Reliable Automated Protein Expression Measurements Using a Hybrid Quadrupole Linear Ion Trap Mass Spectrometer and Cleavable ICAT ® Reagents

Isotope-coded affinity tags 1 have been identified as a method for global measurement of differential protein expression. Use of ICAT ® reagents for high-throughput sample analysis requires reliable automated expression measurement and protein identification requiring minimal or no manual review. Instrument resolution contributes to the reliability of both expression measurement and protein identification. Ion trap instruments are outperformed by time-of-flight instruments in providing fast highresolution scans. In this work, a higher resolution scan is used on a hybrid quadrupole linear ion trap instrument to obtain better resolution data for precursor ions. The resulting data quality enables reliable charge-state determination and accurate mass calculation. The benefits of this data quality for automation of both quantitation and identification are presented.