PNNL

Abstract

We report a new tandem mass spectrometric approach for the improved identification of polypeptides from mixtures (e.g. using genomic databases). The approach involves the dissociation of several species simultaneously in a single experiment and provides both increased speed and sensitivity. The data analysis makes use of the known fragmentation pathways for polypeptides and highly accurate mass-measurements for both the set of parent polypeptides and their fragments. The accurate mass information makes it possible to attribute most fragments to a specific parent species. We provide an initial demonstration of this multiplexed tandem MS approach using an FTICR mass spectrometer with a mixture of seven polypeptides dissociated using infrared irradiation from a CO2 laser. The peptides are successfully identified from the largest genomic data base yet available (C. elegans) which is equivalent in complexity to that for a specific type of differentiated cell in the human genome. Additionally, since only a few enzymatic fragments are necessary to identify unambiguously a protein from an appropriate database, it is anticipated that the multiplexed MSIMS method will allow the more rapid identification of proteins after online separation of mixtures of their enzymatically produced polypeptides.