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]] *Sent:* Thursday, April 6, 2017 9:03 PM *To:* spctools-discuss <[email protected]> *Cc:* [email protected] *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] <javascript:> [mailto: [email protected] <javascript:>] *On Behalf Of *richard chiang *Sent:* Thursday, April 6, 2017 7:16 PM *To:* spctools-discuss <[email protected] <javascript:>> *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 <javascript:>> <note type="input" label="residue, potential modification mass"> 15.9...@M,8.014199@K,10.008269@R</note <javascript:>> <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 <javascript:>] 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] <javascript:>. To post to this group, send email to [email protected] <javascript:>. 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. 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.
