Numerous biological processes are concurrently and coordinately active in every living cell. Each of them encompasses synthetic, catalytic and regulatory functions that are, almost always, carried out by proteins organized further into higher-order structures and networks. For decades, the structures and functions of selected proteins have been studied using biochemical and biophysical methods. However, the properties and behaviour of the proteome as an integrated system have largely remained elusive. Powerful mass-spectrometry-based technologies now provide unprecedented insights into the composition, structure, function and control of the proteome, shedding light on complex biological processes and phenotypes.
At a glance
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This paper demonstrates that complete proteomes of a model organism can be obtained and quantified in different biological states.
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This study aggregates data on diverse human proteomes from the authors and the research community and, like ref. 17, argues that a large part of the genome is accessible to mass-spectrometric detection.
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A pioneering investigation of the degree of correlation between the transcriptome and the proteome — a question that is still unresolved.
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- The BioPlex network: a systematic exploration of the human interactome. Cell 162, 425–440 (2015).
A large-scale investigation of proteins binding to tagged constructs to establish a human interactome.
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This paper describes the characterization of a human interactome using bait proteins that are expressed under endogenous control; its analysis in several quantitative dimensions revealed a preponderance of weak interactions.
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- Mass spectrometry of intact V-type ATPases reveals bound lipids and the effects of nucleotide binding. Science 334, 380–385 (2011).
An elegant demonstration of native mass spectrometry in structural studies of intact membrane complexes.
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- Direct identification of ligand-receptor interactions on living cells and tissues. Nature Biotechnol. 30, 997–1001 (2012). et al.
- Structural probing of a protein phosphatase 2A network by chemical cross-linking and mass spectrometry. Science 337, 1348–1352 (2012).
This study pioneered the use of chemical crosslinking to reveal the topology of an important phosphatase complex.
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- Probing the protein interaction network of Pseudomonas aeruginosa cells by chemical cross-linking mass spectrometry. Structure 23, 762–773 (2015). et al.
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- Tracking cancer drugs in living cells by thermal profiling of the proteome. Science 346, 1255784 (2014).
In this paper, isobaric chemical labelling was used to measure the proportion of proteins that bound to a drug as a function of temperature, on a proteome-wide scale.
- Global analysis of protein structural changes in complex proteomes. Nature Biotechnol. 32, 1036–1044 (2014). et al.
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- Systems genetics of metabolism: the use of the BXD murine reference panel for multiscalar integration of traits. Cell 150, 1287–1299 (2012). et al.
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- Systems proteomics of liver mitochondria function. Science 352, aad0189 (2016).
A demonstration of the combined use of proteomics and genetics to interrogate mitochondrial function.
- Proteogenomics connects somatic mutations to signalling in breast cancer. Nature 534, 55–62 (2016).
This analysis of breast cancer tissues revealed that proteomics is almost on a par with transcriptomics in terms of achievable depth of coverage of gene expression.
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- Plasma proteome profiling to assess human health and disease. Cell Syst. 2, 185–195 (2016). et al.
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- Quantitative variability of 342 plasma proteins in a human twin population. Mol. Syst. Biol. 11, 786 (2015). et al.
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- The Perseus computational platform for comprehensive analysis of (prote)omics data. Nature Methods 13, 731–740 (2016). et al.
- Skyline: an open source document editor for creating and analyzing targeted proteomics experiments. Bioinformatics 26, 966–968 (2010). et al.
- Targeted data extraction of the MS/MS spectra generated by data-independent acquisition: a new concept for consistent and accurate proteome analysis. Mol. Cell. Proteomics 11, O111.016717 (2012). et al.
- OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nature Biotechnol. 32, 219–223 (2014). et al.
- DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics. Nature Methods 12, 258–264 (2015). et al.
- Quantitative phosphoproteomics reveals widespread full phosphorylation site occupancy during mitosis. Sci. Signal. 3, ra3 (2010). et al.
- Proteoform: a single term describing protein complexity. Nature Methods 10, 186–187 (2013). , & The Consortium for Top Down Proteomics.
- Higher-energy C-trap dissociation for peptide modification analysis. Nature Methods 4, 709–712 (2007). et al.
- Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proc. Natl Acad. Sci. USA 101, 9528–9533 (2004). , , , &
- Orbitrap mass spectrometry. Anal. Chem. 85, 5288–5296 (2013). &
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- The nuclear proteome of a vertebrate. Curr. Biol. 25, 2663–2671 (2015). et al.
- Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ. Mol. Cell. Proteomics 13, 2513–2526 (2014). et al.
- Estimation of absolute protein quantities of unlabeled samples by selected reaction monitoring mass spectrometry. Mol. Cell. Proteomics 11, M111.013987 (2012). , , &