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Building DDA spectral library mrmiller  2017-08-18 05:28
 
I'm very familiar with MS but have just started looking at proteins so my problem is probably my unfamiliarity.

I'm struggling with figuring out how to adapt the DDA MS1 filtering to my LC-MS file because of the first steps in the DDA import. I'm not sure how to go about getting the files equivalent to the .group and .wiff files in the tutorial.

I tried using the XML outputs from Protein Prospect to see if it would accept any of those, including the DIG, PRODUCT, and BRIDGE programs.

Thank you,
 
 
Kaipo Tamura responded:  2017-08-18 10:55
Here is a list of the search engines that we currently support: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BlibBuild
I'm not familiar with the ones you mentioned but one option to import the files into Skyline is to create a .ssl file, described here: https://skyline.ms/wiki/home/software/BiblioSpec/page.view?name=BiblioSpec%20input%20and%20output%20file%20formats
Alternatively we could try to add support for the output formats you listed, if provided with example results.

Thanks,
Kaipo
 
mrmiller responded:  2017-08-18 11:18
Protein Prospector is listed on the BiblioSpec input and output file formats page. What program would you suggest to build the library from in silico?
 
Brendan MacLean responded:  2017-08-18 14:31
Interesting. It looks like the formats page Kaipo listed needs to be updated since we do list Protein Prospector here:

https://skyline.ms/wiki/home/software/Skyline/page.view?name=building_spectral_libraries

Note that this page lists our support as (pepXML/mzXML), which means Protein Prospector must have a pepXML/mzXML export options somewhere. Kaipo, I am sure if you look at the pepXML/mzXML format, you will find it supporting pepXML from Protein Prospector.

Our release notes also say we implemented this in Skyline 1.2. (search for Protein Prospector on the release notes page):

https://skyline.ms/notes.url#skyline_1_2

Anyway, it does require you to get pepXML from Protein Prospector.

Hope this helps.

--Brendan