Adding the contam_ prefix doesn't work with an existing database. It only works when downloading the database using Philosopher

[lxavierneves]

Hello,

I'm using Fragpipe v22.0 and loaded a uniprot reference proteome .fasta file then loaded into Fragpipe and clicked to add decoys and contaminants. However I noticed that the contaminants have not been marked with "contam_" in the .fasta file header, therefore have not been removed from my search results.

has this happened to other users?

many thanks,
Leandro

[fcyu]

However I noticed that the contaminants have not been marked with "contam_" in the .fasta file header

It seems to be a bug in Philosopher. Could you share your fasta file?

Thanks,

Fengchao

[anesvi]

If you downloaded Human database, then contaminants that are human proteins would not be marked as contaminants, I believe. Maybe this will explain what you observed?

[lxavierneves]

It's a hamster database and none of the contaminant entries had the contam_ prefix

File below
2024-12-13-decoys-contam-20241211_UP000189706_10036_onePTNperGene.fasta.zip

Many thanks

[lxavierneves]

I've just realised that the original .fasta could be useful as well
20241211_UP000189706_10036_onePTNperGene.zip

[fcyu]

Thanks for sharing the file. It remind me that adding the contam_ prefix only works when you download the database using Philosopher: #510 (comment)

Let me transfer this one to https://github.com/Nesvilab/philosopher/issues

Best,

Fengchao