Analysis of the stochastic variation in LTQ single scan mass spectra.

Rapid Communications in Mass Spectrometry : RCM
Qunhua LiMurray Hackett

Abstract

A better understanding of the scan-to-scan signal intensity variation can lead to more sophisticated algorithms for database searching and de novo peptide sequencing using single scan mass spectra. In this study, we systematically studied the variation in relative intensity of m/z values in the single scan product ion mass spectra (MS2) derived from five representative precursor ions (MS1) collected using an LTQ linear ion trap under constant flow direct infusion conditions with peptide concentrations held constant. We applied a matching algorithm based on a pair hidden Markov model to align the peaks from each scan belonging to the same m/z value prior to assessing the signal intensity variation. The most significant single contributor to scan-to-scan signal intensity variation for high abundance ions was centroider error. Our study also showed that the variation in signal intensity is higher than what would be expected if the ion statistics derived from the dual geometry electron multiplier detector followed a Poisson distribution.

References

Jun 12, 2002·Journal of the American Society for Mass Spectrometry·Jae C SchwartzJohn E P Syka
Feb 15, 2003·Analytical Chemistry·Moshe HavilioZeev Smilansky
Sep 25, 2004·Mass Spectrometry Reviews·Donald J DouglasDunmin Mao
Feb 16, 2006·Analytical Chemistry·Adele R BlacklerChristine C Wu
Nov 1, 1994·Journal of the American Society for Mass Spectrometry·J K EngJ R Yates

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Citations

Jul 4, 2008·Biology Direct·Gelio AlvesYi-Kuo Yu
Dec 1, 2006·Journal of Mass Spectrometry : JMS
Jul 20, 2007·Proteomics·Qiangwei XiaMurray Hackett

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