Alexey Nesvizhskii

I should handle it except possibly one step in philosopher. But it is not needed, really. If you get a crash at that stage, you can rerun from TMT-Integrator step....

Yes, you should convert from RAW to mzML. Philosopher is not optimized for RAW, so it would take a lot longer to run with RAW than mzML (although in your...

Please make sure to sue a recent version of proteowizard/scovert, not more than 6 months old… From: dnwhdals ***@***.***> Sent: Wednesday, September 29, 2021 12:16 PM To: Nesvilab/FragPipe ***@***.***> Cc:...

Can you check you are using the latest philosopher? And also converted to mzML using a recent version of msconvert From: surendradasari ***@***.***> Sent: Monday, October 18, 2021 11:34 AM...

Good. Yes, you need MS1 scans too even though it is TMT analysis (that’s how the Purity score is calculated) Best, Alexey From: surendradasari ***@***.***> Sent: Monday, October 18, 2021...

I observed the same issue with standard search using GenCode database. Need to fix for the next release

Hi Huiyin Is it because we require that there is a gene name? I see more people using TMT/integrator with databases that do not have it. We should add a...

@Maithy15 can you confirm there were 'xml.tmp' files, and you were able to run the tools after cleaning the folder?

@prvst can we print an informative error message when this error happens and there are 'tmp.xml' files in the directory. I am not sure though if we can figure out...

Are you using the latest philosopher? But even with an earlier version, there should not be any proteins in reprint.int that are not present in combined_protein.tsv. I assume you are...