Abstract
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.
Highlights
Challenges of proteomic studies stem from the complexity of the proteome and to its broad dynamic range
Shotgun liquid chromatography coupled with tandem mass spectrometry (LC-mass spectrum (MS)/MS; overview in Figure 3) is most frequently used
Mass spectrometry is better amenable to characterizing peptides; LC-MS/ MS starts by enzymatically digesting proteins into a peptide mixture
Summary
Proteomics is defined as the system-wide characterization of all the proteins in an organism in terms of their sequence, localization, abundance, post-translational modifications, and biomolecular interactions. Examples include the relative quantification of over 4,000 proteins in haploid and diploid yeast, which identified the pheromone signaling pathway as enriched in differential abundance [2]; determination of site- and time-specific dynamics of more than 6,000 phosphorylation sites of HeLa cells stimulated with epidermal growth factor [3]; and characterization of 232 multiprotein complexes in Saccharomyces cerevisiae, which proposed new cellular roles for 344 proteins [4] Such investigations are successfully utilized in functional biology [5,6], genomics [7,8], and biomedical research [9].
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