Hello TPP, I'm a new TPP user, and so far, very happy with the results from simple qualitative proteomic experiments (information dependent acquisitions and straight database searching). I am know going to start some quantitative experiments using light and heavy dimethylation labeling reactions (D-labeled formaldehyde and sodium cyanoborohydride). I've already read many of the discussion threads on this topic, so I guess both XPRESS and/or ASAPratio should work fine in this context. I also read about the way to perform the DB searches using the static and variable modificatios too :-).
I have though a couple of questions before I start processing my samples (whole cell lysate digests and subcelular fractions). 1. At this time, I only have available for my analysis a AB QTRAP 3200 system. Previously, I have worked with this system and analyzed my data (same labeling approach) using Mascot Distiller program-Rover combo. In those conditions, Mascot Distiller gave me the possibility of doing the quantitation on the full MS scan or on what Distiller called the zoom scan, which is the ER (enhanced resolution) scan done on the trap an lower scar rates to determine the charge and 'exact' mass of the precursor. I have gone through the XPRESS and ASAPratio parameters, and this option doesn't seem available. Could somebody tell me whether this option is available, or whether the quantification will be done on the full MS data by default? 2. Occasionally, I fractionate my samples (after digestion and labelling) by SCX, and then inject each fraction into the MS (ONE Wiff file, with X number of samples as fractions present). When I analyzed these data with Mascot Distiller, I run into some problems, specially for those peptides which coeluted into more than one fraction during the SCX separation. Since the same peptide appeared in more than one fraction, Mascot Distiller was not able to correctly extract the signals from the individual samples (fractions) and quantitation was hampered. I was wondering if anyone has done these type of experiments, and whether TPP (with either XPRESS or ASAPratio) can manage this typo of files (One wiff, with multiple sample files, or multiple wiff files acquired independently)? Thanks TPP people, looking forward to for your suggestions and hopefully will move our MS analytical platform to TPP in the near future. Alejandro Cohen -- 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.
