Hello Pete, iProphet has a sibling experiments model and uses the replicate spectra model for replicate PSMs that are in the same experiment.This is enabled by running InteractParser with -X<experiment_label> flag, which labels the spectra in the pepXML file. If you are using xinteract or Petunia web interface the option is -E<experiment_label>. You have to make sure that for each search engine analysis you assign the same label to the same data. The experiment label is flexible and allows you to separate the data into "experiments" as defined by you. It makes sense in your case to make the experiment labels either the "fraction_name" or the "fraction_name"+"replicate". Other than that I think you are on the right path.
Cheers, -David On Tue, Jun 5, 2018 at 3:13 PM, <[email protected]> wrote: > 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. > -- 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.
