Using power spectrum analysis to evaluate 18o-water labeling data acquired from low resolution mass spectrometers

Rovshan G. Sadygov, Yingxin Zhao, Sigmund J. Haidacher, Jonathan M. Starkey, Ronald G. Tilton, Larry Denner

Research output: Contribution to journalArticlepeer-review

17 Scopus citations


We describe a method for ratio estimations in 18O-water labeling experiments acquired from low resolution isotopically resolved data. The method is implemented in a software package specifically designed for use in experiments making use of zoom-scan mode data acquisition. Zoom-scan mode data allow commonly used ion trap mass spectrometers to attain isotopic resolution, which makes them amenable to use in labeling schemes such as 18O-water labeling, but algorithms and software developed for high resolution instruments may not be appropriate for the lower resolution data acquired in zoom-scan mode. The use of power spectrum analysis is proposed as a general approach that may be uniquely suited to these data types. The software implementation uses a power spectrum to remove high-frequency noise and band-filter contributions from coeluting species of differing charge states. From the elemental composition of a peptide sequence, we generate theoretical isotope envelopes of heavy-light peptide pairs in five different ratios; these theoretical envelopes are correlated with the filtered experimental zoom scans. To automate peptide quantification in high-throughput experiments, we have implemented our approach in a computer program, MassXplorer. We demonstrate the application of MassXplorer to two model mixtures of known proteins and to a complex mixture of mouse kidney cortical extract. Comparison with another algorithm for ratio estimations demonstrates the increased precision and automation of MassXplorer.

Original languageEnglish (US)
Pages (from-to)4306-4312
Number of pages7
JournalJournal of Proteome Research
Issue number8
StatePublished - Aug 6 2010


  • O-water labeling
  • bioinformatics
  • correlation of filtered spectrum with a theoretical isotope distribution
  • low-pass and band filtering
  • mass spectrometry
  • power spectral analysis
  • quantification
  • ratio estimation

ASJC Scopus subject areas

  • General Chemistry
  • Biochemistry


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