Hi SunSun, I am not an expert on exactly how this works, but I will answer as best I can. The short answer is that the search engine does NOT know, and it does not NEED to know. All it knows is the n terminal mass of the full tag that you give it.
The longer answer then is that the reporter often is fragmented off with a charge and that is when you see a reporter ion. However, it is also relatively often (maybe even half the time) that it is *not* fragmented off. For those ions you tend to get robust b ions of various lengths. You almost always see just the whole n terminal label too. Y ions are, of course, unaffected. I have never seen spectra that have b ions with reporter removed but the balancing part of the tag still there. I suppose it must happen, especially when there is a basic residue such as and H near the n terminus. But maybe those spectra don’t get very good scores, so you don’t see them. They’re probably there but rare. Maybe some else has more or better information. Regards, Eric *From:* [email protected] [mailto: [email protected]] *On Behalf Of *zeyu sun *Sent:* Sunday, April 26, 2015 10:19 PM *To:* [email protected] *Subject:* [spctools-discuss] Comet/tandem search on isobaric data Hi TPP team, I got a silly question here about using comet and tandem to search TMT data within the TPP workflow. I didn't found anywhere in Comet and Tandem's parameter file to specify the quantitative method, so I simply put TMT as a fix modification on Nterm and K just for the search and use the Libra to do the quantitation later. It all went OK, but I just realize one confusion issue here: because the TMT was defined as a fix modification, how does Comet and Tandem know the TMT will be cleaved off during HCD that there is no TMT modificaiton in MS/MS spectrum? Thank you! SunSun -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
