Proteomics Moves From Expression to Turnover

Update and Future Perspective

Mary K Doherty; Phillip D Whitfield

Expert Rev Proteomics. 2011;8(3):325-334.

Expert Commentary

Proteomics is about more than identifying and quantifying proteins. To truly integrate the discipline with other 'omic' technologies, it is important that methods are found to address the dynamics of the system and how the cell or organism moves from one state to another. This is important for understanding areas as diverse as growth, aging, response to environmental stress and a range of pathologies. A great deal of research has focused on whole-body turnover, which, while extremely valuable, does not address the nuances of the individual cell's ability to adapt to changing circumstances. The landscape has changed considerably over the past 5 years, with new and innovative methods to directly measure individual protein synthesis, degradation and turnover on a global scale. Researchers are also moving from studies solely in cell culture to applied studies in animals and plants. Although the majority of studies still rely on the use of stable isotope-labeled tracers and MS, complementary non-mass spectrometric methods are also emerging.^[59]

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Table 1. Summary of approaches used to determine protein turnover.
Method	Application	Label	System	Ref.
Dynamic SILAC	Determination of protein degradation rates by MS	Amino acid	Yeast Chicken Human cell line	[31,34,42]
PC/QMS	Pulse/chase approach to determine ribosome assembly dynamics	Amino acid	Escherichia coli	[45]
Combined SILAC/iTRAQ	Protein dynamics under non-steady-state conditions	Amino acid	Streptomyces coelicor	[46]
Pulsed SILAC	Measures the relative rate of protein synthesis under different experimental conditions	Amino acid	HeLa cells Yeast	[43]
Ratio methods	Profiling protein turnover under different experimental conditions	Ammonium sulfate	Mycobacterium smegmatis	[47]
SINEW	Whole animal protein turnover	Water	Mouse	[48]
Plant dynamics	Measuring proteome turnover in plants	Water	Arabidopsis	[50]
TAP tagging	Non-mass spectrometric method to profile protein stability		Yeast	[51]
Global Protein Stability	Fluorescent assay using microarrays		Human	[53]

iTRAQ: Isobaric tag for relative and absolute quantitation; MS: Mass spectrometry; PC/QMS: Pulse-chase MS approach; SILAC: Stable isotope labeling of amino acids in cell culture; SINEW: Stable isotope labeling of nonessential amino acids with heavy water; TAP: Tandem affinity purification.

Table 2. Quantification software programs for mass spectrometry.
Name of program	Application	Availability	Ref.
MASCOT	Integral to the MASCOT search engine Generic to all instrument vendors Licensed software	Commercial	[101]
MaxQuant	Primarily for Thermo FT and Orbitrap instruments. Has a combined search and quantification package, which allows the user to upload protein databases. Incorporates GO analysis	Freeware	[102]
MSQuant	Suitable for Applied Biosystems, Thermo and Waters instruments. Supports amino acid and 15N labeling	Freeware	[103]
RELEX	Specific to Thermo instruments	Freeware	[104]
XPRESS	Available as part of the TransProteome Pipeline package. Generic to all instrument vendors	Freeware	[105]

GO: Gene ontology.

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