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A Mixed Integer Linear Optimization Framework for the Identification and Quantification of Targeted Post-translational Modifications of Highly Modified Proteins Using Multiplexed Electron Transfer Dissociation Tandem Mass Spectrometry

In liquid chromatography tandem mass spectrometry (LC-MS/MS), when peptides of the same elemental composition elute at similar times, they co-fragment and produce ‘mixed’ tandem MS. This problem is unusually prevalent for hypermodified proteins, and this article presents the first approach for the interpretation of mixed tandem MS. The algorithm combined with a novel LC-MS/MS approach (Young N. et al., Mol. Cell. Proteom., 8(10), 2009) resulted in the high-throughput analysis of combinatorial histone codes, which was described by Michael Washburn as ‘an impressive development of an enabling technology’ (http://f1000.com/prime/1164285) and led to an NIH Research Service Award (Award Number F32GM093490; $69,687).