• Sign In
  1. Requests

myrimatch/IDPicker data importing

support

View Request

view list print
myrimatch/IDPicker data importing mvillal1  2015-04-28 21:54
 
Hello Skyline developers and community.

I have been trying to create a spectral library from some Myrimatch-IDPicker output files but I am not able (or don't know how) to export them to the idpXML/mzXML formats that Skyline requires. My files are either in pepXML or mzIdentML formats but I don't know how to convert either of these outputs to idpXML or mzXML... Can anyone point me out a way to do this? The raw data comes from a Thermo LTQ-XL which is then processed through the Bumberdash-IdPicker pipeline.

Many thanks!

P.S. I am new to targeted proteomics but Skyline is proven to be a great tool! Keep up the good work and thanks again!

-Ivan.
 
 
Brendan MacLean responded:  2015-04-28 22:10
Hi Ivan,
If you can give us an example of your files, we can probably get them working pretty quickly. I may be mistaken, but I thought we had this working for mzIndentML/mzML from IdPicker, but it certainly has been a while since we saw one of these files. It is certainly possible that something changed since we last worked on this.

I will email you directly with a location to post an example we can look at.

Thanks for posting to the support board.

--Brendan
 
abrahampe responded:  2016-12-12 09:54
Hi Brendan,

I am currently using MyriMatch and I am also not able to import the .mzID files. The error is: .mzid file contains an unsupported score type.

Thanks!

--
Paul
 
Kaipo Tamura responded:  2016-12-12 11:03
Hi Paul,
You can see the list of supported formats here: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild

Currently for MyriMatch we are expecting .idpXML files, though we can add support for MzIdentML. I will contact you through email if you are able to share sample mzid/mzml results.

Thanks,
Kaipo
 
Kaipo Tamura responded:  2016-12-13 11:43
Support for MyriMatch .mzid files turns out to be problematic, since they do not contain usable scores.