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Expert Review of Proteomics Volume 8, 2011 - Issue 6
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Review

Intact proteome fractionation strategies compatible with mass spectrometry

Alan A Doucette Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS, B3H 4R2, Canada;[email protected]
,
John C Tran Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA; Department of Molecular Biosciences, Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
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Mark J Wall Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS, B3H 4R2, Canada; Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS, B3H 4R2, Canada
&
Shayla Fitzsimmons Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS, B3H 4R2, Canada; Department of Chemistry, Dalhousie University, 6274 Coburg Road, Halifax, NS, B3H 4R2, Canada
Pages 787-800 | Published online: 09 Jan 2014

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Wenxuan Cai, Trisha M. Tucholski, Zachery R. Gregorich & Ying Ge. (2016) Top-down Proteomics: Technology Advancements and Applications to Heart Diseases. Expert Review of Proteomics 13:8, pages 717-730.
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Articles from other publishers (36)

Jiwon Yu, Minju Kim & Hae-Min Park. (2023) Recent Advances in Top-Down Proteomics for Proteoform Analysis. KSBB Journal 38:1, pages 12-20.
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Julien Camperi, Maryam Moshref, Lu Dai & Ho Young Lee. (2021) Physicochemical and Functional Characterization of Differential CRISPR-Cas9 Ribonucleoprotein Complexes. Analytical Chemistry 94:2, pages 1432-1440.
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Timothy N. Tiambeng, Zhijie Wu, Jake A. Melby & Ying Ge. 2022. Proteoform Identification. Proteoform Identification 15 30 .
Rituparna Banerjee, Naveena B. Maheswarappa, Sowmya Dasoju & Sushma S. Ande. (2021) OFFGEL and GELFrEE fractionation: Novel liquid-phase protein recovery strategies in proteomics studies. TrAC Trends in Analytical Chemistry 140, pages 116282.
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Jake A. Melby, David S. Roberts, Eli J. Larson, Kyle A. Brown, Elizabeth F. Bayne, Song Jin & Ying Ge. (2021) Novel Strategies to Address the Challenges in Top-Down Proteomics. Journal of the American Society for Mass Spectrometry 32:6, pages 1278-1294.
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James M. Fulcher, Aman Makaju, Ronald J. Moore, Mowei Zhou, David A. Bennett, Philip L. De Jager, Wei-Jun Qian, Ljiljana Paša-Tolić & Vladislav A. Petyuk. (2021) Enhancing Top-Down Proteomics of Brain Tissue with FAIMS. Journal of Proteome Research 20:5, pages 2780-2795.
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Venus Baghalabadi & Alan A. Doucette. (2020) Mass spectrometry profiling of low molecular weight proteins and peptides isolated by acetone precipitation. Analytica Chimica Acta 1138, pages 38-48.
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Madhavi Srikoti, Mark S. Bolgar & Yuri Kazakevich. (2020) Hybrid mode of hydrophobic interaction chromatography of monoclonal antibodies and related biomolecules: Influence of elution conditions on chromatographic performance using poly (alkyl aspartamide) silica columns. Journal of Chromatography B 1140, pages 121984.
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Alan A. Doucette & Jessica L. Nickerson. (2020) Developing front-end devices for improved sample preparation in MS-based proteome analysis. Journal of Mass Spectrometry 55:3, pages e4494.
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Luis A. Macias, Inês C. Santos & Jennifer S. Brodbelt. (2019) Ion Activation Methods for Peptides and Proteins. Analytical Chemistry 92:1, pages 227-251.
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Alan Doucette & Andrew Crowell. 2019. Proteomics Technologies and Applications. Proteomics Technologies and Applications.
Parviz Ghezellou, Vannuruswamy Garikapati, Seyed Mahdi Kazemi, Kerstin Strupat, Alireza Ghassempour & Bernhard Spengler. (2018) A perspective view of top‐down proteomics in snake venom research. Rapid Communications in Mass Spectrometry 33:S1, pages 20-27.
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Leah V. Schaffer, Robert J. Millikin, Rachel M. Miller, Lissa C. Anderson, Ryan T. Fellers, Ying Ge, Neil L. Kelleher, Richard D. LeDuc, Xiaowen Liu, Samuel H. Payne, Liangliang Sun, Paul M. Thomas, Trisha Tucholski, Zhe Wang, Si Wu, Zhijie Wu, Dahang Yu, Michael R. Shortreed & Lloyd M. Smith. (2019) Identification and Quantification of Proteoforms by Mass Spectrometry. PROTEOMICS 19:10, pages 1800361.
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Yu Liang, Yutong Jin, Zhijie Wu, Trisha Tucholski, Kyle A. Brown, Lihua Zhang, Yukui Zhang & Ying Ge. (2019) Bridged Hybrid Monolithic Column Coupled to High-Resolution Mass Spectrometry for Top-Down Proteomics. Analytical Chemistry 91:3, pages 1743-1747.
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Daniel L. Winter, Marc R. Wilkins & William A. Donald. (2019) Differential Ion Mobility–Mass Spectrometry for Detailed Analysis of the Proteome. Trends in Biotechnology 37:2, pages 198-213.
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Bifan Chen, Kyle A. Brown, Ziqing Lin & Ying Ge. (2017) Top-Down Proteomics: Ready for Prime Time?. Analytical Chemistry 90:1, pages 110-127.
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Elisabeth Govaert, Katleen Van Steendam, Sander Willems, Liesbeth Vossaert, Maarten Dhaenens & Dieter Deforce. (2017) Comparison of fractionation proteomics for local SWATH library building. PROTEOMICS 17:15-16, pages 1700052.
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Joseph Gault, Egor Vorontsov, Mathieu Dupré, Valeria Calvaresi, Magalie Duchateau, Diogo B. Lima, Christian Malosse & Julia Chamot-Rooke. 2017. MALDI-TOF and Tandem MS for Clinical Microbiology. MALDI-TOF and Tandem MS for Clinical Microbiology 493 504 .
Wenxuan Cai, Trisha Tucholski, Bifan Chen, Andrew J. Alpert, Sean McIlwain, Takushi Kohmoto, Song Jin & Ying Ge. (2017) Top-Down Proteomics of Large Proteins up to 223 kDa Enabled by Serial Size Exclusion Chromatography Strategy. Analytical Chemistry 89:10, pages 5467-5475.
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Bifan Chen, Ying Peng, Santosh G. Valeja, Lichen Xiu, Andrew J. Alpert & Ying Ge. (2016) Online Hydrophobic Interaction Chromatography–Mass Spectrometry for Top-Down Proteomics. Analytical Chemistry 88:3, pages 1885-1891.
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Nicole M. Lane, Zachery R. Gregorich & Ying Ge. 2016. Manual of Cardiovascular Proteomics. Manual of Cardiovascular Proteomics 187 212 .
Carolyn Kachuk, Kegan Stephen & Alan Doucette. (2015) Comparison of sodium dodecyl sulfate depletion techniques for proteome analysis by mass spectrometry. Journal of Chromatography A 1418, pages 158-166.
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Irene van den Broek & William D van Dongen. (2015) LC–MS-based quantification of intact proteins: perspective for clinical and bioanalytical applications. Bioanalysis 7:15, pages 1943-1958.
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Szymon Filip, Konstantinos Vougas, Jerome Zoidakis, Agnieszka Latosinska, William Mullen, Goce Spasovski, Harald Mischak, Antonia Vlahou & Joachim Jankowski. (2015) Comparison of Depletion Strategies for the Enrichment of Low-Abundance Proteins in Urine. PLOS ONE 10:7, pages e0133773.
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Santosh G. Valeja, Lichen Xiu, Zachery R. Gregorich, Huseyin Guner, Song Jin & Ying Ge. (2015) Three Dimensional Liquid Chromatography Coupling Ion Exchange Chromatography/Hydrophobic Interaction Chromatography/Reverse Phase Chromatography for Effective Protein Separation in Top-Down Proteomics. Analytical Chemistry 87:10, pages 5363-5371.
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Ki Hun Kim, Philip D. Compton, John C. Tran & Neil L. Kelleher. (2015) Online Matrix Removal Platform for Coupling Gel-Based Separations to Whole Protein Electrospray Ionization Mass Spectrometry. Journal of Proteome Research 14:5, pages 2199-2206.
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Stephen J. Hattan, Jie Du & Kenneth C. Parker. (2015) Bifunctional Glass Membrane Designed to Interface SDS-PAGE Separations of Proteins with the Detection of Peptides by Mass Spectrometry. Analytical Chemistry 87:7, pages 3685-3693.
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Ünige A. Laskay, Kristina Srzentić, Michel Monod & Yury O. Tsybin. (2014) Extended bottom-up proteomics with secreted aspartic protease Sap9. Journal of Proteomics 110, pages 20-31.
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Lichen Xiu, Santosh G. Valeja, Andrew J. Alpert, Song Jin & Ying Ge. (2014) Effective Protein Separation by Coupling Hydrophobic Interaction and Reverse Phase Chromatography for Top-down Proteomics. Analytical Chemistry 86:15, pages 7899-7906.
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Zachery R. Gregorich & Ying Ge. (2014) Top-down proteomics in health and disease: Challenges and opportunities. PROTEOMICS 14:10, pages 1195-1210.
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Nadia Ucciferri & Silvia Rocchiccioli. 2014. Pseudogenes. Pseudogenes 187 195 .
Xin Chen & Ying Ge. (2013) Ultrahigh pressure fast size exclusion chromatography for top-down proteomics. PROTEOMICS 13:17, pages 2563-2566.
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Stephan A. Müller, Sven Findeiß, Sandy R. Pernitzsch, Dirk K. Wissenbach, Peter F. Stadler, Ivo L. Hofacker, Martin von Bergen & Stefan Kalkhof. (2013) Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics. Journal of Proteomics 86, pages 27-42.
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Kasper Engholm-Keller & Martin R. Larsen. (2013) Technologies and challenges in large-scale phosphoproteomics. PROTEOMICS 13:6, pages 910-931.
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. 2013. Low-Abundance Proteome Discovery. Low-Abundance Proteome Discovery 323 332 .
Miroslava Stastna & Jennifer E. Van Eyk. (2012) Analysis of protein isoforms: Can we do it better?. PROTEOMICS 12:19-20, pages 2937-2948.
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