Fengchao
Fengchao
Thanks for the report. It was because the intensity value is overflowed. I didn't expect the data will have such a high intensity. Maybe I should cap it to 8388607...
Hi @jmcalist . I guess you mixed different issues here. Can you send all log files? Best, Fengchao
> Just to confirm, for the previous reply of 'can you try increasing the protein FDR threshold', does this refer to changing --prot 0.01 to --prot 0.05 in the FDR...
Thanks for your log files. It looks like none of your jobs finished without any error. MSFragger failed with the Thermo raw file parser's errors like ```shell [pool-1-thread-7] ERROR com.dmtavt.batmass.io.thermo.ThermoGrpcServerProcess...
Converting them to mzML would make the running faster and more robust. But you need to make sure that you used the correct settings in the conversion. Here is the...
I have no idea since I am not familiar with the Philosopher source code.
Hi Shinya, It was actually due to a different reason. Could you share your .d folders with us? Thanks, Fengchao
Yes, please. Here is the link to upload the .d: https://www.dropbox.com/request/TG1snTlVtJNHY1vuzReD Thanks, Fengchao
Hi Shinya, Thank you for sharing the files. I think PTMProphet, which is used to perform PTM localization, has issues with C terminal modifications. For example, the localization probability of...
If PTMProphet is disabled, you will still have the PTMs localized in the peptides, but there will be no probability to measure the confidence. Best, Fengchao