Abstract
Quantitative mass spectrometry (MS)-based proteomics continues to evolve through advances in sample preparation, chemical and biochemical reagents, instrumentation, and software. The breadth of proteomes and biological applications combined with unique experimental goals makes optimizing MS-based proteomics workflows a daunting task. Several MS-based instrument platforms are commercially available with LC-MS/MS being the most common for quantitative proteomics studies. Although the direction of LC-MS/MS instrumentation development is toward more user-friendly interfaces, there remain fundamental aspects of the technology that can be optimized for improving data quality. The intent of this chapter is to provide an introductory framework for understanding some of the more significant LC-MS/MS experimental conditions that can influence quantitative MS-based proteomics measurements, including electrospray ionization (ESI) bias and ion transmission efficiency. Because each commercial LC-MS/MS system is unique with regard to ESI source, transmission optics, ion isolation and trapping, ion fragmentation, and mass analysis, the use of design of experiments (DoE) is discussed as a potential approach for efficiently optimizing multiple inter-related factors.
Published Version
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