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Mass spectrometry-based proteomics in biomedical research: emerging technologies and future strategies

Published online by Cambridge University Press:  23 September 2010

Geraldine M. Walsh ,
Jason C. Rogalski ,
Cordula Klockenbusch  and
Juergen Kast
Geraldine M. Walsh
Affiliation:
The Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada. The Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada.
Jason C. Rogalski
Affiliation:
The Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada. The Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada.
Cordula Klockenbusch
Affiliation:
The Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada.
Juergen Kast*
Affiliation:
The Biomedical Research Centre, University of British Columbia, Vancouver, BC, Canada. The Centre for Blood Research, University of British Columbia, Vancouver, BC, Canada. Department of Chemistry, University of British Columbia, Vancouver, BC, Canada.
*
*Corresponding author: Juergen Kast, The Biomedical Research Centre, 2222 Health Sciences Mall, Vancouver, BC, CanadaV6T 1Z3. E-mail: kast@brc.ubc.ca
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Abstract

In recent years, the technology and methods widely available for mass spectrometry (MS)-based proteomics have increased in power and potential, allowing the study of protein-level processes occurring in biological systems. Although these methods remain an active area of research, established techniques are already helping answer biological questions. Here, this recent evolution of MS-based proteomics and its applications are reviewed, including standard methods for protein and peptide separation, biochemical fractionation, quantitation, targeted MS approaches such as selected reaction monitoring, data analysis and bioinformatics. Recent research in many of these areas reveals that proteomics has moved beyond simply cataloguing proteins in biological systems and is finally living up to its initial potential – as an essential tool to aid related disciplines, notably health research. From here, there is great potential for MS-based proteomics to move beyond basic research, into clinical research and diagnostics.

Type
Review Article
Information
Expert Reviews in Molecular Medicine , Volume 12 , January 2010 , e30
Copyright
Copyright © Cambridge University Press 2010

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Further reading, resources and contacts

Delahunty, C. and Yates, J.R. 3rd (2005) Protein identification using 2D-LC-MS/MS. Methods 35, 248-255 Describes in detail the strong cation exchange/reversed-phase method that is widely used for 2D LC-MS/MS analysis.Google Scholar
Fang, Y., Robinson, D.P. and Foster, L.J. (2010) Quantitative analysis of proteome coverage and recovery rates for upstream fractionation methods in proteomics. Journal of Proteome Research 9, 1902-1912 Rigorously compares the three most commonly used protein-level first-dimension separation techniques CF, IPG and GeLC.CrossRefGoogle ScholarPubMed
Markham, K., Bai, Y. and Schmitt-Ulms, G. (2007) Co-immunoprecipitations revisited: an update on experimental concepts and their implementation for sensitive interactome investigations of endogenous proteins. Analytical and Bioanalytical Chemistry 389, 461-473 Deals with immunoprecipitations and MS to identify interaction partners and mentions several valid guidelines to avoid possible pitfalls.Google Scholar
Rogers, L.D. and Foster, L.J. (2009) Phosphoproteomics – finally fulfilling the promise?. Molecular Biosystems 5, 1122-1129 An in-depth review about the development of phosphoproteomics in recent years.Google Scholar
Dengjel, J., Kratchmarova, I. and Blagoev, B. (2009) Receptor tyrosine kinase signaling: a view from quantitative proteomics. Molecular Biosystems 5, 1112-1121 An overview about recent approaches to study receptor tyrosine kinase signalling using MS-based proteomics.Google Scholar
Elliott, M.H. et al. (2009) Current trends in quantitative proteomics. Journal of Mass Spectrometry 44, 1637-1660 A thorough and well-written synopsis of the current state of quantitative proteomics, which discusses the strengths and weaknesses of the methods in more depth than they have been covered here.Google Scholar
Lange, V. et al. (2008) Selected reaction monitoring for quantitative proteomics: a tutorial. Molecular System Biology 4, 222 An informative tutorial explaining many aspects of SRM, including transition design and optimisation as well as the application of SRM for quantitative proteomics.Google Scholar
Yocum, A.K. and Chinnaiyan, A.M. (2009) Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry. Briefings in Functional Genomics and Proteomics 8, 145-157 A useful review on SRM that includes advice on method development as well as a section on other MS-based targeted approaches.Google Scholar
Issaq, H.J. and Veenstra, T.D. (2008) Would you prefer multiple reaction monitoring or antibodies with your biomarker validation?. Expert Reviews of Proteomics 5, 761-763 An engaging discussion of the possible applications of SRM in clinical biomarker validation assays.Google Scholar
Malik, R. et al. (2010) From proteome lists to biological impact – tools and strategies for the analysis of large MS data sets. Proteomics 10, 1270-1283 An excellent review of available tools to extract biologically relevant information from large proteomic datasets.Google Scholar
Wang, M. et al. (2008) Label-free mass spectrometry-based protein quantification technologies in proteomic analysis. Briefings in Functional Genomics and Proteomics 7, 329-339 An overview of available label-free MS-based approaches to protein quantification.Google Scholar
Delahunty, C. and Yates, J.R. 3rd (2005) Protein identification using 2D-LC-MS/MS. Methods 35, 248-255 Describes in detail the strong cation exchange/reversed-phase method that is widely used for 2D LC-MS/MS analysis.Google Scholar
Fang, Y., Robinson, D.P. and Foster, L.J. (2010) Quantitative analysis of proteome coverage and recovery rates for upstream fractionation methods in proteomics. Journal of Proteome Research 9, 1902-1912 Rigorously compares the three most commonly used protein-level first-dimension separation techniques CF, IPG and GeLC.CrossRefGoogle ScholarPubMed
Markham, K., Bai, Y. and Schmitt-Ulms, G. (2007) Co-immunoprecipitations revisited: an update on experimental concepts and their implementation for sensitive interactome investigations of endogenous proteins. Analytical and Bioanalytical Chemistry 389, 461-473 Deals with immunoprecipitations and MS to identify interaction partners and mentions several valid guidelines to avoid possible pitfalls.Google Scholar
Rogers, L.D. and Foster, L.J. (2009) Phosphoproteomics – finally fulfilling the promise?. Molecular Biosystems 5, 1122-1129 An in-depth review about the development of phosphoproteomics in recent years.Google Scholar
Dengjel, J., Kratchmarova, I. and Blagoev, B. (2009) Receptor tyrosine kinase signaling: a view from quantitative proteomics. Molecular Biosystems 5, 1112-1121 An overview about recent approaches to study receptor tyrosine kinase signalling using MS-based proteomics.Google Scholar
Elliott, M.H. et al. (2009) Current trends in quantitative proteomics. Journal of Mass Spectrometry 44, 1637-1660 A thorough and well-written synopsis of the current state of quantitative proteomics, which discusses the strengths and weaknesses of the methods in more depth than they have been covered here.Google Scholar
Lange, V. et al. (2008) Selected reaction monitoring for quantitative proteomics: a tutorial. Molecular System Biology 4, 222 An informative tutorial explaining many aspects of SRM, including transition design and optimisation as well as the application of SRM for quantitative proteomics.Google Scholar
Yocum, A.K. and Chinnaiyan, A.M. (2009) Current affairs in quantitative targeted proteomics: multiple reaction monitoring-mass spectrometry. Briefings in Functional Genomics and Proteomics 8, 145-157 A useful review on SRM that includes advice on method development as well as a section on other MS-based targeted approaches.Google Scholar
Issaq, H.J. and Veenstra, T.D. (2008) Would you prefer multiple reaction monitoring or antibodies with your biomarker validation?. Expert Reviews of Proteomics 5, 761-763 An engaging discussion of the possible applications of SRM in clinical biomarker validation assays.Google Scholar
Malik, R. et al. (2010) From proteome lists to biological impact – tools and strategies for the analysis of large MS data sets. Proteomics 10, 1270-1283 An excellent review of available tools to extract biologically relevant information from large proteomic datasets.Google Scholar
Wang, M. et al. (2008) Label-free mass spectrometry-based protein quantification technologies in proteomic analysis. Briefings in Functional Genomics and Proteomics 7, 329-339 An overview of available label-free MS-based approaches to protein quantification.Google Scholar