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


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.

  • Faca VM
  • Hanash SM
  • Krasnoselsky AL
  • Pitteri SJ
  • Zhang Q
PubMed ID
Appears In
J Proteome Res, 2008, 7 (6)