mzTAB File Type for Spectral Library

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mzTAB File Type for Spectral Library melissa martinez  2018-04-27 13:49
 
Hello,

Despite the many types of data that are acceptable to build a spectral library using Skyline, I've recently run into some compatibility issues with mzTAB files. A couple years ago HUPO selected mzTAB as the standard data file type for proteomics data sharing. Some data repositories, like MASSIVE from UCSD, require converting all peptide files into mzTAB files and that is all that's available to download.

Could you please consider making Skyline capable of using this file type for the peptide IDs? If this is the chosen file type for proteomics data sharing, I imagine it'll be seen more and more.

Thank you very much!

-Melissa
 
 
Brendan MacLean responded:  2018-04-27 21:18
Hi Melissa,
Good point. We usually wait for someone to ask. You are the first, but it sounds like we can get examples from MASSIVE. If you would like to provide your own example of an mzTAB format file that you would like to see turned into a spectral library for Skyline, please point us to it on-line or post it to our file drop point:

http://skyline.ms/files.url

Thanks for the suggestion.

--Brendan
 
Jason Held responded:  2018-05-16 11:24
I was just looking into how to import mzTABs into Skyline and came across this. I'd second that it'd be really useful.

Jason
 
Kaipo Tamura responded:  2018-05-22 15:31
Hi Jason,
I've written the code to build a spectral library from an mzTab file, but need data to test it - would you mind sharing an mzTab file along with the corresponding spectrum files (e.g. mzML/mzXML)? Brendan posted a URL above where you can post an example.

Thanks,
Kaipo
 
Jason Held responded:  2018-05-24 09:11
Thanks! However, I am having issues making an mzTAB with results out of Massive. Will circle back when I get that sorted out.

Cheers
 
Brendan MacLean responded:  2018-05-24 09:36
Hi Jason,
We were able to find some examples on Massive ourselves and Kaipo was able to make some use of those. If no one else is producing mzTab at this point, I think we have figured out how to get examples from Massive. If you have your own mzTab, we'd be interested in seeing that as well.

Thanks for expressing your interest.

--Brendan