Harald Barsnes

Aha, so it's not PeptideShaker that fails when loading the data (as for the Comet output), but MS Amanda itself that fails when searching the data? Not much we can...

> Regarding the error on another computer, everything seems to go well (searchgui), but then there is a failure and the ongoing process (searchgui + peptideshaker) is interrupted. You can...

Seems like you shared the wrong mzml file? At least PeptideShaker is asking for ModA1_GlucoseWBA.mzML and you only shared ModC1_GlioxalWBA.mzML?

I'm now able to process your data but it ends in the following message: ``` Tue Nov 22 15:20:38 CET 2022 Importing sequences from UniprotSprotTD_concatenated_target_decoy.fasta. Tue Nov 22 15:20:50 CET...

> the X! tandem says the spectrum doesn't meet the necessary criteria, but I've changed several settings and it still doesn't work. I did the test with the same spectrum...

> The potential modifications found by the program can actually happen as we are using experimental models to check chemical derivatizations. So, what happens is that the same peptide (in...

> After some time that I didn't use the program I did it again, but the peptide shaker fails to open. I send the report and I was able to...

Hi Juan, Thanks for letting us know about this one! Here is a beta version that should solve the problem: https://genesis.ugent.be/maven2/eu/isas/peptideshaker/PeptideShaker/2.2.18-beta/PeptideShaker-2.2.18-beta.zip Hopefully this version will allow you to generate a...

The issue has been resolved in PeptideShaker 2.2.18 which has now been officially released.

As far as I know, this is not something we support at the moment. It should not be too difficult to implement, but I'm afraid we do not have the...