Mass Spectrometry Instrumentation in Proteomics


Mass spectrometry has evolved into a crucial technology for the field of proteomics, enabling the comprehensive study of proteins in biological systems. Innovative developments have yielded flexible and versatile mass spectrometric tools, including quadrupole time‐of‐flight, linear ion trap, Orbitrap and ion mobility instruments. Together they offer various and complementary capabilities in terms of ionisation, sensitivity, speed, resolution, mass accuracy, dynamic range and methods of fragmentation. Mass spectrometers can acquire qualitative and quantitative information on a large scale to study protein expression, protein interactions and modifications, in complexes, organelles, cells and tissues. The currently available technological platforms and approaches offer a wide selection for proteomics experiments from low to high throughput, from shotgun discovery to targeted validation. In terms of desired outcome, cost and time, choosing between available instrumentation and methodologies is key to find the best analytical strategy suiting a particular proteomics experiment.

Key Concepts:

  • The basic elements of a mass spectrometer are an ionisation source, mass analyser and detector.

  • Mass spectrometers central to proteomics‐based research are mostly ‘hybrid’ instruments combining the capabilities of different types of mass analysers.

  • Key properties of MS instruments for proteomics are sensitivity, speed, resolution, mass accuracy, dynamic range and methods of fragmentation.

  • Bottom‐up LC–MS‐based shotgun approaches have become the dominant form of analysing complex samples in various proteomics approaches

  • Mass spectrometry is a crucial tool in proteomics research, but proper experimental design and sample preparation remains key; garbage in–garbage out.

  • The choice for a particular instrument is dependant on the chosen workflow, ranging from low throughput to shotgun discovery and targeted validation strategies.

Keywords: matrix‐assisted laser desorption/ionisation (MALDI); electrospray ionisation (ESI); liquid chromatography tandem mass spectrometry (LC–MS/MS); orbitrap; triple quadrupole; quadrupole time‐of‐flight; ion trap; proteomics strategies; ion mobility

Figure 1.

The three main elements of a mass spectrometer and the most commonly used mass analyser components in proteomics.

Figure 2.

The current two most frequently used analytical strategies for expression proteomics: (a) gel‐based proteomics and (b) LC–MS‐driven (shotgun) proteomics.



Beck M, Schmidt A, Malmstroem J et al. (2011) The quantitative proteome of a human cell line. Molecular Systems Biology 7: 549.

Blagoev B, Kratchmarova I, Ong SE et al. (2003) A proteomics strategy to elucidate functional protein–protein interactions applied to EGF signaling. Nature Biotechnology 21: 315–318.

Eng JK, McGormack AL and Yates JR (1994) An attempt to correlate tandem mass spectra of peptides with amino acid sequences in protein databases. Journal of the American Chemical Society 5: 976–989.

Fenn JB, Mann M, Meng CK and Whitehouse CM (1989) Electrospray ionization for mass spectrometry of large biomolecules. Science 246: 64–71.

Geromanos SJ, Vissers JP, Silva JC et al. (2009) The detection, correlation, and comparison of peptide precursor and product ions from data independent LC–MS with data dependant LC–MS/MS. Proteomics 9: 1683–1695.

Gevaert K, Goethals M, Martens L et al. (2003) Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N‐terminal peptides. Nature Biotechnology 21: 566–569.

Gevaert K, Van Damme J, Goethals M et al. (2002) Chromatographic isolation of methionine‐containing peptides for gel‐free proteome analysis: identification of more than 800 Escherichia coli proteins. Molecular and Cellular Proteomics 1: 896–903.

Gygi SP, Rist B, Gerber SA et al. (1999) Quantitative analysis of complex protein mixtures using isotope‐coded affinity tags. Nature Biotechnology 17: 994–999.

Hu Q, Noll RJ, Li H et al. (2005) The Orbitrap: a new mass spectrometer. Journal of Mass Spectrometry 40: 430–443.

Kanu AB, Dwivedi P, Tam M, Matz L and Hill HH Jr (2008) Ion mobility‐mass spectrometry. Journal of Mass Spectrometry 43: 1–22.

Karas M and Hillenkamp F (1988) Laser desorption ionization of proteins with molecular mass exceeding 10,000 daltons. Analytical Chemistry 60: 2299–2301.

Link AJ, Eng J, Schieltz DM et al. (1999) Direct analysis of protein complexes using mass spectrometry. Nature Biotechnology 17: 676–682.

Makarov A (2000) Electrostatic axially harmonic orbital trapping: a high performance technique of mass analysis. Analytical Chemistry 72: 1156–1162.

Michalski A, Cox J and Mann M (2011) More than 100,000 detectable peptide species elute in single shotgun proteomics runs but the majority is inaccessible to data‐dependent LC‐MS/MS. Journal of Proteome Research 10: 1785–1793.

Ong SE, Blagoev B, Kratchmarova I et al. (2002) Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics. Molecular and Cellular Proteomics 1: 376–386.

Picotti P, Bodenmiller B, Mueller LN, Domon B and Aebersold R (2009) Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics. Cell 138: 795–806.

Rigaut G, Shevchenko A, Rutz B et al. (1999) A generic protein purification method for protein complex characterization and proteome exploration. Nature Biotechnology 17: 1030–1032.

Schmidt A, Claassen M and Aebersold R (2009) Directed mass spectrometry: towards hypothesis‐driven proteomics. Current Opinion in Chemical Biology 13: 510–517.

Silva JC, Denny R, Dorschel CA et al. (2005) Quantitative proteomic analysis by accurate mass retention time pairs. Analytical Chemistry 77: 2187–2200.

Silva JC, Gorenstein MV, Li GZ, Vissers JP and Geromanos SJ. (2006) Absolute quantification of proteins by LCMSE: a virtue of parallel MS acquisition. Molecular and Cellular Proteomics 5: 144–156.

Syka JE, Coon JJ, Schroeder MJ, Shabanowitz J and Hunt DF (2004) Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. Proceedings of the National Academy of Sciences of the USA 101: 9528–9533.

Tran JC, Zamdborg L, Ahlf DR et al. (2011) Mapping intact protein isoforms in discovery mode using top‐down proteomics. Nature doi: 10.1038/nature10575.

Zhao Y and Jensen ON (2009) Modification‐specific proteomics: strategies for characterization of post‐translational modifications using enrichment techniques. Proteomics 9: 4632–4641.

Zubarev RA, Kelleher NL and McLafferty FW (1998) Electron capture dissociation of multiply charged protein cations. A nonergodic process. Journal of the American Chemical Society 120: 3265–3266.

Further Reading

Domon B and Aebersold R (2010) Options and considerations when selecting a quantitative proteomics strategy. Nature Biotechnology 28: 710–721.

Gavin AC, Bösche M, Krause R et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415: 141–147.

Ho Y, Gruhler A, Heilbut A et al. (2002) Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature 415: 180–183.

Jensen ON (2000) Modification‐specific proteomics: strategies for systematic studies of post‐translationally modified proteins. In: Blackstock W and Mann M (eds) Proteomics: A Trends Guide, pp. 36–42. London, UK: Elsevier Science.

Pandey A and Mann M (2000) Proteomics to study genes and genomes. Nature 405: 837–846.

Silberring J and Ekman R (eds) (2002) Mass Spectrometry and Hyphenated Techniques in Neuropeptide Research. New York, NY: Wiley Interscience.

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Sprenger, Richard R, and Roepstorff, Peter(Apr 2012) Mass Spectrometry Instrumentation in Proteomics. In: eLS. John Wiley & Sons Ltd, Chichester. [doi: 10.1002/9780470015902.a0006194.pub2]