Faster mass spectrometry-based protein inference: junction trees are more efficient than sampling and marginalization by enumeration.

IEEE/ACM Transactions on Computational Biology and Bioinformatics
Oliver Serang, William Stafford Noble

Abstract

The problem of identifying the proteins in a complex mixture using tandem mass spectrometry can be framed as an inference problem on a graph that connects peptides to proteins. Several existing protein identification methods make use of statistical inference methods for graphical models, including expectation maximization, Markov chain Monte Carlo, and full marginalization coupled with approximation heuristics. We show that, for this problem, the majority of the cost of inference usually comes from a few highly connected subgraphs. Furthermore, we evaluate three different statistical inference methods using a common graphical model, and we demonstrate that junction tree inference substantially improves rates of convergence compared to existing methods. The python code used for this paper is available at http://noble.gs.washington.edu/proj/fido.

References

Nov 25, 2003·Analytical Chemistry·Alexey I NesvizhskiiRuedi Aebersold
May 10, 2006·BMC Bioinformatics·Norbert DojerJerzy Tiuryn
Dec 14, 2006·Molecular & Cellular Proteomics : MCP·Thomas S PriceTilo Grosser
Sep 29, 2007·Nature Methods·Alexey I NesvizhskiiRuedi Aebersold
Oct 24, 2007·Nature Methods·Lukas KällMichael J MacCoss
May 29, 2008·Journal of Proteome Research·Christopher Y ParkWilliam S Noble
Aug 18, 2010·Journal of Proteome Research·Oliver SerangWilliam Stafford Noble
Jul 27, 2012·Statistics and Its Interface·Oliver Serang, William Noble
Nov 1, 1994·Journal of the American Society for Mass Spectrometry·J K EngJ R Yates

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Citations

Aug 4, 2009·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Yong Fuga LiHaixu Tang
Aug 11, 2015·Journal of Proteome Research·Oliver Serang, Lukas Käll
Dec 11, 2013·Proteomics·Pieter KelchtermansLennart Martens
Jul 15, 2015·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Oliver Serang
Aug 24, 2016·FEMS Microbiology Ecology·Katharina M KeiblingerKatharina Riedel
Nov 28, 2012·BMC Bioinformatics·Yong Fuga Li, Predrag Radivojac

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