I have been doing similar work but with acetone instead of formaldehyde. I am using Tandem as a search engine. In the tandem.params file for the search, I specify static modifications for the light e.g. 42.0xx@[,42.0xx@K. Then specify the mass difference between the heavy-light label as a variable modification, e.g. 6.0xx@[,6.0xx@K.
For quantitation, I use ASAPRatio. In that section I select "n" (small n) and K on the line called "Change labeled residues to", check off the heavy elutes before the light. For "Specified residue mass 1" I select "n" and type in the monoisotopic mass for the heavy isotope complete label modification mass on the n-terminus, in my case it is 48.0xx, and for "Specified residue mass 2" select K and enter 176.xx which is the monoisotopic residue mass of a lysine with the heavy label. During the TPP training course, the example data set was iCAT and it was mentioned that you also had to add the residue mass of oxidized Met or it wouldn't consider those peptides. I presume this is the case for all datasets and I don't know whether it is the case for all modified residues such as deamidated N, Q etc. that were part of the mods in the search. I have not tried Xpress on my data. The results are given a p-value which to my understanding is a measure of whether the result is truly enriched or part of the background set. The result seems to be that the closer the ratios are to 1 the higher the p-values. Which is to me confusing. I would think that if a particular protein ratio which results from integrating peak areas of the light and heavy for all the peptides assigned to a protein, and that data is very tight, then even if the ratio is 1 the p-value should indicate that. But it doesn't. If you look at the Aebersold paper on ASAPRatio the table near the end shows this trend in p-values also. Brian On Mon, Nov 5, 2012 at 4:42 PM, tonydufour <[email protected]> wrote: > What is the best way to use TPP to quantify a murine dataset that was > dimethylated light and heavy (0 and 6)??? > > -- > You received this message because you are subscribed to the Google Groups > "spctools-discuss" group. > To view this discussion on the web visit > https://groups.google.com/d/msg/spctools-discuss/-/FF5m-ilo0DoJ. > To post to this group, send email to [email protected]. > To unsubscribe from this group, send email to > [email protected]. > 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 [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en.
