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Review
. 2013 Dec;12(12):3444-52.
doi: 10.1074/mcp.O113.034181. Epub 2013 Nov 1.

Status of large-scale analysis of post-translational modifications by mass spectrometry

Jesper V Olsen  1 , Matthias Mann
Affiliations
Review

Status of large-scale analysis of post-translational modifications by mass spectrometry

Jesper V Olsen et al. Mol Cell Proteomics. 2013 Dec.

Abstract

Cellular function can be controlled through the gene expression program, but often protein post-translational modifications (PTMs) provide a more precise and elegant mechanism. Key functional roles of specific modification events--for instance, during the cell cycle--have been known for decades, but only in the past 10 years has mass-spectrometry-(MS)-based proteomics begun to reveal the true extent of the PTM universe. In this overview for the special PTM issue of Molecular and Cellular Proteomics, we take stock of where MS-based proteomics stands in the large-scale analysis of protein modifications. For many PTMs, including phosphorylation, ubiquitination, glycosylation, and acetylation, tens of thousands of sites can now be confidently identified and localized in the sequence of the protein. The quantification of PTM levels between different cellular states is likewise established, with label-free methods showing particular promise. It is also becoming possible to determine the absolute occupancy or stoichiometry of PTM sites on a large scale. Powerful software for the bioinformatic analysis of thousands of PTM sites has been developed. However, a complete inventory of sites has not been established for any PTM, and this situation will persist into the foreseeable future. Furthermore, although PTM coverage by MS-based methods is impressive, it still needs to be improved, especially in tissues and in clinically relevant systems. The central challenge for the field is to develop streamlined methods for determining biological functions for the myriad of modifications now known to exist.

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Figures

Fig. 1.
Fig. 1.
Overview of PTM analysis and challenges. The principal steps in the workflow for PTM analysis are depicted on the left. On the right, the main types of modifications, alternative proteases, PTM enrichment methods, and quantification types are symbolized. For each step, some of the main challenges are listed.
Fig. 2.
Fig. 2.
A vision for PTM analysis. Proteomics of PTMs would greatly benefit from a more complete repertoire of enrichment tools and reagents. With further development of mass spectrometric capabilities, however, it would be desirable to detect modified peptides without specific enrichment. This would make it possible to study many PTMs simultaneously and estimate their stoichiometry directly. Robust PTM analysis with high throughput could deliver patient classification and unique information on treatment efficacy. Finally, very deep and quantitatively accurate PTM analysis will provide a crucial basis for systems biology.
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References

    1. Clamp M., Fry B., Kamal M., Xie X., Cuff J., Lin M. F., Kellis M., Lindblad-Toh K., Lander E. S. (2007) Distinguishing protein-coding and noncoding genes in the human genome. Proc. Natl. Acad. Sci. U.S.A. 104, 19428–19433 - PMC - PubMed
    1. Tran J. C., Zamdborg L., Ahlf D. R., Lee J. E., Catherman A. D., Durbin K. R., Tipton J. D., Vellaichamy A., Kellie J. F., Li M., Wu C., Sweet S. M., Early B. P., Siuti N., LeDuc R. D., Compton P. D., Thomas P. M., Kelleher N. L. (2011) Mapping intact protein isoforms in discovery mode using top-down proteomics. Nature 480, 254–258 - PMC - PubMed
    1. Stenflo J., Fernlund P., Egan W., Roepstorff P. (1974) Vitamin K dependent modifications of glutamic acid residues in prothrombin. Proc. Natl. Acad. Sci. U.S.A. 71, 2730–2733 - PMC - PubMed
    1. Ficarro S. B., McCleland M. L., Stukenberg P. T., Burke D. J., Ross M. M., Shabanowitz J., Hunt D. F., White F. M. (2002) Phosphoproteome analysis by mass spectrometry and its application to Saccharomyces cerevisiae. Nat. Biotechnol. 20, 301–305 - PubMed
    1. Beausoleil S. A., Jedrychowski M., Schwartz D., Elias J. E., Villen J., Li J., Cohn M. A., Cantley L. C., Gygi S. P. (2004) Large-scale characterization of HeLa cell nuclear phosphoproteins. Proc. Natl. Acad. Sci. U.S.A. 101, 12130–12135 - PMC - PubMed

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