-jRICad2U4?rlkey=xk2nmpf09u6ox0vsc7pe9pdie&st=f42djql8&dl=0.

[ruwoltMax]

Thank you two so much! I'm gonna give it a try asap.

Cheers,
Max.