deisotoping in msconvert affects iTRAQ reporter ion labels; can deisotoping only occur for >= 140 m/z

[Gautam Saxena]

Deisotoping (in the msconvert option) significantly improves search results for iTRAQ data. However, it also has very bad affects on the reporter ions. Is there a way to get msconvert to only do deisotoping for those spectra in which the m/z >= 140 (ie above the reporter ion levels)? Is this something that can be customized? If not, is there a good workaround to this problem -- eg running msconvert for ms2 below 140 (no desitoping) and again for above 140 (with deisotoping) and somehow merging the mzXML files?

[Eric Deutsch]

Sounds like a pretty easy and worthwhile feature to add. Maybe you can convince one of the ProteoWizard folks to add it.

 

In the mean time you could create one set of mzMLs with deisotoping for searching, and then swap in a second set of mzMLs without to execute Libra.

 

Eric

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[Gautam Saxena]

Dear ProteoWizard,

I know msconvert is open source, so if we had the skills and expertise, we could make what appears to be an easy change, but therein lies the problem. Given our lack of expertise here, is there a proper way to request this feature enhancement so that it can be implemented "correctly"?