Cyrus, For XPRESS, minimally you just need to specify: - which residues are labeled - the mass difference between the light and heavy forms of the label
We have the precursor m/z of the identified peptide and can calculate the precursor m/z of the isotopic pair just by knowing which residues are labeled and what the mass difference is between the light and heavy label. So I think you've got it right. K as the labeled residue and 6.02012902 as the mass difference. The notion of needing info on the fixed and variable modifications used to perform the search just are not pertinent for quantification by XPRESS. - Jimmy On Fri, Feb 10, 2012 at 12:09 PM, Cyrus Khambatta <xmasevenoo...@gmail.com> wrote: > Hi, > > I have a quick question about quantificaiton of SILAC samples using 13- > C6-Lysine as my heavy isotope. > I also tried reading through previous threads, and couldn't find a > direct answer to this question. > > My questions: > (1) Does XPRESS support either fixed or variable modifications? > (2) I can see that ASAPRatio does, but I can't get that tool to work > properly. What am I doing wrong? > > > FOR XPRESS ANALYSIS > > Fixed Modifications: > Carbamidomethylation(C), Monoisotopic mass = 160.0306487 > > Variable Modifications: > Oxidized Methionine(M), Monoisotopic mass = 147.035 > Pyroglutamic Acid(E), Monoisotopic mass = 112.0160439 > > I'm using 13-C6-Lysine as my heavy isotope, Monoisotopic mass = > 134.115092 > > The settings I'm using in XPRESS: > > Change XPRESS mass tolerance: 0.1 > Change XPRESS residue mass difference: K, 6.02012902 > > How do I input the fixed and/or variable modifications listed above? > > FOR ASAP RATIO ANALYSIS > > Change labeled residues to: K > m/z range to include in summation of peak: 0.05 > Specified residue mass 1: M, 147.035 > Specified residue mass 2: C, 160.0306487 > Specified residue mass 3: E, 112.0160439 > > Results: > (1) XPRESS quantifies a ratio of heavy/light and gives me a ratio, > however this analysis does not take into account any fixed or variable > modifications discussed above. > (2) ASAPRatio result is always "-1 +/- -1" and no chromatogram is > displayed when I click on that link. > > Any ideas what I may be doing wrong? > > Thank you VERY MUCH for your help, > Cyrus > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To post to this group, send email to spctools-discuss@googlegroups.com. > To unsubscribe from this group, send email to > spctools-discuss+unsubscr...@googlegroups.com. > 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 spctools-discuss@googlegroups.com. To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
