Computational Mass Spectrometry–Based Proteomics

Proteomics is defined as the system-widecharacterization of all the proteins in anorganism in terms of their sequence,localization, abundance, post-translationalmodifications, and biomolecular interac-tions. Modern proteomic investigationsare increasingly quantitative and compre-hensive [1]. Examples include the relativequantification of over 4,000 proteins inhaploid and diploid yeast, which identifiedthe pheromone signaling pathway asenriched in differential abundance [2];determination of site- and time-specificdynamics of more than 6,000 phosphory-lation sites of HeLa cells stimulated withepidermal growth factor [3]; and charac-terization of 232 multiprotein complexesin Saccharomyces cerevisiae, which proposednew cellular roles for 344 proteins [4].Such investigations are now successfullyutilized in functional biology [5,6], geno-mics [7,8], and biomedical research [9].Challenges of proteomic studies stemfrom the complexity of the proteome andto its broad dynamic range. For example,the human genome contains around20,000 protein coding genes. Their trans-lation, combined with splicing or proteol-ysis, yields an estimated 50,000–500,000proteins, and over 10 million differentprotein forms can be derived by somaticDNA rearrangements and post-transla-tional modifications [10]. The abundanceof protein species in human plasma spansmore than 10 orders of magnitude [11].Unlike oligonucleotides, proteins cannotbe amplified, and therefore the objectivesof proteomics are achieved by sensitiveand scalable technologies identifying andquantifying proteins [12]. The overallmass spectrometry–based proteomic work-flow is summarized in Figure 1.