Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets

Proteomics. 2010 Jul;10(14):2712-8. doi: 10.1002/pmic.200900473.


In a typical shotgun proteomics experiment, a significant number of high-quality MS/MS spectra remain "unassigned." The main focus of this work is to improve our understanding of various sources of unassigned high-quality spectra. To achieve this, we designed an iterative computational approach for more efficient interrogation of MS/MS data. The method involves multiple stages of database searching with different search parameters, spectral library searching, blind searching for modified peptides, and genomic database searching. The method is applied to a large publicly available shotgun proteomic data set.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Cell Line, Tumor
  • Computational Biology / methods*
  • Databases, Protein*
  • Humans
  • Mass Spectrometry / standards*
  • Peptides / analysis
  • Peptides / chemistry
  • Proteomics / methods*


  • Peptides