I am using xpress algorithms to get peak areas under curve (label free). I did some homework in this forum, and it turns out that it is doable by xpress according to this post:
https://groups.google.com/forum/#!searchin/spctools-discuss/label$20free$20xpress/spctools-discuss/RQPvyz3hIa4/bAVLoHxjinwJ In the above post, it is suggested to run xinteract with -X-M option, and then grab only "light area" in the pepxml file. So I did it using the command: xinteract -x20 -Opt -PREC -X-M-m0.05 -NResult.pep.xml somefile.raw.pep.xml (tpp v4.5 rapture rev 2) Inside Result.pep.xml file, I found description of xpress algorithm: <xpressratio_summary version="2.1 (TPP v4.5 RAPTURE rev 2, Build 201307022022 (linux))" author="Jimmy Eng" same_scan_range="Y" labeled_residues="MLIGHT" xpress_light="0" massdiff="MLIGHT,1.00" masstol="0.05" min_num_chromatogram_points="6" min_num_isotope_peaks="0"/> My questions are: 1. Basically -M option defaults "MLIGHT" as labeled, not every amino acid; Should I indicates all amino acid residues by using -n option? 2. My raw data has been searched by setting parent mass tolerance of 20ppm. I am wondering if it is reasonable to set mass tolerance to 0.05 dalton here by using -m option. 3. for: min_num_chromatogram_points="6", is it to leave it just like this or change to some other values? 4. Is there any way to get protein level quantitation by use of peak area of peptides? I have these questions since, when I manually check the peak areas by xcalibur, it turns out to be very different than what xpress gives to me. So I figured that something must be wrong with my setting. Can somebody help me out on these issues? -- 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 post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at http://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/groups/opt_out.
