Fengchao
Fengchao
Unfortunately, no. The incompatibility is not due to the file format but the additional ion mobility dimension. Converting it to mzML doesn't help. We will add the support and let...
HI Sandra, I am not sure if I understand your question correctly, but can you try the "excluded mods" option in "Quant (MS1)" if you are doing LFQ. If it...
It just uses the sequence of the assigned protein in the fasta file. Best, Fengchao
The second one is also correct because there is a peptide `ALKLQLDNQY` in the protein. We don't distinguish `I` and `L` when mapping peptides to proteins because they have the...
Yes, this is a known bug: https://github.com/Nesvilab/philosopher/issues/430
Fixed in https://github.com/Nesvilab/philosopher/pull/517 Huge thanks to @hollenstein Best, Fengchao
Not available in the current version. If we added it in the future, will keep you posted. Best, Fengchao
Could you upgrade FragPipe and MSFragger to the latest version and try again? Thanks, Fengchao
Could you share the log file? Thanks, Fengchao
Thanks for the log file. I think the error was because the MS1 and MS2 have different set of FAIMS CV. Best, Fengchao