Hi David, Thanks for your advice - I've had success using the experiment flag in Petunia, and have found that using an experiment label including fraction, replicate and also enzyme (used for digest) works well when processed through iProphet/protein prophet.
However, my problem now is that the 'models' tab when I open the resulting interact.ipro.prot.xml file is not visible - so I don't know where to set the cutoff for 1% FDR I notice in my .params folder that there is no interact.ipro.prot html file - but no errors appear while protein prophet is running. Please could you shed any light on how I can make the models visible? Perhaps I've deleted some file in the .params folder that's required to generate the html? Thanks Pete 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.
