Automated interpretation of mass spectra of complex mixtures by matching of isotope peak distributions

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Abstract
Mass spectrometry is now firmly established as a powerful technique for the identification and characterization of proteins when used in conjunction with sequence databases. Various approaches involving stable‐isotope labeling have been developed for quantitative comparisons between paired samples in proteomic expression analysis by mass spectrometry. However, interpretation of such mass spectra is far from being fully automated, mainly due to the difficulty of analyzing complex patterns resulting from the overlap of multiple peaks arising from the assortment of natural isotopes. In order to facilitate the interpretation of a complex mass spectrum of such a mixture, such as an MS spectrum of a stable‐isotope‐enriched ion species, we report on the development of a software application, ‘Matching’ (web accessible), that enables the automatic matching of theoretical isotope envelopes to multiple ion peaks in a raw spectrum. It is particularly useful for resolving the relative abundances of narrow‐split paired peaks caused by enrichment with a stable isotope, such as 18O, 13C, 2H, or 15N. Copyright © 2004 John Wiley & Sons, Ltd.
Funding Information
  • Center for Genetic Engineering and Biotechnology of Havana
  • Special Coordination Fund for the Promotion of Science and Technology
  • Ministry of Education, Culture, Sports, Science and Technology of Japan
  • Ministry of Health, Labour and Welfare of Japan