Ultra-sensitive, high throughput and quantitative proteomics measurements

We describe the broad basis and application of an approach for very high throughput, ultra-sensitive, and quantitative proteomic measurements based upon the use of ultra-high performance separations and mass spectrometry (MS). An overview of the accurate mass and time (AMT) tag approach and a description of the incorporated data analysis pipeline necessary for efficient proteomic studies are presented. Adjunct technologies, including stable-isotope labeling methodologies and improvements in the utilization of liquid chromatography (LC)-MS peak intensity information for quantitative purposes are also discussed. Related areas include the use of automated sample handling for improving analysis reproducibility, methods for using information from the separation for more confident peptide peak identification, and the utilization of smaller diameter capillary columns having lower volumetric flow rates to increase electrospray ionization efficiency and allow for more predictable and quantitative results. The developments are illustrated in the context of studies of complex biological systems.