Hi Antonio, To use StPeter, you must perform peptide validation and protein inference first. These are done, minimally, with the PeptideProphet and ProteinProphet tools, respectively. They are needed because StPeter quantifies proteins, not peptides, and thus you need to first perform protein inference.
We do have a tutorial for StPeter, sorry if our links don't line up precisely from the launch location you started at. Updating the documentation site is a work in progress. Try here: http://tools.proteomecenter.org/wiki/index.php?title=Tutorial:StPeter1 Unfortunately, it does assume using the GUI. StPeter (and the other TPP tools) should all have command line usage statements if you simply type them without parameters. But it is easiest to try solving your Apache2 problems. And regarding your last question, no, the precursor intensity is never used as part of StPeter. The quantification is done entirely with spectral indexes which utilize the intensity of fragment ions, not precursor ions. Cheers, Mike On Saturday, May 19, 2018 at 5:03:25 PM UTC-7, Antonio Ortega wrote: > > Hi all! My name is Antonio Ortega, and I am a Master student in > Bioinfomatics at the University of Copenhagen, currently doing my Master > Thesis on proteomics and mass spectrometry. > > I was wondering how can I use StPeter as a quantification tool if I pass > as input the output of search engines like MSGF or Comet. I can see in the > tutorial that Stpeter receives as input protXML files, however Comet > produces pepXML output and MSGF produces mzid files that apparently can be > converted to pepXML with idconvert > > https://groups.google.com/forum/#!topic/spctools-discuss/tbkcovbFxEc > > Why is the intermediate proXML file produced by PeptideProphet, iProphet > and ProteinProphet needed? Is there any step by step tutorial on how to use > these tools from the command line? The tutorial here > http://tools.proteomecenter.org/wiki/index.php?title=TPP_Tutorial applies > for people using the GUI Petunia, however, Apache2 gives me a forbidden > access error when I try to access the TPP port., so I cannot follow the > instructions there. > > Regarding the method, the fragment ion intensity of the j spectrum of > peptide k corresponds to the intensity of the precursor that generated > spectrum j right? And this number can be found in .mgf spectrum files as > the second number in the PEPMASS field right? > PEPMASS=XXXX YYY > being YYY equal to the intensity. > > Thank you very much for your help in advance and keep up the good work! > > Best regards > > > Antonio > > -- 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.
