It make sense to me now, Eric. Thanks! I looked into some of my spectra, most b ions did have iTRAQ still attached to it. However, I was able to find some b ions that did not have iTRAQ attached, those of course were not considered as matches. But there were not that much such ions, and they were mostly in low intensity, so I guess they won't affect the search result anyway.
SunSun On Friday, May 1, 2015 at 12:08:58 AM UTC+8, Eric Deutsch wrote: > > 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:* spctools...@googlegroups.com <javascript:> [mailto: > spctools...@googlegroups.com <javascript:>] *On Behalf Of *zeyu sun > *Sent:* Sunday, April 26, 2015 10:19 PM > *To:* spctools...@googlegroups.com <javascript:> > *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 spctools-discu...@googlegroups.com <javascript:>. > To post to this group, send email to spctools...@googlegroups.com > <javascript:>. > 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
