Harald Barsnes

As far as I can tell from the log file there are two search engines failing: MyriMatch and Comet. For MyriMatch, the problem seems to be the FASTA file and...

>To get indexed spectra, I have set the output format to .mzML (indexed) in ThermoRawFileParser, this creates a Cement1.mzML file and a Cement1.cms file. However, comet is looking for Cement1.mzml...

> Indeed, the executable file does not exist even though there are other windows-like files (.ddl, CMD.exe) in this directory. It seems like SearchGUI thinks it is running inside an...

@biocc Thanks for letting us know! You can find new beta releases that should solve the problem here: https://genesis.ugent.be/maven2/eu/isas/searchgui/SearchGUI/4.2.0-beta/SearchGUI-4.2.0-beta-windows.zip and https://genesis.ugent.be/maven2/eu/isas/searchgui/SearchGUI/4.2.0-beta/SearchGUI-4.2.0-beta-mac_and_linux.tar.gz If this is not the case, please open a...

Issue assumed resolved with PeptideShaker v3.0.0. If this is not the case, please let us know and we'll reopen the issue.

Can you try right-clicking the jar file instead and choose "Open with..."? and then see if you can choose Java JDK 19 there? You can also try to override the...

Issue assumed resolved. It this is not the case, please let us know and we'll reopen the issue.

No idea, but does not look good. I'd recommend contacting the MS-GF+ developers: https://github.com/MSGFPlus/msgfplus/issues.

> Maybe SearchGUI could check for MSGF+ errors and abort? Maybe, but it very much depends on how the individual search engines detect and report errors that may occur. For...

Hi Hannes, I'm afraid this is not something we are planning on implementing in the near future. But in any case the spectrum data would have to be converted to...