I really need to learn more! Completely in bewilderment. Actually x!tandem gave me a search result and peptideprophet went well. Maybe I got wrong totally
在 2017年4月7日星期五 UTC+8下午12:40:01，Eric Deutsch写道： > > Yes, but note that the documentation you quote is for SILAC data. While in > your original message, you were asking about iTRAQ data. SILAC and iTRAQ > are completely different. These SILAC settings don’t apply to iTRAQ. Unless > you’re combining the two.. > > > > > > *From:* richard chiang [mailto:[email protected] <javascript:>] > *Sent:* Thursday, April 6, 2017 9:03 PM > *To:* spctools-discuss <[email protected] <javascript:>> > *Cc:* [email protected] <javascript:> > *Subject:* Re: [spctools-discuss] Parameters in X!tandem inputfile for > itraq 8 > > > > Thank you! I am not quite understand your meaning. I just modified it > according follows, although I am not sure if it was right. > residue, modification mass <http://www.thegpm.org/TANDEM/api/rmm.html>: > > In order to facilitate the analysis of SILAC data, the capability of > having multiple sets of modifications analyzed simultaneously has been > added. To specify additional sets of modifications, use the same parameter > name with the addition of an incrementing count (starting at 1): > > > residue, modification mass 1 > residue, modification mass 2 > ... > residue, modification mass N > I will do a further reading to bettter understand it. And your anwser give > me another confussion,if a signal modification is enough, how should the > libra program to differentiate the proteins for quantification later. > 在 2017年4月7日星期五 UTC+8上午10:53:51，Eric Deutsch写道： > > Hi, I don’t think that will get you anything useful, although you could > try it to see if you get anything that way. All you want is a single > modification on n-term and K as in the other thread. > > > > I’m guessing what happens is that the reporter ions like to hold the > charge and most peptides will still fragment somewhere along the backbone. > So.. if the reporter ion stays attached, then you see the mass of both the > reporter and balance group plus residues until the break. But, if the > reporter ions breaks off, then the charge stays on the reporter ion and you > see it, while the molecule with the residues plus the balance group has no > charge and so you don’t see it. So the molecules you’re thinking of are > there, but they rarely carry a charge so you don’t see them. That’s my > guess. If anyone who really knows can set us straight, that would be great. > > > > Regards, > > Eric > > > > > > > > *From:* [email protected] [mailto:[email protected]] > *On Behalf Of *richard chiang > *Sent:* Thursday, April 6, 2017 7:16 PM > *To:* spctools-discuss <[email protected]> > *Subject:* [spctools-discuss] Parameters in X!tandem inputfile for itraq 8 > > > > Hi, > I am trying to anlysis itraq8 Ms/Ms data with xtandm, and got confused by > a previouse disscussion iTRAQ data through xtandem! using TPP. > <https://groups.google.com/forum/#!searchin/spctools-discuss/tandem$20parameters%7Csort:date/spctools-discuss/e4wihr_i8JE/1SNYto9jMVgJ> > Should not the parameters in tandem.paraams.xml like follows,since balance > groups have been removed by the second Ms > > <note type="input" label="residue, modification mass">57.0...@C</note> > <note type="input" label="residue, potential modification mass"> > 15.9...@M,8.014199@K,10.008269@R</note> > <note type="input" label="residue, modification mass 1">113@K</note> > <note type="input" label="residue, modification mass 2">114@K</note> > <note type="input" label="residue, modification mass 3">116@K</note> > <note type="input" label="residue, modification mass 4">117@K</note> > <note type="input" label="residue, modification mass 5">118@K</note> > <note type="input" label="residue, modification mass 6">121@K</note> > <note type="input" label="residue, potential modification > motif"></note> > <note> You can specify a variable modification only when present > in a motif. For instance, 0....@N!{P}[ST] is a deamidation modification > on N only if it is present in an N[any but P][S or T] motif (N-glycosite). > </note> > <note type="input" label="protein, N-terminal residue modification > mass 1">113@K</note> > <note type="input" label="protein, N-terminal residue modification > mass 2">114@K</note> > <note type="input" label="protein, N-terminal residue modification > mass 3">116@K</note> > <note type="input" label="protein, N-terminal residue modification > mass 4">117@K</note> > <note type="input" label="protein, N-terminal residue modification > mass 5">118@K</note> > <note type="input" label="protein, N-terminal residue modification > mass 6">121@K</note> > > Sincerely, > Richard > > -- > 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 https://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. 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