Harald Barsnes

I've just redeployed the beta version which should now also support terminal PTMs: https://genesis.ugent.be/maven2/eu/isas/peptideshaker/PeptideShaker/2.2.18-beta/PeptideShaker-2.2.18-beta.zip

> I suppose PS is looking for peptides of the form "PEPCA" not "PEPC[+57.0214]A" with fixed modifications? We're just parsing all of the modifications provided in the peptide sequences. These...

> We're just parsing all of the modifications provided in the peptide sequences. Seems like we currently treat all modifications in pin files as variable. Hence, I need to detect...

> Here is a link to the PeptideShaker project zip file Seems to only contain the psdb file? Better if you could share the pin file and the search settings...

I've just redeployed the beta version which should now also support fixed PTMs: https://genesis.ugent.be/maven2/eu/isas/peptideshaker/PeptideShaker/2.2.18-beta/PeptideShaker-2.2.18-beta.zip

> Whoops... copied the wrong file. Here is a link for the zipped results files/parameters: https://www.dropbox.com/s/9lyf2qoobwhe7t3/Archive.zip?dl=0 Thanks! As far as I can tell it all seems to be working fine...

> It seems to be working for me as well! 😄 I've been able to load TMT-modified, as well as unmodified datasets, and also load in Sage results with other...

> I think additional enzyme support is probably the biggest blocker? Yes, I think so. Would also be great to get the precursors without charge state information issue addressed? (As...

You can set up your own enzymes via the Edit > Enzymes menu option in the main SearchGUI window. The created enzyme will then afterwards be available in the drop-down...

Ah, thanks for letting me know! There was a minor bug in our code that has now been fixed and a new version released (v4.1.23). Still not sure how the...