Charge state determination of peptide tandem mass spectra using support vector machine (SVM)

IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society
An-Min ZouFang-Xiang Wu

Abstract

A single mass spectrometry experiment could produce hundreds of thousands of tandem mass spectra. Several search engines have been developed to interpret tandem mass spectra. All search engines need to determine the masses of peptide ions from their mass/charge ratios. Unfortunately, mass spectrometers do not detect the charges of ions. A current strategy is to search candidate peptides multiple times, once for each possible charge state (typically +2 or +3 ). However, this strategy not only wastes the search time, but also increases the risk of false positive peptide identification. This paper aims at discriminating doubly charged spectra from triply charged ones. Twenty-eight features are introduced to describe the discriminant characteristics of doubly charged and triply charged spectra. The support vector machine (SVM) technique is used to train the classifier on these 28 features. To verify the proposed method, computational experiments are conducted on two types of datasets: ISB dataset generated from the low-resolution ion-trap instrument and TOV dataset generated from the high-resolution quadrupole-time-of-flight instrument. For each type of dataset, the SVM-based classifiers are trained and tested on 20 randomly sample...Continue Reading

References

Feb 17, 2001·Journal of Mass Spectrometry : JMS
Feb 27, 2001·Mass Spectrometry Reviews·J Godovac-Zimmermann, L R Brown
Dec 18, 2001·Journal of Mass Spectrometry : JMS·T BrotinJ P Dutasta
Dec 18, 2001·Journal of Mass Spectrometry : JMS
Mar 21, 2003·Journal of Proteome Research·Rovshan G SadygovJohn R Yates
Oct 15, 2003·Rapid Communications in Mass Spectrometry : RCM·Robertson Craig, Ronald C Beavis
Jul 21, 2004·Bioinformatics·Marshall BernJohn R Yates
Sep 2, 2004·Nature Reviews. Molecular Cell Biology·Hanno Steen, Matthias Mann
Feb 2, 2008·IEEE Transactions on Neural Networks·A A GrafS Borer
Feb 6, 2008·Analytical Chemistry·Seungjin NaCheolju Lee
Jan 1, 1993·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·L Vincent
Jun 27, 2008·BMC Bioinformatics·Fang-Xiang WuGuy G Poirier
Feb 28, 2009·BMC Bioinformatics·An-Min ZouGuy G Poirier
Nov 1, 1994·Journal of the American Society for Mass Spectrometry·J K EngJ R Yates

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Citations

Aug 2, 2011·Proteomics·Wenjun LinWenjun Zhang
May 3, 2015·IEEE Transactions on Nanobioscience· Yan Yan Fang-Xiang Wu
Aug 5, 2010·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Konstantina S Nikita, Dimitrios I Fotiadis
Jun 20, 2012·IEEE Transactions on Information Technology in Biomedicine : a Publication of the IEEE Engineering in Medicine and Biology Society·Lei LiuHongzhi Zhang
Oct 24, 2017·Journal of Proteome Research·Sebastian DorlViktoria Dorfer

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