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J Proteome Res. 2008 Jun;7(6):2546-52. doi: 10.1021/pr7007219. Epub 2008 Apr 18.

Isoform analysis of LC-MS/MS data from multidimensional fractionation of the serum proteome.

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  • 1Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.


We developed a visualization approach for the identification of protein isoforms, precursor/mature protein combinations, and fragments from LC-MS/MS analysis of multidimensional fractionation of serum and plasma proteins. We also describe a pattern recognition algorithm to automatically detect and flag potentially heterogeneous species of proteins in proteomic experiments that involve extensive fractionation and result in a large number of identified serum or plasma proteins in an experiment. Examples are given of proteins with known isoforms that validate our approach and present a subset of precursor/mature protein pairs that were detected with this approach. Potential applications include identification of differentially expressed isoforms in disease states.

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