Fengchao

I apologize if there are any miscommunications. I meant that something was wrong in your data. Could you share `CR10Pm.mzML` with me to take a look? Thanks, Fengchao

Thanks for sharing the mzML file. The reason for the error is that your mzML file does not have the required tags. Taking the following MS2 scan for example ```xml...

The error was because either the `ext` folder was not in the MSFragger-4.1.jar folder or mono was not installed on your Linux: https://fragpipe.nesvilab.org/docs/tutorial_setup_fragpipe.html. To read the raw format, mono is...

Ah, this is because IonQuant detected and read the mzML files, which had the compensation voltage issues, from the same folder. Could you move the mzML files to other places...

I am not sure what exactly the "export all PSMs of all proteins" means, but clicking the "all proteins" will select all proteins, and then all PSMs will be shown...

Yes, we can let IonQuant take that information and propagate to the combined table. Best, Fengchao

Hi @ShinjaChakraborty , you could start with one of the built-in glyco-N workflows. Here is a tutorial if you need it: https://fragpipe.nesvilab.org/docs/tutorial_glyco.html Best, Fengchao

Same reason, there are no IDs ```shell WARNING: Mixture model quality test failed for charge (2+). WARNING: Mixture model quality test failed for charge (3+). WARNING: Mixture model quality test...

Hi Matt, Sorry for the long delay. I finally got a chance to implement this feature. If there is not too much trouble, could you share some typical Waters and...

Mapping the mzML/pepXML to the pin file is actually OK as long as we have a consistent way to extract the scan number (from native ID if it is encoded...