Importing PEAKS mzIdentML files

[AnotherKiwi]

I've tried importing the mzIdentML file exported by PEAKS Studio 8 for use by Scaffold (both v 1.0 and 1.1 - see attached screenshot) but PeptideShaker fails to find PSM in the file. The PeptideShaker output shows:

Tue Aug 16 11:57:16 NZST 2016 Reading identification files. Tue Aug 16 11:57:16 NZST 2016 Parsing peptides_1_1_0.mzid. Tue Aug 16 11:57:16 NZST 2016 No PSM found in peptides_1_1_0.mzid. Tue Aug 16 11:57:16 NZST 2016 No identifications retained.

Can you please advise if it is possible to import PEAKS results files into PeptideShaker? If so, what am I doing wrong?

Thanks Stephen

[hbarsnes]

Hi Stephen,

My guess is that we don't parse the PSM scores used by PEAKS. Could you send us an example mzid file from PEAKS so that we can try to locate the problem? We would also need the mgf file used as input in order to ensure that we can map the PSMs back to the spectra.

Best regards, Harald

[AnotherKiwi]

Hi Harald

The mzid file and MGFs used for the search are attached. I must confess to being a complete newbie with mzIdentML files so I'm not sure whether PEAKS exports all the required information. I'll be interested to hear your verdict!

Kind regards Stephen

XTandem Test_PEAKS PTM_16.zip

[hbarsnes]

Hi Stephen,

Seems like the PEAKS mzid file exposed an issue in the way we parsed mzid files. Already corrected, just need to check that the fix it generic enough. Will release a new version later this week.

Best regards, Harald

[AnotherKiwi]

Thanks Harald

I look forward to trying incorporating PEAKS results in the new version.

Kind regards Stephen

[1Moe]

Hi Harald and Stephen,

might hijack this topic and see if I could get some help. Trying to import a mzid file from peptideshaker into peakview but peakview complaines and doesn't accept the format.

mzid file can be downloaded here: https://drive.google.com/drive/folders/0BybCLLWRgDsUX2VTc0F1ZlpCMnM

See below for the PeakView error message (very non-descriptive, unfortunately): Cheers Moe

The given key was not present in the dictionary.

at ABSciex.PeakViewPlugin.SwathMenu.SwathLoadIonLibraryAction.LoadIonLibrary() at ABSciex.PeakViewPlugin.SwathMenu.SwathLoadIonLibraryAction.Execute() at Clearcore2.Utility.UI.UICommands.CommandAction.ExecuteCommand(Command command) at Clearcore2.Utility.UI.UICommands.Command.Execute(CommandExecutor executor) at Clearcore2.Utility.UI.UICommands.CommandExecutor.ExecuteCommand()

PeakView Version: 2.2.0.0 OS Version: Microsoft Windows NT 6.1.7601 Service Pack 1 OS Size: 64-bit DotNet Loader Version: 4.0.30319.42000

[hbarsnes]

Hi Moe,

The PeptideShaker mzid files should be ok. At least they pass all the mzid validation tests. It looks like PeakView is not supporting one (or more) of the CV terms used in the PeptideShaker mzid file. We used to have similar issues with Skyline. In order to fix it you'll have to contact the PeakView developers. Should be straightforward for them to adapt their code.

Best regards, Harald

[hbarsnes]

Hi Stephen, hi Moe,

PeptideShaker v1.13.1 has just been released supporting the loading of mzid files from PEAKS Studio. If this is not the case, please let us know and we'll reopen the issue.

Best regards, Harald

[AnotherKiwi]

Hi Harald I'll give v1.13.1 a try and let you know if I still have problems. Thanks very much for the excellent support! Cheers Stephen