Comprehensive Analysis of a Multidimensional Liquid Chromatography Mass Spectrometry Dataset Acquired on a Quadrupole Selecting, Quadrupole Collision Cell, Time-of-flight Mass Spectrometer

Abstract

A thorough analysis of the protein interaction partners of the yeast GTPase Gsp1p was carried out by a multidimensional chromatography strategy of strong cation exchange fractionation of peptides followed by reverse phase LC-ESI-MSMS using a QSTAR instrument. This dataset was then analyzed using the latest developmental version of Protein Prospector. The Prospector search results were also compared with results from the search engine “Mascot” using a new results comparison program within Prospector named …