Hi, I have two treatment groups and want to identify (& quantify) the peptides.
1. Metabolic label with N15 sample (3 replicates) 2. Normal N14 sample (3 replicates). I extracted & digested the protein using S-trap kit and fractionated each sample into 8 fractions using Pierce high Ph fractionation kit, resulting 48 samples (2 Treatment group X 3 replicates X 8 Fractions) in total. I matched all of the data using Comet and X!Tandem, using two different (N14 and N15) parameters - which produced separate .mzML files for each. Now I am confused how to combine all fractions, replicates and parameters into single result file. I am thinking to go for N14 parameter first - merge all fractions and replicates of comet/tandem in peptide prophet, merge peptide-prophet results of Comet and Tandem in i-prophet afterwards. Do the same for N15 parameter, and combine i-prophets of N15 and N14 in protein prophet. I will run Xpress later on, for quantification. Can you please advice me is it OK? or any other way to do? ASIF -- 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 [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/spctools-discuss/b462a19a-78e5-4de7-86c4-2530dea4b711n%40googlegroups.com.
