Note to users. If you're seeing this message, it means that your browser cannot find this page's style/presentation instructions -- or possibly that you are using a browser that does not support current Web standards. Find out more about why this message is appearing, and what you can do to make your experience of our site the best it can be.


Science 14 April 2006:
Vol. 312. no. 5771, pp. 212 - 217
DOI: 10.1126/science.1124619

Review

Mass Spectrometry and Protein Analysis

Bruno Domon1 and Ruedi Aebersold1,2,3

Mass spectrometry is a central analytical technique for protein research and for the study of biomolecules in general. Driven by the need to identify, characterize, and quantify proteins at ever increasing sensitivity and in ever more complex samples, a wide range of new mass spectrometry–based analytical platforms and experimental strategies have emerged. Here we review recent advances in mass spectrometry instrumentation in the context of current and emerging research strategies in protein science.

1 Institute of Molecular Systems Biology, ETH Zurich, CH-8093 Zurich, Switzerland.
2 Faculty of Sciences, University of Zurich, CH-8006 Zurich, Switzerland.
3 Institute for Molecular Systems Biology, Seattle, WA 98103, USA.

Read the Full Text


THIS ARTICLE HAS BEEN CITED BY OTHER ARTICLES:
Protein quantification across hundreds of experimental conditions.
Z. Khan, J. S. Bloom, B. A. Garcia, M. Singh, and L. Kruglyak (2009)
PNAS 106, 15544-15548
   Abstract »    Full Text »    PDF »
Identification and Quantification of Glycoproteins Using Ion-Pairing Normal-phase Liquid Chromatography and Mass Spectrometry.
W. Ding, H. Nothaft, C. M. Szymanski, and J. Kelly (2009)
Mol. Cell. Proteomics 8, 2170-2185
   Abstract »    Full Text »    PDF »
Unique Ion Signature Mass Spectrometry, a Deterministic Method to Assign Peptide Identity.
J. Sherman, M. J. McKay, K. Ashman, and M. P. Molloy (2009)
Mol. Cell. Proteomics 8, 2051-2062
   Abstract »    Full Text »    PDF »
Characterization of the rapamycin-sensitive phosphoproteome reveals that Sch9 is a central coordinator of protein synthesis.
A. Huber, B. Bodenmiller, A. Uotila, M. Stahl, S. Wanka, B. Gerrits, R. Aebersold, and R. Loewith (2009)
Genes & Dev. 23, 1929-1943
   Abstract »    Full Text »    PDF »
Lysine Acetylation Targets Protein Complexes and Co-Regulates Major Cellular Functions.
C. Choudhary, C. Kumar, F. Gnad, M. L. Nielsen, M. Rehman, T. C. Walther, J. V. Olsen, and M. Mann (2009)
Science 325, 834-840
   Abstract »    Full Text »    PDF »
Identification of L-ferritin in Neuromelanin Granules of the Human Substantia Nigra: A TARGETED PROTEOMICS APPROACH.
F. Tribl, E. Asan, T. Arzberger, T. Tatschner, E. Langenfeld, H. E. Meyer, G. Bringmann, P. Riederer, M. Gerlach, and K. Marcus (2009)
Mol. Cell. Proteomics 8, 1832-1838
   Abstract »    Full Text »    PDF »
Large Scale Comparative Proteomics of a Chloroplast Clp Protease Mutant Reveals Folding Stress, Altered Protein Homeostasis, and Feedback Regulation of Metabolism.
B. Zybailov, G. Friso, J. Kim, A. Rudella, V. R. Rodriguez, Y. Asakura, Q. Sun, and K. J. van Wijk (2009)
Mol. Cell. Proteomics 8, 1789-1810
   Abstract »    Full Text »    PDF »
Comparative Analysis of the Membrane Proteome of Closely Related Metastatic and Nonmetastatic Tumor Cells.
C. Roesli, B. Borgia, C. Schliemann, M. Gunthert, H. Wunderli-Allenspach, R. Giavazzi, and D. Neri (2009)
Cancer Res. 69, 5406-5414
   Abstract »    Full Text »    PDF »
Proteome coverage prediction with infinite Markov models.
M. Claassen, R. Aebersold, and J. M. Buhmann (2009)
Bioinformatics 25, i154-i160
   Abstract »    Full Text »    PDF »
Thematic Review Series: Proteomics. An integrated omics analysis of eicosanoid biology.
M. W. Buczynski, D. S. Dumlao, and E. A. Dennis (2009)
J. Lipid Res. 50, 1015-1038
   Abstract »    Full Text »    PDF »
Combination of MS Protein Identification and Bioassay of Chromatographic Fractions to Identify Biologically Active Substances from Complex Protein Sources.
S. Kuromitsu, H. Yokota, M. Hiramoto, M. Yuri, M. Naitou, N. Nakamura, S. Kawabata, M. Kobori, M. Katoh, K. Furuchi, et al. (2009)
Mol. Cell. Proteomics 8, 1318-1323
   Abstract »    Full Text »    PDF »
Common Sense Approaches to Urinary Biomarker Study Design.
M. A. Knepper (2009)
J. Am. Soc. Nephrol. 20, 1175-1178
   Full Text »    PDF »
Mass Spectrometry-based Proteomic Profiling of Lung Cancer.
S. Ocak, P. Chaurand, and P. P. Massion (2009)
Proceedings of the ATS 6, 159-170
   Abstract »    Full Text »    PDF »
Environmental Proteomics: a Paradigm Shift in Characterizing Microbial Activities at the Molecular Level.
M. Keller and R. Hettich (2009)
Microbiol. Mol. Biol. Rev. 73, 62-70
   Abstract »    Full Text »    PDF »
Quantitative strategies to fuel the merger of discovery and hypothesis-driven shotgun proteomics.
K. G. Kline, G. L. Finney, and C. C. Wu (2009)
Brief Funct Genomic Proteomic 8, 114-125
   Abstract »    Full Text »    PDF »
Quantitative Proteomics Reveals GIMAP Family Proteins 1 and 4 to Be Differentially Regulated during Human T Helper Cell Differentiation.
J.-J. Filen, S. Filen, R. Moulder, S. Tuomela, H. Ahlfors, A. West, P. Kouvonen, S. Kantola, M. Bjorkman, M. Katajamaa, et al. (2009)
Mol. Cell. Proteomics 8, 32-44
   Abstract »    Full Text »    PDF »
Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics.
H. Choi, D. Fermin, and A. I. Nesvizhskii (2008)
Mol. Cell. Proteomics 7, 2373-2385
   Abstract »    Full Text »    PDF »
Peptizer, a Tool for Assessing False Positive Peptide Identifications and Manually Validating Selected Results.
K. Helsens, E. Timmerman, J. Vandekerckhove, K. Gevaert, and L. Martens (2008)
Mol. Cell. Proteomics 7, 2364-2372
   Abstract »    Full Text »    PDF »
Label-free Quantitative Analysis of One-dimensional PAGE LC/MS/MS Proteome: Application on Angiotensin II-Stimulated Smooth Muscle Cells Secretome.
B.-B. Gao, L. Stuart, and E. P. Feener (2008)
Mol. Cell. Proteomics 7, 2399-2409
   Abstract »    Full Text »    PDF »
Mass Spectrometry Special Feature: Precision proteomics: The case for high resolution and high mass accuracy.
M. Mann and N. L. Kelleher (2008)
PNAS 105, 18132-18138
   Abstract »    Full Text »    PDF »
An Integrated, Directed Mass Spectrometric Approach for In-depth Characterization of Complex Peptide Mixtures.
A. Schmidt, N. Gehlenborg, B. Bodenmiller, L. N. Mueller, D. Campbell, M. Mueller, R. Aebersold, and B. Domon (2008)
Mol. Cell. Proteomics 7, 2138-2150
   Abstract »    Full Text »    PDF »
Identifying specific protein interaction partners using quantitative mass spectrometry and bead proteomes.
L. Trinkle-Mulcahy, S. Boulon, Y. W. Lam, R. Urcia, F.-M. Boisvert, F. Vandermoere, N. A. Morrice, S. Swift, U. Rothbauer, H. Leonhardt, et al. (2008)
J. Cell Biol. 183, 223-239
   Abstract »    Full Text »    PDF »
Data analysis and bioinformatics tools for tandem mass spectrometry in proteomics.
E. W. Deutsch, H. Lam, and R. Aebersold (2008)
Physiol Genomics 33, 18-25
   Abstract »    Full Text »    PDF »
Metadegradomics: Toward in Vivo Quantitative Degradomics of Proteolytic Post-translational Modifications of the Cancer Proteome.
A. Doucet, G. S. Butler, D. Rodriguez, A. Prudova, and C. M. Overall (2008)
Mol. Cell. Proteomics 7, 1925-1951
   Abstract »    Full Text »    PDF »
Consequences of C4 Differentiation for Chloroplast Membrane Proteomes in Maize Mesophyll and Bundle Sheath Cells.
W. Majeran, B. Zybailov, A. J. Ytterberg, J. Dunsmore, Q. Sun, and K. J. van Wijk (2008)
Mol. Cell. Proteomics 7, 1609-1638
   Abstract »    Full Text »    PDF »
Transgenic, Fluorescent Leishmania mexicana Allow Direct Analysis of the Proteome of Intracellular Amastigotes.
D. Paape, C. Lippuner, M. Schmid, R. Ackermann, M. E. Barrios-Llerena, U. Zimny-Arndt, V. Brinkmann, B. Arndt, K. P. Pleissner, P. R. Jungblut, et al. (2008)
Mol. Cell. Proteomics 7, 1688-1701
   Abstract »    Full Text »    PDF »
Quantitative Proteomics of a Chloroplast SRP54 Sorting Mutant and Its Genetic Interactions with CLPC1 in Arabidopsis.
H. Rutschow, A. J. Ytterberg, G. Friso, R. Nilsson, and K. J. van Wijk (2008)
Plant Physiology 148, 156-175
   Abstract »    Full Text »    PDF »
Targeted Quantitative Analysis of Streptococcus pyogenes Virulence Factors by Multiple Reaction Monitoring.
V. Lange, J. A. Malmstrom, J. Didion, N. L. King, B. P. Johansson, J. Schafer, J. Rameseder, C.-H. Wong, E. W. Deutsch, M.-Y. Brusniak, et al. (2008)
Mol. Cell. Proteomics 7, 1489-1500
   Abstract »    Full Text »    PDF »
Matching isotopic distributions from metabolically labeled samples.
S. McIlwain, D. Page, E. L. Huttlin, and M. R. Sussman (2008)
Bioinformatics 24, i339-i347
   Abstract »    Full Text »    PDF »
Investigating MS2/MS3 Matching Statistics: A Model For Coupling Consecutive Stage Mass Spectrometry Data For Increased Peptide Identification Confidence.
P. J. Ulintz, B. Bodenmiller, P. C. Andrews, R. Aebersold, and A. I. Nesvizhskii (2008)
Mol. Cell. Proteomics 7, 71-87
   Abstract »    Full Text »    PDF »
Tandem Mass Spectrometry in Physiology.
T. Pisitkun, J. D. Hoffert, M.-J. Yu, and M. A. Knepper (2007)
Physiology 22, 390-400
   Abstract »    Full Text »    PDF »
N-Glycosylation Site Occupancy in Serum Glycoproteins Using Multiple Reaction Monitoring Liquid Chromatography-Mass Spectrometry.
A. J. Hulsmeier, P. Paesold-Burda, and T. Hennet (2007)
Mol. Cell. Proteomics 6, 2132-2138
   Abstract »    Full Text »    PDF »
Isotope-labeled Protein Standards: Toward Absolute Quantitative Proteomics.
V. Brun, A. Dupuis, A. Adrait, M. Marcellin, D. Thomas, M. Court, F. Vandenesch, and J. Garin (2007)
Mol. Cell. Proteomics 6, 2139-2149
   Abstract »    Full Text »    PDF »
PepSplice: cache-efficient search algorithms for comprehensive identification of tandem mass spectra.
F. F. Roos, R. Jacob, J. Grossmann, B. Fischer, J. M. Buhmann, W. Gruissem, S. Baginsky, and P. Widmayer (2007)
Bioinformatics 23, 3016-3023
   Abstract »    Full Text »    PDF »
MglA Regulates Francisella tularensis subsp. novicida (Francisella novicida) Response to Starvation and Oxidative Stress.
T. Guina, D. Radulovic, A. J. Bahrami, D. L. Bolton, L. Rohmer, K. A. Jones-Isaac, J. Chen, L. A. Gallagher, B. Gallis, S. Ryu, et al. (2007)
J. Bacteriol. 189, 6580-6586
   Abstract »    Full Text »    PDF »
Current trends in computational inference from mass spectrometry-based proteomics.
B.-J. M. Webb-Robertson and W. R. Cannon (2007)
Brief Bioinform 8, 304-317
   Abstract »    Full Text »    PDF »
The Implications of Proteolytic Background for Shotgun Proteomics.
P. Picotti, R. Aebersold, and B. Domon (2007)
Mol. Cell. Proteomics 6, 1589-1598
   Abstract »    Full Text »    PDF »
Blocking S-adenosylmethionine synthesis in yeast allows selenomethionine incorporation and multiwavelength anomalous dispersion phasing.
M. G. Malkowski, E. Quartley, A. E. Friedman, J. Babulski, Y. Kon, J. Wolfley, M. Said, J. R. Luft, E. M. Phizicky, G. T. DeTitta, et al. (2007)
PNAS 104, 6678-6683
   Abstract »    Full Text »    PDF »
Protein Sequences from Mastodon and Tyrannosaurus Rex Revealed by Mass Spectrometry.
J. M. Asara, M. H. Schweitzer, L. M. Freimark, M. Phillips, and L. C. Cantley (2007)
Science 316, 280-285
   Abstract »    Full Text »    PDF »
Quantitative Proteomics Profiling of Sarcomere Associated Proteins in Limb and Extraocular Muscle Allotypes.
S. Fraterman, U. Zeiger, T. S. Khurana, M. Wilm, and N. A. Rubinstein (2007)
Mol. Cell. Proteomics 6, 728-737
   Abstract »    Full Text »    PDF »
Advances in neuromembrane proteomics: efforts towards a comprehensive analysis of membrane proteins in the brain.
K. J. Grant and C. C. Wu (2007)
Brief Funct Genomic Proteomic
   Abstract »    Full Text »    PDF »
Proteomics of specific treatment-related alterations in Fabry disease: A strategy to identify biological abnormalities.
D. F. Moore, O. V. Krokhin, R. C. Beavis, M. Ries, C. Robinson, E. Goldin, R. O. Brady, J. A. Wilkins, and R. Schiffmann (2007)
PNAS 104, 2873-2878
   Abstract »    Full Text »    PDF »
Thematic review series: Systems Biology Approaches to Metabolic and Cardiovascular Disorders. Proteomics approaches to the systems biology of cardiovascular diseases.
T. A. Drake and P. Ping (2007)
J. Lipid Res. 48, 1-8
   Abstract »    Full Text »    PDF »
Potential Applications and Limitations of Proteomics in the Study of Neurological Disease.
Y. Kinoshita, T. Uo, S. Jayadev, G. A. Garden, T. P. Conrads, T. D. Veenstra, and R. S. Morrison (2006)
Arch Neurol 63, 1692-1696
   Full Text »    PDF »
Analysis of Human Phagocyte Flavocytochrome b558 by Mass Spectrometry.
R. M. Taylor, D. Baniulis, J. B. Burritt, J. M. Gripentrog, C. I. Lord, M. H. Riesselman, W. S. Maaty, B. P. Bothner, T. E. Angel, E. A. Dratz, et al. (2006)
J. Biol. Chem. 281, 37045-37056
   Abstract »    Full Text »    PDF »
The Chloride Intracellular Channel Protein CLIC5 Is Expressed at High Levels in Hair Cell Stereocilia and Is Essential for Normal Inner Ear Function.
L. H. Gagnon, C. M. Longo-Guess, M. Berryman, J.-B. Shin, K. W. Saylor, H. Yu, P. G. Gillespie, and K. R. Johnson (2006)
J. Neurosci. 26, 10188-10198
   Abstract »    Full Text »    PDF »
Thematic review series: Systems Biology Approaches to Metabolic and Cardiovascular Disorders. Lipidomics: a global approach to lipid analysis in biological systems.
A. D. Watson (2006)
J. Lipid Res. 47, 2101-2111
   Abstract »    Full Text »    PDF »
Proteomics in Clinical Trials and Practice: Present Uses and Future Promise.
N. S. Azad, N. Rasool, C. M. Annunziata, L. Minasian, G. Whiteley, and E. C. Kohn (2006)
Mol. Cell. Proteomics 5, 1819-1829
   Abstract »    Full Text »    PDF »
Preconditioning Enters the Era of "Physiological Proteomics".
R. A. Cohen and M. E. McComb (2006)
Circ. Res. 99, 663-665
   Full Text »    PDF »
A suite of algorithms for the comprehensive analysis of complex protein mixtures using high-resolution LC-MS.
M. Bellew, M. Coram, M. Fitzgibbon, M. Igra, T. Randolph, P. Wang, D. May, J. Eng, R. Fang, C. Lin, et al. (2006)
Bioinformatics 22, 1902-1909
   Abstract »    Full Text »    PDF »



To Advertise     Find Products


Science. ISSN 0036-8075 (print), 1095-9203 (online)