Quantitation With Virtual Expert Mass Spectrometrist

Quantitative analysis of proteins and peptides by mass spectrometry has been greatly advanced by the development of proteomic technologies within recent years. Particularly, labeling of peptides and proteins with stable isotopes such as ² H, ¹⁵ N, and ¹³ C facilitated the unbiased comparison of protein amounts in distinct samples in a single mass spectrometric experiment. These methods can be applied to detect quantitative changes in protein amounts and posttranslational modifications such as phosphorylation. Quantitation of mass spectra requires accurate and efficient bioinformatics tools, which can match corresponding peptides, determine peak intensities, and calculate relative amounts. In this chapter, we describe the use of virtual expert mass spectrometrist for the quantitation of mass spectra from samples with peptides and proteins encoded with stable isotopes.