Hi Mike Thanks for your fast answer! I am sorry I couldn't get back to you earlier. I understand protein inference must be carried out prior to running StPeter. However, I still don't understand the Spectral Index (SI) definition from the original Griffin paper https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2805705/ . I would appreciate if you could shed some light.
The spectral index (SI) for a protein is the cumulative fragment ion > intensity for each spectrum of each peptide giving rise to a protein, which > can be represented using the equation from Griffin et al. where *i* is > the fragment ion intensity of peptide *k*, *j* is the *j*th spectral > count of *sc* total spectral counts for peptide *k* and *pn* is the > number of peptides identified for that protein <https://lh3.googleusercontent.com/-fxXf4Vlx0m4/WxJHqr8AafI/AAAAAAAANwQ/uaPdP9JDycE4hCuE0amGXvJv_hYcLpUVACLcBGAs/s1600/SI.png> I don't understand what's the fragment ion intensity of peptide *k. *Please correct me if I am wrong here. Peptide *k* is a precursor ion and it has a single intensity (measured in MS1). After going through MS1, it fragments generating multiple fragment ions. So according to my understanding, there's a single precursor ion intensity and several fragment ion intensities for peptide *k*. Therefore, I don't comprehend what's *i* in the equation above. I understand that *i* is summed over for all *sc *spectra identified as coming from peptide *k,* and then for all *pn* peptides coming from protein *K.* This total sum whould make protein's K SI. Thanks for your help and time!! :) Best Antonio onsdag den 23. maj 2018 kl. 01.05.15 UTC+2 skrev Michael Hoopmann: > > 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 > <http://www.google.com/url?q=http%3A%2F%2Ftools.proteomecenter.org%2Fwiki%2Findex.php%3Ftitle%3DTutorial%3AStPeter1&sa=D&sntz=1&usg=AFQjCNEogKp8slamhq2lozPqyziMcnFZyA> > > 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 [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.
