Skyline uses another program called "BlibBuild.exe" to construct the spectral library.

I ran BlibBuild.exe under a debugger, and I can tell you that the thing that it is complaining about in your file is where it says "MS:100XXX".

I hope this helps. I don't know whether this is something that we need to fix about BlibBuild (certainly the error message could be made more helpful).

Hi Nick,

Thanks for the help. "MS:100XXX" was something we used as a placeholder while working on the new mzid 1.2 format changes, but should of course have been removed.

After removing the incorrect CV term I'm able to start loading the file, but I now get the following error message instead: "ERROR: Can't determine cutoff score, unknown analysis type".

Any tips on this one as well?

Best regards,
Harald

Hi Harald,

When building libraries, BlibBuild first tries to identify the software that produced the mzIdentML file in order to determine how to do further processing (e.g. what scores to look for). We will need to add support for this case.

Thanks,
Kaipo

Hi Kaipo,

Thanks for the information. I'm attaching the revised mzid file from PeptideShaker in case you can extract what you need from this file.

In case you don't know PeptideShaker (http://peptideshaker.googlecode.com), it is a tool for the interpretation of proteomics identification results from multiple search engines. At the moment we support X!Tandem, MS-GF+, MS Amanda, MyriMatch, Comet and OMSSA, and more are on the way. All of these search engines are supported via SearchGUI (http://searchgui.googlecode.com), which is where we mainly take our input from.

After processing the individual search results these are combined into a single PeptideShaker result. Both the combined PeptideShaker result and the individual search result scores are included in the mzid file.

Please let me know if you need any additional information about either PeptideShaker or the content of the mzid file.

Best regards,
Harald

Hi Kaipo and Harald,


Will new coming updated version support mzid file from PeptideShaker? or is there any test release from Skyline Daily? PeptideShaker also can export pride.xml that is a file format Skyline supports. When I tested it, it seems Skyline doesn't support it. Any suggestion or help would be appreciated!


Gil

Hi Gil,

Support for PeptideShaker outputs will probably not make it into the upcoming version, but hopefully the version after this.

Thanks,
Kaipo

Hi Kaipo,

Thanks. Hope we have the support soon.

Gil

I'd just like to add my name to the people looking forward to this implementation. I use PeptideShaker all the time and would love to see it supported in Skyline, which is also one of my favourite programs...