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

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

Research output: Contribution to journalArticle

15 Citations (Scopus)

Abstract

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
Volume9
Issue number8
DOIs
StatePublished - Aug 6 2010

Fingerprint

Mass spectrometers
Power spectrum
Spectrum analysis
Labeling
Spectrum Analysis
Software
Peptides
Water
Experiments
Complex Mixtures
Software packages
Isotopes
Computer program listings
Automation
Data acquisition
Throughput
Ions
Noise
Chemical analysis
Kidney

Keywords

  • 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

  • Biochemistry
  • Chemistry(all)

Cite this

Using power spectrum analysis to evaluate 18o-water labeling data acquired from low resolution mass spectrometers. / Sadygov, Rovshan; Zhao, Yingxin; Haidacher, Sigmund J.; Starkey, Jonathan; Tilton, Ronald; Denner, Larry.

In: Journal of Proteome Research, Vol. 9, No. 8, 06.08.2010, p. 4306-4312.

Research output: Contribution to journalArticle

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