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Patil LM, Parkinson DH, Zuniga NR, Lin HJL, Naylor BC, Price JC. Combining offline high performance liquid chromatography fractionation of peptides and intact proteins to enhance proteome coverage in bottom-up proteomics. J Chromatogr A 2023; 1701:464044. [PMID: 37196519 DOI: 10.1016/j.chroma.2023.464044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2022] [Revised: 04/10/2023] [Accepted: 05/02/2023] [Indexed: 05/19/2023]
Abstract
Offline peptide separation (PS) using high-performance liquid chromatography (HPLC) is currently used to enhance liquid chromatography-tandem mass spectrometry (LC-MS/MS) detection of proteins. In search of more effective methods for enhancing MS proteome coverage, we developed a robust method for intact protein separation (IPS), an alternative first-dimension separation technique, and explored additional benefits that it offers. Comparing IPS to the traditional PS method, we found that both enhance detection of unique protein IDs to a similar magnitude, though in diverse ways. IPS was especially effective in serum, which has a small number of extremely high abundance proteins. PS was more effective in tissues with fewer dominating high-abundance proteins and was more effective in enhancing detection of post-translational modifications (PTMs). Combining the IPS and PS methods together (IPS+PS) was especially beneficial, enhancing proteome detection more than either method could independently. The comparison of IPS+PS versus six PS fractionation pools increased total number of proteins IDs by nearly double, while also significantly increasing number of unique peptides detected per protein, percent peptide sequence coverage of each protein, and detection of PTMs. This IPS+PS combined method requires fewer LC-MS/MS runs than current PS methods would need to obtain similar improvements in proteome detection, and it is robust, time- and cost-effective, and generally applicable to various tissue and sample types.
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Affiliation(s)
- Leena M Patil
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - David H Parkinson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Nathan R Zuniga
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Hsien-Jung L Lin
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - Bradley C Naylor
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
| | - John C Price
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA.
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2
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Carbonara K, Andonovski M, Coorssen JR. Proteomes Are of Proteoforms: Embracing the Complexity. Proteomes 2021; 9:38. [PMID: 34564541 PMCID: PMC8482110 DOI: 10.3390/proteomes9030038] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 08/24/2021] [Accepted: 08/29/2021] [Indexed: 12/17/2022] Open
Abstract
Proteomes are complex-much more so than genomes or transcriptomes. Thus, simplifying their analysis does not simplify the issue. Proteomes are of proteoforms, not canonical proteins. While having a catalogue of amino acid sequences provides invaluable information, this is the Proteome-lite. To dissect biological mechanisms and identify critical biomarkers/drug targets, we must assess the myriad of proteoforms that arise at any point before, after, and between translation and transcription (e.g., isoforms, splice variants, and post-translational modifications [PTM]), as well as newly defined species. There are numerous analytical methods currently used to address proteome depth and here we critically evaluate these in terms of the current 'state-of-the-field'. We thus discuss both pros and cons of available approaches and where improvements or refinements are needed to quantitatively characterize proteomes. To enable a next-generation approach, we suggest that advances lie in transdisciplinarity via integration of current proteomic methods to yield a unified discipline that capitalizes on the strongest qualities of each. Such a necessary (if not revolutionary) shift cannot be accomplished by a continued primary focus on proteo-genomics/-transcriptomics. We must embrace the complexity. Yes, these are the hard questions, and this will not be easy…but where is the fun in easy?
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Affiliation(s)
| | | | - Jens R. Coorssen
- Faculties of Applied Health Sciences and Mathematics & Science, Departments of Health Sciences and Biological Sciences, Brock University, 1812 Sir Isaac Brock Way, St. Catharines, ON L2S 3A1, Canada; (K.C.); (M.A.)
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3
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Zhang D, Zhang Q, Bai L, Han D, Liu H, Yan H. Fabrication of an ionic-liquid-based polymer monolithic column and its application in the fractionation of proteins from complex biosamples. J Sep Sci 2018; 41:1923-1929. [PMID: 29368444 DOI: 10.1002/jssc.201701369] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2017] [Revised: 01/09/2018] [Accepted: 01/10/2018] [Indexed: 12/28/2022]
Abstract
An ionic-liquid-based polymer monolithic column was synthesized by free radical polymerization within the confines of a stainless-steel column (50 mm × 4.6 mm id). In the processes, ionic liquid and stearyl methacrylate were used as dual monomers, ethylene glycol dimethacrylate as the cross-linking agent, and polyethylene glycol 200 and isopropanol as co-porogens. Effects of the prepolymerization solution components on the properties of the resulting monoliths were studied in detail. Scanning electron microscopy, nitrogen adsorption-desorption measurements, and mercury intrusion porosimetry were used to investigate the morphology and pore size distribution of the prepared monoliths, which showed that the homemade ionic-liquid-based monolith column possessed a relatively uniform macropore structure with a total macropore specific surface area of 44.72 m2 /g. Compared to a non-ionic-liquid-based monolith prepared under the same conditions, the ionic-liquid-based monolith exhibited excellent selectivity and high performance for separating proteins from complex biosamples, such as egg white, snailase, bovine serum albumin digest solution, human plasma, etc., indicating promising applications in the fractionation and analysis of proteins from the complex biosamples in proteomics research.
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Affiliation(s)
- Doudou Zhang
- College of Pharmaceutical Sciences, Hebei University, Baoding, P. R. China
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, P. R. China
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, P. R. China
| | - Qian Zhang
- College of Pharmaceutical Sciences, Hebei University, Baoding, P. R. China
| | - Ligai Bai
- College of Pharmaceutical Sciences, Hebei University, Baoding, P. R. China
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, P. R. China
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, P. R. China
| | - Dandan Han
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, P. R. China
| | - Haiyan Liu
- College of Pharmaceutical Sciences, Hebei University, Baoding, P. R. China
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, P. R. China
- Key Laboratory of Pharmaceutical Quality Control of Hebei Province, Hebei University, Baoding, P. R. China
| | - Hongyuan Yan
- Key Laboratory of Medicinal Chemistry and Molecular Diagnosis, Ministry of Education, Hebei University, Baoding, P. R. China
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4
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Protein separations using enhanced-fluidity liquid chromatography. J Chromatogr A 2017; 1523:257-264. [DOI: 10.1016/j.chroma.2017.07.060] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 07/17/2017] [Accepted: 07/18/2017] [Indexed: 11/21/2022]
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5
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Eeltink S, Wouters S, Dores-Sousa JL, Svec F. Advances in organic polymer-based monolithic column technology for high-resolution liquid chromatography-mass spectrometry profiling of antibodies, intact proteins, oligonucleotides, and peptides. J Chromatogr A 2017; 1498:8-21. [PMID: 28069168 DOI: 10.1016/j.chroma.2017.01.002] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 11/22/2016] [Accepted: 01/02/2017] [Indexed: 11/27/2022]
Abstract
This review focuses on the preparation of organic polymer-based monolithic stationary phases and their application in the separation of biomolecules, including antibodies, intact proteins and protein isoforms, oligonucleotides, and protein digests. Column and material properties, and the optimization of the macropore structure towards kinetic performance are also discussed. State-of-the-art liquid chromatography-mass spectrometry biomolecule separations are reviewed and practical aspects such as ion-pairing agent selection and carryover are presented. Finally, advances in comprehensive two-dimensional LC separations using monolithic columns, in particular ion-exchange×reversed-phase and reversed-phase×reversed-phase LC separations conducted at high and low pH, are shown.
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Affiliation(s)
- Sebastiaan Eeltink
- Vrije Universiteit Brussel, Department of Chemical Engineering, Pleinlaan 2, B-1050 Brussels, Belgium.
| | - Sam Wouters
- Vrije Universiteit Brussel, Department of Chemical Engineering, Pleinlaan 2, B-1050 Brussels, Belgium
| | - José Luís Dores-Sousa
- Vrije Universiteit Brussel, Department of Chemical Engineering, Pleinlaan 2, B-1050 Brussels, Belgium
| | - Frantisek Svec
- Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing, China
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Combining TBP-based rOFFGEL-IEF with FASP and nLC–ESI-LTQ-MS/MS for the analysis of cisplatin-binding proteins in rat kidney. Talanta 2014; 120:433-42. [DOI: 10.1016/j.talanta.2013.11.084] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 11/22/2013] [Accepted: 11/28/2013] [Indexed: 11/23/2022]
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7
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Maixner F, Overath T, Linke D, Janko M, Guerriero G, van den Berg BHJ, Stade B, Leidinger P, Backes C, Jaremek M, Kneissl B, Meder B, Franke A, Egarter-Vigl E, Meese E, Schwarz A, Tholey A, Zink A, Keller A. Paleoproteomic study of the Iceman's brain tissue. Cell Mol Life Sci 2013; 70:3709-22. [PMID: 23739949 PMCID: PMC11113858 DOI: 10.1007/s00018-013-1360-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2012] [Revised: 03/27/2013] [Accepted: 04/30/2013] [Indexed: 01/02/2023]
Abstract
The Tyrolean Iceman, a Copper-age ice mummy, is one of the best-studied human individuals. While the genome of the Iceman has largely been decoded, tissue-specific proteomes have not yet been investigated. We studied the proteome of two distinct brain samples using gel-based and liquid chromatography-mass spectrometry-based proteomics technologies together with a multiple-databases and -search algorithms-driven data-analysis approach. Thereby, we identified a total of 502 different proteins. Of these, 41 proteins are known to be highly abundant in brain tissue and 9 are even specifically expressed in the brain. Furthermore, we found 10 proteins related to blood and coagulation. An enrichment analysis revealed a significant accumulation of proteins related to stress response and wound healing. Together with atomic force microscope scans, indicating clustered blood cells, our data reopens former discussions about a possible injury of the Iceman's head near the site where the tissue samples have been extracted.
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Affiliation(s)
- Frank Maixner
- Institute for Mummies and the Iceman, EURAC research, 39100 Bolzano, Italy
| | - Thorsten Overath
- Division for Systematic Proteome Research, Institute for Experimental Medicine, Christian-Albrechts-Universität Kiel, 24105 Kiel, Germany
| | - Dennis Linke
- Division for Systematic Proteome Research, Institute for Experimental Medicine, Christian-Albrechts-Universität Kiel, 24105 Kiel, Germany
| | - Marek Janko
- Center of Smart Interfaces, TU Darmstadt, 64287 Darmstadt, Germany
| | - Gea Guerriero
- Department Environment and Agro-biotechnologies (EVA), Centre de Recherche Public-Gabriel Lippmann, 41, rue du Brill, 4422 Belvaux, Luxembourg
| | - Bart H. J. van den Berg
- Division for Systematic Proteome Research, Institute for Experimental Medicine, Christian-Albrechts-Universität Kiel, 24105 Kiel, Germany
| | - Bjoern Stade
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität Kiel, 24105 Kiel, Germany
| | - Petra Leidinger
- Department of Human Genetics, Saarland University, 66421 Saar Homburg, Germany
| | - Christina Backes
- Department of Human Genetics, Saarland University, 66421 Saar Homburg, Germany
| | | | - Benny Kneissl
- Software Engineering and Bioinformatics, Johannes Gutenberg-University of Mainz, 55128 Mainz, Germany
| | - Benjamin Meder
- Department of Internal Medicine III, University of Heidelberg, 69120 Heidelberg, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität Kiel, 24105 Kiel, Germany
| | - Eduard Egarter-Vigl
- Department of Pathological Anatomy and Histology, General Hospital Bolzano, 39100 Bolzano, Italy
| | - Eckart Meese
- Department of Human Genetics, Saarland University, 66421 Saar Homburg, Germany
| | - Andreas Schwarz
- Department of Neurosurgery, General Hospital Bolzano, 39100 Bolzano, Italy
| | - Andreas Tholey
- Division for Systematic Proteome Research, Institute for Experimental Medicine, Christian-Albrechts-Universität Kiel, 24105 Kiel, Germany
| | - Albert Zink
- Institute for Mummies and the Iceman, EURAC research, 39100 Bolzano, Italy
| | - Andreas Keller
- Department of Human Genetics, Saarland University, 66421 Saar Homburg, Germany
- Siemens Healthcare, 91052 Erlangen, Germany
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Stobaugh JT, Fague KM, Jorgenson JW. Prefractionation of Intact Proteins by Reversed-Phase and Anion-Exchange Chromatography for the Differential Proteomic Analysis of Saccharomyces cerevisiae. J Proteome Res 2012. [DOI: 10.1021/pr300701x] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Jordan T. Stobaugh
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - Kaitlin M. Fague
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
| | - James W. Jorgenson
- University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, United States
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9
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Donato P, Cacciola F, Tranchida PQ, Dugo P, Mondello L. Mass spectrometry detection in comprehensive liquid chromatography: basic concepts, instrumental aspects, applications and trends. MASS SPECTROMETRY REVIEWS 2012; 31:523-559. [PMID: 22383300 DOI: 10.1002/mas.20353] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2011] [Revised: 11/10/2011] [Accepted: 11/10/2011] [Indexed: 05/31/2023]
Abstract
The review, as can be deduced from the title, focuses on both theoretical and practical aspects of the use of mass spectrometry as a third, added dimension to a comprehensive LC (LC × LC) system, generating the most powerful analytical tool today for non-volatile analytes. The first part deals with the technical requirements for linkage of an LC × LC system to an MS one, including the choice of the mobile phase (buffer and salts), flow rate (splitting), type of ionization (interface); advantages and disadvantages of off-line and on-line methods are discussed, as well. A discussion of the various aspects of instrumentation is provided, both from a chromatographic and mass spectrometry standpoint, with particular emphasis directed to the choice of column sets, spatial resolution, mass resolving power, mass accuracy, and tandem-MS capabilities. The extent to which mass spectrometry may be of aid in unraveling column-outlet multicompound bands is highlighted, along with its effectiveness as a chromatographic detector of excellent sensitivity, universality yet with potential in terms of selectivity and amenability to quantitative analysis over a wide dynamic range. The following section of the review contains significant applications of comprehensive two-dimensional LC coupled to MS in different areas of research, with details on interfaces, column stationary phases, modulation and MS parameters. It is not the intention of the authors to provide a comprehensive description of the techniques, but merely to discuss only those aspects which are essential for successful applications of the LC-MS combination. The reader will be acquainted with the enormous potential of this hyphenated technique, and the factors and instrumental developments that have concurred to make it emerge to a central role in specialized fields, such as proteomics.
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Affiliation(s)
- Paola Donato
- University Campus Bio-Medico, Via Álvaro del Portillo 21, 00128 Rome, Italy
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10
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Hung CW, Tholey A. Tandem Mass Tag Protein Labeling for Top-Down Identification and Quantification. Anal Chem 2011; 84:161-70. [DOI: 10.1021/ac202243r] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Chien-Wen Hung
- Institut für Experimentelle Medizin—AG Systematische Proteomforschung, Christian-Albrechts-Universität, Niemannsweg 11, 24105 Kiel, Germany
| | - Andreas Tholey
- Institut für Experimentelle Medizin—AG Systematische Proteomforschung, Christian-Albrechts-Universität, Niemannsweg 11, 24105 Kiel, Germany
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11
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Knief C, Delmotte N, Vorholt JA. Bacterial adaptation to life in association with plants - A proteomic perspective from culture to in situ conditions. Proteomics 2011; 11:3086-105. [PMID: 21548095 DOI: 10.1002/pmic.201000818] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2010] [Revised: 02/01/2011] [Accepted: 02/17/2011] [Indexed: 12/13/2022]
Abstract
Diverse bacterial taxa that live in association with plants affect plant health and development. This is most evident for those bacteria that undergo a symbiotic association with plants or infect the plants as pathogens. Proteome analyses have contributed significantly toward a deeper understanding of the molecular mechanisms underlying the development of these associations. They were applied to obtain a general overview of the protein composition of these bacteria, but more so to study effects of plant signaling molecules on the cytosolic proteome composition or metabolic adaptations upon plant colonization. Proteomic analyses are particularly useful for the identification of secreted proteins, which are indispensable to manipulate a host plant. Recent advances in the field of proteome analyses have initiated a new research area, the analysis of more complex microbial communities. Such studies are just at their beginning but hold great potential for the future to elucidate not only the interactions between bacteria and their host plants, but also of bacteria-bacteria interactions between different bacterial taxa when living in association with plants. These include not only the symbiotic and pathogenic bacteria, but also the commensal bacteria that are consistently found in association with plants and whose functions remain currently largely uncovered.
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Affiliation(s)
- Claudia Knief
- Institute of Microbiology, ETH Zurich, Zurich, Switzerland
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