Comprehensive Analysis of a Multidimensional Liquid Chromatography Mass Spectrometry Dataset Acquired on a Quadrupole Selecting, Quadrupole Collision Cell, Time-of-flight Mass Spectrometer II. NEW DEVELOPMENTS IN PROTEIN PROSPECTOR ALLOW FOR RELIABLE AND COMPREHENSIVE AUTOMATIC ANALYSIS OF LARGE DATASETS*□S
نویسندگان
چکیده
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 “SearchCompare.” The results from this study demonstrate that the high quality data produced on a quadrupole selecting, quadrupole collision cell, time-of-flight (QqTOF) geometry instrument allows for confident assignment of the vast majority of interpretable spectra by current search engines. Molecular & Cellular Proteomics 4:1194–1204, 2005.
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