PNNL

Abstract

Significant technological advances in quantitative proteomics approaches and instrumentation, as well as in related (bio)informatics data analysis have been achieved over the past decade. The so-called “bottom-up” proteomics approach that accounts for nearly all proteomics measurements combines high efficiency separations with MS to characterize highly complex peptide mixtures. Currently the most powerful approach in terms of overall separation power and sensitivity involves gradient elution reversed phase liquid chromatography (LC) coupled to high mass measurement accuracy MS, particularly Fourier transform-ion cyclotron resonance mass spectrometry (FTICR MS). These LC-MS platforms allow large number of peptides to be distinguished. While the dynamic range achievable in any mass spectrum constrains the number of detectable species, the use of separations and their effective integration with MS greatly increases the overall proteomics analysis dynamic range, but at the cost of lower throughput. In this article, we highlight aspects of separations, electrospray ionization (ESI) phenomena, and MS developments that are interrelated and important for making more sensitive and higher throughput quantitative proteomics measurements.