Harald Barsnes

Hi! I'm afraid this is a known issue with our backend code that we have not yet been able to solve. In other words, it is not due to your...

Hi! The problem here (at least the one shown in the screenshot) is that MS-GF+ filters out all of the spectra. You can either switch to a different search engine...

Yes, you are indeed correct in that it seems like our mzid parsing is formatting-specific. I guess we never considered that anyone would want to write an mzid file without...

> Technically XML is supposed to be whitespace agnostic "Should" is the keyword there. ;) But yes, this is clearly something that ought to be fixed in our home made...

I'm afraid this is a known backend issue to which the only known solution is to increase the amount of memory provided to PeptideShaker. You can do this via the...

Another option you can try is to use only one thread/core. This will however dramatically slow down the processing. But could be worth it if it allows you to complete...

Hi! Seems like there is an error when parsing the spectrum titles for some of your MS-GF+ mzIdentML files. Any chance you can share one of these files so that...

Oh, and I would also need the corresponding spectrum file (in order to be able to load the data and reproduce the issue).

I can confirm that I'm able to reproduce the issue. Seems to be an error with the indexing of protein c-terminal peptides. I will have to dig deeper and get...

Did you do the raw file conversion separately outside of SearchGUI? As the mzid file you shared indicates that mgf was used as input, while SearchGUI's internal conversion (using ThermoRawFileParser)...