Split search files based on reporter ions

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Proton Member
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Split search files based on reporter ions

Postby fmr33 » Mon Jun 22, 2015 7:17 am

Hello all,

I am currently doing DDA using TMT labeling and then moving forward with SRM with peptides we are interested in. I currently do my search using SEQUEST in Proteome Discoverer and the look at my data in Scaffold Q+. I use skyline to make my methods for SRM and would like to first bring my DDA data into skyline split by the reporter ion. At the moment I can only pull in a sample that has all of the reporter ions present.

After all that explanation what I am wondering is: Is there a way to take my .mgf or .dat file and split it into multiple files according to to the reporter ion. Scaffold Q+ is able to do this for me but I can't find a way to export that data into a usable file format to then bring into skyline. Any help or guidance would be helpful even if it is a different workflow say using the Trans Proteomic Pipeline. Thank you.

E. Coli Lysate Member
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Postby Craig » Tue Jun 23, 2015 7:14 am

Do you know any scripting languages? If so, .mgf files are just plain text, so you could fairly easily write something that checks the reporter ions and writes the spectrum to the appropriate sub-.mgf file.

John F
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Postby John F » Thu Jun 25, 2015 12:29 pm

Within MSconvert, there is a relatively new option for filtering which should help you called mzPresent. mzPresent was developed for glycoproteomic work, but should work great for this type of application as well. I'm not familiar with what files you would need to import for Scaffold data, but you should be able to adapt mzPresent for your application. We were using the following settings to make an mgf of all MS2 spectra with any reporter ion for glycosylation (204.08 or 366.14 here):

msconvert "*.RAW" --mgf --filter "mzPresent 0.01 MZ 0.1 bpi-relative [204.08, 366.14] include"

more info (also a citation for mzPresent) in: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3617326/
msconvert documentation: http://proteowizard.sourceforge.net/tools.shtml
good luck!

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Postby Christopher » Sat Jun 27, 2015 8:21 pm

The msconvert option mentioned above sounds quite easy. If you can't get it to work, you could also achieve this pretty simply in R using the mzR package on an mzXML or mzML version of your data file.

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