Quantifying proteomes and their post-translational modifications by stable isotope label-based mass spectrometry - PubMed (original) (raw)

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Quantifying proteomes and their post-translational modifications by stable isotope label-based mass spectrometry

Anna E Merrill et al. Curr Opin Chem Biol. 2013 Oct.

Abstract

Stable isotope labeling coupled with mass spectrometry has revolutionized the scope and impact of protein expression studies. Label incorporation can occur metabolically or chemically, and each method bears specific strengths and weaknesses. Quantitative proteomics confidently identifies specific interactions between proteins and other biological species, such as nucleic acids and metabolites. Extending label-based methods to phosphorylation-modified forms of proteins enables the construction of signaling networks and their temporal responses to stimuli. The integration of multiple data types offers systems-level insight on coordinated biological processes. Finally, the development of methods applicable to tissue quantification suggests the emerging role of label-based, quantitative mass spectrometry in translational science.

Copyright © 2013 Elsevier Ltd. All rights reserved.

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Figures

Figure 1

Figure 1

Stable isotope incorporation strategies for relative proteome quantification by mass spectrometry. Two predominant methods for label-based quantification are isobaric tagging and SILAC. Isobaric tags label the N-termini and lysine residues of peptides resulting from protein extraction and proteolytic digestion. All labels in a set bear the same intact mass, meaning that peptides from differentially-labeled samples will appear at the same precursor m/z. Only upon fragmentation are the reporter ions released to permit quantification. Alternatively, in metabolic approaches such as SILAC, heavy isotope-labeled amino acids are incorporated during protein synthesis. Samples can be mixed together prior to cell lysis so that all downstream processing steps are performed on all samples simultaneously. SILAC-labeled peptides are quantified from full MS scans across the elution profile.

Figure 2

Figure 2

Cell type-specific activation of kinase families. A phosphoproteomic comparison of human embryonic stem (ES) cells with human fibroblast (newborn foreskin fibroblast, NFF) cells revealed a pool of phosphorylation sites that was differentially regulated between the cell lines. These phosphorylation sites serve as kinase substrates whose cognate protein kinases can be predicted computationally. The activation of entire families of kinases can depend on cell type. For example, CMGC kinases are highly-activated in ES cells, while CAMK and AGC kinase substrates are enriched in NFF cells.

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