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 [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.
