Multidimensional proteomics for cell biology

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Abstract

The proteome is a dynamic system in which each protein has interconnected properties — dimensions — that together contribute to the phenotype of a cell. Measuring these properties has proved challenging owing to their diversity and dynamic nature. Advances in mass spectrometry-based proteomics now enable the measurement of multiple properties for thousands of proteins, including their abundance, isoform expression, turnover rate, subcellular localization, post-translational modifications and interactions. Complementing these experimental developments are new data analysis, integration and visualization tools as well as data-sharing resources. Together, these advances in the multidimensional analysis of the proteome are transforming our understanding of various cellular and physiological processes.

Key Points

  • The proteome is complex as a result of the interconnected, dynamic properties of proteins, which include abundance, isoform expression, subcellular localization, interactions, turnover rate and post-translational modifications, among others.

  • Only through analysing the variation in many of these properties can a full understanding of crucial biological regulatory mechanisms be achieved. Such analyses have so far been restricted by technical limitations and cost.

  • Data analysis and data sharing are crucial to maximise the effect of mass spectrometry-based proteomic analyses, as is making such data available to cell biologists in free to access, web-based and graphically rich formats.

  • Our understanding of cellular processes will be enhanced by predicting the interdependence of protein properties. For example, knowing that a protein with a certain modification, if localized in the cytosol, will be degraded. Future innovations will enable more comprehensive measurement of a wider range of protein properties.

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Figure 1: Multidimensional proteome analysis of cells and tissues.
Figure 2: Methods for protein turnover analysis.
Figure 3: Approaches for the analysis of protein interactions.

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Acknowledgements

A.I.L. is a Wellcome Trust Principal Research Fellow and M.L. is a Royal Society of Edinburgh Scottish Government Personal Research Fellow.

Author information

Correspondence to Mark Larance or Angus I. Lamond.

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Competing interests

The authors declare no competing financial interests.

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Supplementary information

Supplementary information S1 (box)

Stable isotope labelling techniques for proteome analysis. (PDF 285 kb)

Supplementary information S2 (figure)

Web-based data sharing of multi-dimensional proteomics datasets. (PDF 193 kb)

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FURTHER INFORMATION

EPD

Chorus

Cytoscape

GPMDB

Human Protein Atlas

Human Proteome Map

MaxQB

MOPED

PaxDB

Phosida

ProteomeXchange Consortium

ProteomicsDB

Glossary

Label-free quantification

Protein quantification without exogenous stable isotope labelling, using data derived either from the number of tandem mass spectrometry (MS/MS) spectra, the number of peptides identified and/or the intensity of each peptide observed.

Data-independent acquisition

(DIA). Otherwise known as 'SWATH'; a technique to acquire mass spectrometry data in predefined m/z windows across an entire liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis for consistent quantification across many samples.

Differential centrifugation

Separation of particles on the basis of size and density using several steps of pelleting by centrifugation at increasing g force.

Equilibrium gradient centrifugation

Separation of particles along a gradient on the basis of their density, using a large centrifugal force until the particles reach equilibrium at the point in the gradient of the same density as their own.

Non-equilibrium gradient centrifugation

Similar to equilibrium gradient centrifugation but the application of centrifugal force is stopped before the particles reach equilibrium.

Protein correlation profiling

(PCP). The clustering of protein profiles to predict components in a particular protein complex or cellular localization.

Endoplasmic reticulum-associated protein degradation

(ERAD). A proteasome-dependent protein degradation pathway for the degradation of endoplasmic reticulum proteins.

Click reactions

Cycloaddition reactions involving chemical groups that are not found in nature, typically azide or alkyne groups. Their incorporation into cellular proteins enables labelling with biotin or fluorescent tags via the cycloaddition reaction.

Selected reaction monitoring

(SRM). A mass spectrometry method to focus the instrument on a specific fragment ion derived from a peptide ion of interest. Methods can be generated to analyse many fragment ions from the same peptide and many peptide ion precursors in a single liquid chromatography tandem mass spectrometry (LC-MS/MS) analysis.

Third-stage tandem mass spectrum

(MS3). A spectrum acquired after further fragmentation of isolated peptide fragments from a tandem mass spectrometry analysis.

Laboratory information management system

(LIMS). A database to store experimental data and associated metadata, typically including details of experimental design.

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Larance, M., Lamond, A. Multidimensional proteomics for cell biology. Nat Rev Mol Cell Biol 16, 269–280 (2015) doi:10.1038/nrm3970

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