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151
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Proteomics for quality-control processes in transfusion medicine. Anal Bioanal Chem 2010; 398:111-24. [DOI: 10.1007/s00216-010-3799-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2010] [Revised: 04/24/2010] [Accepted: 04/27/2010] [Indexed: 12/23/2022]
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152
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Botelho D, Wall MJ, Vieira DB, Fitzsimmons S, Liu F, Doucette A. Top-Down and Bottom-Up Proteomics of SDS-Containing Solutions Following Mass-Based Separation. J Proteome Res 2010; 9:2863-70. [DOI: 10.1021/pr900949p] [Citation(s) in RCA: 125] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Diane Botelho
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3
| | - Mark J. Wall
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3
| | - Douglas B. Vieira
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3
| | - Shayla Fitzsimmons
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3
| | - Fang Liu
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3
| | - Alan Doucette
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J3
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153
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Kellie JF, Tran JC, Lee JE, Ahlf DR, Thomas HM, Ntai I, Catherman AD, Durbin KR, Zamdborg L, Vellaichamy A, Thomas PM, Kelleher NL. The emerging process of Top Down mass spectrometry for protein analysis: biomarkers, protein-therapeutics, and achieving high throughput. MOLECULAR BIOSYSTEMS 2010; 6:1532-9. [PMID: 20711533 DOI: 10.1039/c000896f] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Top Down mass spectrometry (MS) has emerged as an alternative to common Bottom Up strategies for protein analysis. In the Top Down approach, intact proteins are fragmented directly in the mass spectrometer to achieve both protein identification and characterization, even capturing information on combinatorial post-translational modifications. Just in the past two years, Top Down MS has seen incremental advances in instrumentation and dedicated software, and has also experienced a major boost from refined separations of whole proteins in complex mixtures that have both high recovery and reproducibility. Combined with steadily advancing commercial MS instrumentation and data processing, a high-throughput workflow covering intact proteins and polypeptides up to 70 kDa is directly visible in the near future.
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Affiliation(s)
- John F Kellie
- Technology Development Team, Center for Top Down Proteomics, University of Illinois at Urbana-Champaign, USA
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154
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Lee JE, Kellie JF, Tran JC, Tipton JD, Catherman AD, Thomas HM, Ahlf DR, Durbin KR, Vellaichamy A, Ntai I, Marshall AG, Kelleher NL. A robust two-dimensional separation for top-down tandem mass spectrometry of the low-mass proteome. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2009; 20:2183-91. [PMID: 19747844 PMCID: PMC2830800 DOI: 10.1016/j.jasms.2009.08.001] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2009] [Revised: 08/01/2009] [Accepted: 08/03/2009] [Indexed: 05/13/2023]
Abstract
For fractionation of intact proteins by molecular weight (MW), a sharply improved two-dimensional (2D) separation is presented to drive reproducible and robust fractionation before top-down mass spectrometry of complex mixtures. The "GELFrEE" (i.e., gel-eluted liquid fraction entrapment electrophoresis) approach is implemented by use of Tris-glycine and Tris-tricine gel systems applied to human cytosolic and nuclear extracts from HeLa S3 cells, to achieve a MW-based fractionation of proteins from 5 to >100 kDa in 1 h. For top-down tandem mass spectroscopy (MS/MS) of the low-mass proteome (5-25 kDa), between 5 and 8 gel-elution (GE) fractions are sampled by nanocapillary-LC-MS/MS with 12 or 14.5 tesla Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometers. Single injections give about 40 detectable proteins, about half of which yield automated ProSight identifications. Reproducibility metrics of the system are presented, along with comparative analysis of protein targets in mitotic versus asynchronous cells. We forward this basic 2D approach to facilitate wider implementation of top-down mass spectrometry and a variety of other protein separation and/or characterization approaches.
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Affiliation(s)
- Ji Eun Lee
- University of Illinois Urbana–Champaign, Department of Chemistry and The Institute for Genomic Biology, Urbana, Illinois, USA
| | - John F. Kellie
- University of Illinois Urbana–Champaign, Department of Chemistry and The Institute for Genomic Biology, Urbana, Illinois, USA
| | - John C. Tran
- University of Illinois Urbana–Champaign, Department of Chemistry and The Institute for Genomic Biology, Urbana, Illinois, USA
| | - Jeremiah D. Tipton
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA
| | - Adam D. Catherman
- University of Illinois Urbana–Champaign, Department of Chemistry and The Institute for Genomic Biology, Urbana, Illinois, USA
| | - Haylee M. Thomas
- University of Illinois Urbana–Champaign, Department of Chemistry and The Institute for Genomic Biology, Urbana, Illinois, USA
| | - Dorothy R. Ahlf
- University of Illinois Urbana–Champaign, Department of Chemistry and The Institute for Genomic Biology, Urbana, Illinois, USA
| | - Kenneth R. Durbin
- University of Illinois Urbana–Champaign, Department of Chemistry and The Institute for Genomic Biology, Urbana, Illinois, USA
| | - Adaikkalam Vellaichamy
- University of Illinois Urbana–Champaign, Department of Chemistry and The Institute for Genomic Biology, Urbana, Illinois, USA
| | - Ioanna Ntai
- University of Illinois Urbana–Champaign, Department of Chemistry and The Institute for Genomic Biology, Urbana, Illinois, USA
| | - Alan G. Marshall
- Ion Cyclotron Resonance Program, National High Magnetic Field Laboratory, Florida State University, Tallahassee, Florida, USA
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida, USA
| | - Neil L. Kelleher
- University of Illinois Urbana–Champaign, Department of Chemistry and The Institute for Genomic Biology, Urbana, Illinois, USA
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155
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Abu-Farha M, Elisma F, Zhou H, Tian R, Zhou H, Asmer MS, Figeys D. Proteomics: From Technology Developments to Biological Applications. Anal Chem 2009; 81:4585-99. [DOI: 10.1021/ac900735j] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Mohamed Abu-Farha
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Fred Elisma
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Houjiang Zhou
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Ruijun Tian
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Hu Zhou
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Mehmet Selim Asmer
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Daniel Figeys
- Ottawa Institute of Systems Biology (OISB), University of Ottawa, Ottawa, Ontario, Canada, and Department of Biochemistry, Microbiology and Immunology, University of Ottawa, Ottawa, Ontario, Canada
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156
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Evaluation of a solution isoelectric focusing protocol as an alternative to ion exchange chromatography for charge-based proteome prefractionation. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:807-13. [DOI: 10.1016/j.jchromb.2009.02.024] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2008] [Revised: 12/10/2008] [Accepted: 02/07/2009] [Indexed: 11/19/2022]
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