Code developments to improve the efficiency of automated MS/MS spectra interpretation

J Proteome Res. May-Jun 2002;1(3):211-5. doi: 10.1021/pr015514r.


We report the results of our work to facilitate protein identification using tandem mass spectra and protein sequence databases. We describe a parallel version of SEQUEST (SEQUEST-PVM) that is tolerant toward arithmetic exceptions. The changes we report effectively separate search processes on slave nodes from each other. Therefore, if one of the slave nodes drops out of the cluster due to an error, the rest of the cluster will carry the search process to the end. SEQUEST has been widely used for protein identifications. The modifications made to the code improve its stability and effectiveness in a high-throughput production environment. We evaluate the overhead associated with the parallelization of SEQUEST. A prior version of software to preprocess LC/MS/MS data attempted to differentiate the charge states of ions. Singly charged ions can be accurately identified, but the software was unable to reliably differentiate tandem mass spectra of +2 and +3 charge states. We have designed and implemented a computational approach to narrow charge states of precursor ions from nominal resolution ion-trap tandem mass spectra. The preprocessing code, 2to3, determines the charge state of the precursor ion using its mass-to-charge ratio (m/z) and fragment ions contained in the tandem mass spectrum. For each possible charge state the program calculates the expected fragment ions that account for precursor ion m/z values. If any one of the numbers is less than an empirically determined threshold value then the spectrum corresponding to that charge state is removed. If both numbers are higher than the threshold value then +2 and +3 copies of the spectrum are kept. We present the comparison of results from protein identification experiments with and without using 2 to 3. It is shown that by determining the charge state and eliminating poor quality spectra 2to3 decreases the number of spectral files to be searched without affecting the search results. The decrease reduces computer requirements and researcher efforts for analysis of the results.

MeSH terms

  • Crystallins / analysis*
  • Crystallins / genetics
  • Databases, Protein
  • Humans
  • Mass Spectrometry / methods*
  • Peptide Hydrolases / analysis*
  • Peptide Hydrolases / genetics
  • Proteasome Endopeptidase Complex*
  • Saccharomyces cerevisiae / metabolism
  • Software*
  • Time Factors


  • Crystallins
  • Peptide Hydrolases
  • Proteasome Endopeptidase Complex
  • ATP dependent 26S protease