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Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

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Abstract

Mass-spectrometry-based proteomics is continuing to make major contributions to the discovery of fundamental biological processes and, more recently, has also developed into an assay platform capable of measuring hundreds to thousands of proteins in any biological system. The field has progressed at an amazing rate over the past five years in terms of technology as well as the breadth and depth of applications in all areas of the life sciences. Some of the technical approaches that were at an experimental stage back then are considered the gold standard today, and the community is learning to come to grips with the volume and complexity of the data generated. The revolution in DNA/RNA sequencing technology extends the reach of proteomic research to practically any species, and the notion that mass spectrometry has the potential to eventually retire the western blot is no longer in the realm of science fiction. In this review, we focus on the major technical and conceptual developments since 2007 and illustrate these by important recent applications.

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Abbreviations

AP:

Affinity purification

DDA:

Data-dependent acquisition

ESI:

Electrospray ionization

HCD:

Higher-energy collision-induced dissociation

HDAC:

Histone deacetylase

HPLC:

High-pressure liquid chromatography

ICP:

Inductively coupled plasma

IMAC:

Immobilized metal affinity chromatography

iTRAQ:

Isobaric tags for absolute and relative quantification

LC:

Liquid chromatography

MRM:

Multiple reaction monitoring

MS:

Mass spectrometry

MS/MS:

Tandem mass spectrometry

PAI:

Protein abundance index

PrEST:

Protein epitope signature tag

PSAQ:

Protein standard absolute quantification

PSM:

Peptide-to-spectrum match

PTM:

Post-translational modification

QTOF:

Quadrupole time of flight

SILAC:

Stable isotope labeling with amino acids in cell culture

SRM:

Selected reaction monitoring

TMT:

Tandem mass tag

UPLC:

Ultra-high-pressure liquid chromatography

XIC:

Extracted ion chromatogram

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Acknowledgments

The authors wish to thank Frank Weissbrodt for help with creating the graphics. We apologize to all authors whose interesting work could not be cited owing to space or conceptual constraints.

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Authors and Affiliations

  1. Cellzome AG, Meyerhofstrasse 1, 69117, Heidelberg, Germany

    Marcus Bantscheff & Mikhail M. Savitski

  2. Chair of Proteomics and Bioanalytics, Technische Universität München, Emil Erlenmeyer Forum 5, 85354, Freising, Germany

    Simone Lemeer & Bernhard Kuster

  3. Center for Integrated Protein Science Munich (CIPSM), 80539, Munich, Germany

    Bernhard Kuster

Authors
  1. Marcus Bantscheff
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  2. Simone Lemeer
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  3. Mikhail M. Savitski
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  4. Bernhard Kuster
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Corresponding authors

Correspondence to Marcus Bantscheff or Bernhard Kuster.

Additional information

Published in the topical issue Quantitative Mass Spectrometry in Proteomics with guest editors Bernhard Kuster and Marcus Bantscheff.

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Bantscheff, M., Lemeer, S., Savitski, M.M. et al. Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present. Anal Bioanal Chem 404, 939–965 (2012). https://doi.org/10.1007/s00216-012-6203-4

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  • DOI: https://doi.org/10.1007/s00216-012-6203-4

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