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X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry

Budin, Nicolas
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Published in Analytical chemistry. 2009, vol. 81, no. 18, p. 7604-7610
Abstract The diversity of experimental workflows involving LC-MS/MS and the extended range of mass spectrometers tend to produce extremely variable spectra. Variability reduces the accuracy of compound identification produced by commonly available software for a spectral library search. We introduce here a new algorithm that successfully matches MS/MS spectra generated by a range of instruments, acquired under different conditions. Our algorithm called X-Rank first sorts peak intensities of a spectrum and second establishes a correlation between two sorted spectra. X-Rank then computes the probability that a rank from an experimental spectrum matches a rank from a reference library spectrum. In a training step, characteristic parameter values are generated for a given data set. We compared the efficiency of the X-Rank algorithm with the dot-product algorithm implemented by MS Search from the National Institute of Standards and Technology (NIST) on two test sets produced with different instruments. Overall the X-Rank algorithm accurately discriminates correct from wrong matches and detects more correct substances than the MS Search. Furthermore, X-Rank could correctly identify and top rank eight chemical compounds in a commercially available test mix. This confirms the ability of the algorithm to perform both a straight single-platform identification and a cross-platform library search in comparison to other tools. It also opens the possibility for efficient general unknown screening (GUS) against large compound libraries.
Keywords *AlgorithmsChromatography, LiquidOrganic Chemicals/*analysisTandem Mass Spectrometry/*methods
PMID: 19702277
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Research group La protéomique au service de la clinique (270)
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MYLONAS, Roman et al. X-Rank: a robust algorithm for small molecule identification using tandem mass spectrometry. In: Analytical chemistry, 2009, vol. 81, n° 18, p. 7604-7610. doi: 10.1021/ac900954d https://archive-ouverte.unige.ch/unige:19995

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Deposited on : 2012-04-23

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