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Mass spectrometry–based proteomics turns quantitative

Abstract

The field of proteomics is built on technologies to analyze large numbers of proteins—ideally the entire proteome—in the same experiment. Mass spectrometry (MS) has been successfully used to characterize proteins in complex mixtures, but results so far have largely been qualitative. Two recently developed methodologies offer the opportunity to obtain quantitative proteomic information. Comparing the signals from the same peptide under different conditions yields a rough estimate of relative protein abundance between two proteomes. Alternatively, and more accurately, peptides are labeled with stable isotopes, introducing a predictable mass difference between peptides from two experimental conditions. Stable isotope labels can be incorporated 'post-harvest', by chemical approaches or in live cells through metabolic incorporation. This isotopic handle facilitates direct quantification from the mass spectra. Using these quantitative approaches, precise functional information as well as temporal changes in the proteome can be captured by MS.

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Figure 1: Extracting quantitative data from mass spectra.
Figure 2: PCP to determine the centrosomal proteome.
Figure 3: Stages of incorporation of stable isotope labels and their impact on quantitative accuracy.
Figure 4: Quantification of proteins with extensive sequence identity.
Figure 5: Identification of specific bait-prey interactions in affinity-precipitation experiments.
Figure 6: Temporal changes in the nucleolar proteome upon transcriptional inhibition.

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Acknowledgements

We gratefully acknowledge our colleagues at the Broad Institute of MIT and Harvard, the Center for Experimental BioInformatics at University of Southern Denmark and the Max Planck Institute for Biochemistry for useful discussions and support. We thank S.A. Carr, B. Küster, L.J. Foster and F. White for critical comments.

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Correspondence to Shao-En Ong or Matthias Mann.

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Ong, SE., Mann, M. Mass spectrometry–based proteomics turns quantitative. Nat Chem Biol 1, 252–262 (2005). https://doi.org/10.1038/nchembio736

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