Hi, I'd really appreciate advice regarding the most valid way to combine my searches with peptide / i / protein prophet.
I have 3 samples, 3 fractions per sample, and each fraction was digested with multiple enzymes. Each of these digests were injected twice. The resulting data were then searched with different search engines; all in an attempt to increase number of protein IDs. My idea of the workflow was as follows: 1. combine results of 1 search engine for duplicate injections of a single fraction using peptide prophet 2. combine results of multiple search engines using iprophet 3. combine iprophet results from different enzymatic digestions of a single fraction of a single sample using protein prophet (to group sibling peptides) I'm unclear whether/when it is valid for me to combine: a) different fractions (note - fractions are expected to have some overlap in peptide and protein IDs) b) different samples (note- samples are biological replicates, and are expected to contain the same peptides / proteins) The reason I would like to combine them all together, is so that I can have a single protein FDR for the whole experiment. Thanks! Pete -- 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 post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
