Fengchao

icon indicating a website link https://fyupro.com/ icon indicating an email [email protected]

icon company University of Michigan icon location Ann Arbor, MI icon location Research Investigator at University of Michigan. Developer of FragPipe, MSFragger, IonQuant, etc.

Results 417 comments of Fengchao

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

Fine. This real E. Coli protein from UniProt also triggered the bug. [real_uniprot_ecoli_protein.zip](https://github.com/Nesvilab/FragPipe/files/9941584/real_uniprot_ecoli_protein.zip)

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

I used my own E. Coli fasta file. Adding decoys and contaminants using Philosopher. And then, the human contaminants are not marked as contaminants. > this dynamic tagging only works...

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

In the released 4.4.0 version, the following marked line is not accurate. Philosopher can not mark the contaminant sequences for any existing fasta files. It can only mark when it...

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

The "tutorial" I mentioned is the wiki page here https://github.com/Nesvilab/philosopher/wiki/Database Best, Fengchao

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

The bug is still there: https://github.com/Nesvilab/philosopher/issues/528, https://github.com/Nesvilab/philosopher/issues/529, https://github.com/Nesvilab/philosopher/issues/516, https://github.com/Nesvilab/philosopher/issues/510#issuecomment-2483454242, and https://github.com/Nesvilab/philosopher/issues/498

combined_protein.tsv with empty sample columns

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

combined_protein.tsv with empty sample columns

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...