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                                            Fengchao

FASTA database: 6 × 9-mer peptides — usable with MSFragger?

If you make them looks like a protein, yes. Best, Fengchao

FASTA database: 6 × 9-mer peptides — usable with MSFragger?

Yes. Or even better ``` >sp|peptide_1|peptide_1 peptide_1 AGAGAGAGA ``` Best, Fengchao

Process 'MSFragger' finished, exit code: 1 Process returned non-zero exit code, stopping

Your data seems to be corrupted. ``` Could not load file C:\200ng_BSF_1106PepSep1_9_two_column_Slot1-18_1_4034.d. The file may be corrupted. ``` Best, Fengchao

tutorial on os x

Hi @lgp0509 , Thank you so much for the efforts and updates. Compiling TPP and Philosopher on OS X is what I always want to do but don't have time...

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

Hi HuiSong, It is a known bug: https://github.com/Nesvilab/philosopher/issues/813, https://github.com/Nesvilab/philosopher/issues/530, https://github.com/Nesvilab/philosopher/issues/516, https://github.com/Nesvilab/philosopher/issues/510#issuecomment-2483454242, and https://github.com/Nesvilab/philosopher/issues/498. This function was not well implemented at the beginning by the Philosopher developer. Hopefully, we will have...

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

It is a known issue. Same as https://github.com/Nesvilab/philosopher/issues/530 Need Felipe @prvst to fix the Philosopher. 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/530, https://github.com/Nesvilab/philosopher/issues/516, https://github.com/Nesvilab/philosopher/issues/510#issuecomment-2483454242, and https://github.com/Nesvilab/philosopher/issues/498

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

Just an update. Philosopher-v4.5.1-RC21 still has this issue. Best, Fengchao

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

When you prepare a **non**-human database, all human contaminant are **NOT** marked as contaminant, which is not supposed to be. See my first message in this thread to reproduce it....

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

Can you try this fasta file: [test.zip](https://github.com/Nesvilab/FragPipe/files/9941566/test.zip)