Fengchao

It might because Philosopher cannot recognize the protein header in the fasta file. Felipe @prvst , can you take a look when you have time? Thanks, Fengchao

> @mwfoster I got an internal request to remove the contaminants from all the output tables. If you want to still have them, please add the contaminants to the FASTA...

Hi Jongmin, I think you didn't run Philosopher' label quant and free quant, which are required by TMT-Integrator. Can you load one of the TMT workflow and try again? Best,...

Hi Jongmin, Can you send me your log file? Please zip it. Then, drag it to GitHub issue page, or email it to [email protected]. GitHub somehow won't show the zip...

Hi Jongmin, Thanks for your log. But there is no free quant or label quant in your log. Can you double check? Best, Fengchao

Thanks Jongmin, Yes, the latest log has free quant and label quant, and both of them finished successfully. But TMT-Integer still says that can't find the "Purity" column. Can you...

Thanks Jongmin. Then, it is a Philosopher bug. Felipe @prvst , can you take a look? Thanks, Fengchao

Hi Alexey, Yes, I will add a checkbox to FragPipe. Hi Jongmin, Sarah will contact you directly regarding the files you uploaded. Thanks, Fengchao

Everything looks good except there is no entries in the tsv files. Felipe @prvst , can you take a look? They said that FragPipe 16, which implied the Philosopher 4.0.0,...

Hi Felipe @prvst , The `interact-*.pep.xml` from Percolator won't have such replacement. Will your changes break the Percolator related workflows? BTW, what kind of characters does PeptideProphet replaced? Best, Fengchao