Thanks David, I wasn't aware of the experiment label - that sounds ideal. I'll give it a try
On Wednesday, 6 June 2018 00:34:47 UTC-7, David Shteynberg wrote: > > 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, <pbell....@gmail.com <javascript:>> 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 spctools-discu...@googlegroups.com <javascript:>. >> To post to this group, send email to spctools...@googlegroups.com >> <javascript:>. >> 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 spctools-discuss+unsubscr...@googlegroups.com. To post to this group, send email to spctools-discuss@googlegroups.com. Visit this group at https://groups.google.com/group/spctools-discuss. For more options, visit https://groups.google.com/d/optout.
