Hi all, I'm trying to use tSIM-ddMS2 to identify specific peptides in my sample, but I also want SILAC quantification of those peptides using XPRESS. I've made sure the MS1 isolation window is wide enough to see both Light and Heavy peptide peaks for everything in my inclusion list (30 daltons, so my heavy peptides which are +8 or +10 are detected). However, when I search with Comet and XPRESS, there is no quantitative ratio provided, just -1.0. XPRESS appears to be looking in the wrong place for the light and heavy peptides, but I am not sure why or how to redirect it to the right parts of my MS1 spectra. If I look at the precursor scans manually via QualBrowser, both peaks are definitely being detected.
Has anyone here tried using XPRESS to do SILAC quantitation in targeted runs before? Here is a folder with my data, search parameters, and database just in case. https://drive.google.com/drive/folders/1142YHaxB1RC6HMcfuy_MdEN8T-sSLDSl?usp=sharing Thanks! -Will -- 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 spctools-discuss+unsubscr...@googlegroups.com. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/445ec267-3132-40ca-89c7-9d62b7c0a993n%40googlegroups.com.
