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 *From:* [email protected] [mailto: [email protected]] *On Behalf Of *Gautam Saxena *Sent:* Friday, January 18, 2013 7:28 PM *To:* [email protected] *Subject:* [spctools-discuss] deisotoping in msconvert affects iTRAQ reporter ion labels; can deisotoping only occur for >= 140 m/z 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? -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To view this discussion on the web visit https://groups.google.com/d/msg/spctools-discuss/-/ka_LbRhkNXMJ. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
