Fengchao

Yes, please upload the other log file containing the whole process, first. Thanks. Fengchao

You set the `TMT-6` but the variable modifications does not seems to be TMT-6: ```shell variable_mod_09 = 417.22485 K 2 variable_mod_12 = 417.22485 n^ 1 ``` May I ask what...

Thanks for the clarification. The current version of IonQuant filters out the PSMs without any variable modifications corresponding to the isobaric label. That was why using IonQuant as the intensity...

No prob! And no need to create another issue, I will use this one to track the changes. Best, Fengchao

> What do you think is the reason for the other problem I met, where it fails to generate a PTM-specific report? Because the format was wrong: `n(417.2249),K(417.2249)\:probe`. It should...

Hi Stefan, Thank you very much for your suggestion. If you want to visualize the annotated spectra, you can open the FP-PDV window by clicking "Open visualization window" in the...

I have implemented the feature to report the matched fragments. Let MSFragger generate the `tsv` report will have those two new columns. If you want to try the pre-released version,...

Hi Owen, Thank you very much for your feedback. We will discuss internally about adding these columns to the TMT report. Best, Fengchao

Seems to be the same as https://github.com/Nesvilab/FragPipe/issues/1836, https://github.com/Nesvilab/FragPipe/issues/1543, and https://github.com/Nesvilab/FragPipe/issues/1431 > the user uses an administrator installed Python, then installs Python packages using a non-administrator account, and that combination causes...

The TMT intensity extraction tool was set to "Skip extraction. Run TMT-Integrator only", which caused the error. Please change it back to the default settings. Best, Fengchao