Systems Proteomics for Translational Network Medicine

Proteomics encompasses diverse methods by which to study proteins, their abundance, structure, posttranslational modifications, and physical or functional interacting partners to map the proteome, the protein complement of a genome. Although such methods can be applied to individual proteins, proteomics facilitates large-scale analysis of complete proteomes or targeted subproteomes (Table 1). Moreover, proteomics enables comparisons between distinct conditions/states, from defined biological sources, across discrete timelines. In general, a proteomic cartography pipeline involves sample acquisition, followed by protein isolation, separation, resolution, and identification (Figure). Along this continuum, each successive module harbors a multistep process, whereby proteomic methodologies can be implemented.Figure. Network systems proteomic pipeline. Strategy extending proteomic profiling from mapping and quantification of protein identities to ontological categorization, pathway analysis and network generation for inclusive systems interpretation.View this table:Table 1. Systems Proteomics LexiconOnce proteins are isolated from the source of interest, 2 major separation strategies have evolved to address proteome complexity.1,2 Traditional gel-based approaches, particularly 2-dimensional gel electrophoresis involving isoelectric focusing followed orthogonally by sodium dodecyl sulfate - polyacrylamide gel electrophoresis, were the earliest methods adopted for protein separation and resolution, comparative assessment of relative abundance, and initial reduction of protein complexity before mass spectrometry (MS). Although 2-dimensional gel electrophoresis remains common, the advent of quantitative MS techniques has led to increased application of various gel-based and gel-free alternatives, whereby protein or peptide complexity is addressed by separation and resolution before or in conjunction with MS, whereas quantification is subsequently measured from MS precursor or fragment ion spectra. Choice of separation strategy is influenced by study objectives and resources, often guided by advantages and limitations to each approach. Quantitative MS methods tend to be less time- and labor-intensive while offering greater potential throughput and data acquisition, yet in instances where 2-dimensional gel electrophoresis approaches are applied in parallel, use of …