Harald Barsnes

The first thing you can try is increasing the amount of memory given to PeptideShaker. This should reduce the chance of this error occurring. You can do this via the...

I'm afraid that we do not work with Docker containers ourselves and therefore do not have much experience with them. My advice will therefore be of a more general type....

Hi Baopu, I'm afraid that pep.xml is not as standardized as one may think. We therefore have to implement individual support for the different search engines producing pep.xml files, for...

Hi Baopu, I had a look at the files you shared plus the additional data from PRIDE. Adding support for loading MSFragger pep.xml files should not be too difficult, however...

Hi Baopu, I'm afraid that we do not currently have the resources to implement this type of PTM search in our tools. I will however keep the issue open in...

Hi Feng, Can you please share the PeptideShaker log file? You can find it via the PeptideShaker Welcome dialog > Settings & Help > Help > Bug Report. You may...

Hi Feng, I'm afraid you are experiencing several issues with the backend for which there is no known fix at the moment. We are however working on refactoring this part...

You can change the temp directories via PathSettingsCLI: https://github.com/compomics/searchgui/wiki/SearchCLI#pathsettingscli If I remember correctly, you can also use the PathSettingsCLI parameters directly as part of a standard SearchCLI command line. You...

> If I set paths with PathSettings cli, or SearchCLI where will it get saved ? > > I suppose it gets save in: > > ./SearchGUI-4.2.8/resources/conf/paths.txt Correct. > Can...

> I hope this dooesn't comes accross as pedantic, we really like SearchGui and Peptide Shaker, we really like the way it's evolving, I think the ability to decide where...