Please note - I've discovered a similar problem (no models html file generated) in the following thread: https://groups.google.com/forum/#!searchin/spctools-discuss/interact$20prot%7Csort:date/spctools-discuss/Yrg2yEO4otg/8u0bNKzpAAAJ
Cheers Pete On Monday, 11 June 2018 14:58:53 UTC-7, [email protected] wrote: > > 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, <[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.
