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Girel S, Meister I, Glauser G, Rudaz S. Hyphenation of microflow chromatography with electrospray ionization mass spectrometry for bioanalytical applications focusing on low molecular weight compounds: A tutorial review. MASS SPECTROMETRY REVIEWS 2024. [PMID: 38952056 DOI: 10.1002/mas.21898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 06/10/2024] [Accepted: 06/20/2024] [Indexed: 07/03/2024]
Abstract
Benefits of miniaturized chromatography with various detection modes, such as increased sensitivity, chromatographic efficiency, and speed, were recognized nearly 50 years ago. Over the past two decades, this approach has experienced rapid growth, driven by the emergence of mass spectrometry applications serving -omics sciences and the need for analyzing minute volumes of precious samples with ever higher sensitivity. While nanoscale liquid chromatography (flow rates <1 μL/min) has gained widespread recognition in proteomics, the adoption of microscale setups (flow rates ranging from 1 to 100 μL/min) for low molecular weight compound applications, including metabolomics, has been surprisingly slow, despite the inherent advantages of the approach. Highly heterogeneous matrices and chemical structures accompanied by a relative lack of options for both selective sample preparation and user-friendly equipment are usually reported as major hindrances. To facilitate the wider implementation of microscale analyses, we present here a comprehensive tutorial encompassing important theoretical and practical considerations. We provide fundamental principles in micro-chromatography and guide the reader through the main elements of a microflow workflow, from LC pumps to ionization devices. Finally, based on both our literature overview and experience, illustrated by some in-house data, we highlight the critical importance of the ionization source design and its careful optimization to achieve significant sensitivity improvement.
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Affiliation(s)
- Sergey Girel
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
| | - Isabel Meister
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Swiss Center of Applied Human Toxicology (SCAHT), Basel, Switzerland
| | - Gaetan Glauser
- Neuchâtel Platform of Analytical Chemistry, University of Neuchâtel, Neuchâtel, Switzerland
| | - Serge Rudaz
- Institute of Pharmaceutical Sciences of Western Switzerland, University of Geneva, Geneva, Switzerland
- Swiss Center of Applied Human Toxicology (SCAHT), Basel, Switzerland
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2
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Abstract
INTRODUCTION Due to its excellent sensitivity, nano-flow liquid chromatography tandem mass spectrometry (LC-MS/MS) is the mainstay in proteome research; however, this comes at the expense of limited throughput and robustness. In contrast, micro-flow LC-MS/MS enables high-throughput, robustness, quantitative reproducibility, and precision while retaining a moderate degree of sensitivity. Such features make it an attractive technology for a wide range of proteomic applications. In particular, large-scale projects involving the analysis of hundreds to thousands of samples. AREAS COVERED This review summarizes the history of chromatographic separation in discovery proteomics with a focus on micro-flow LC-MS/MS, discusses the current state-of-the-art, highlights advances in column development and instrumentation, and provides guidance on which LC flow best supports different types of proteomic applications. EXPERT OPINION Micro-flow LC-MS/MS will replace nano-flow LC-MS/MS in many proteomic applications, particularly when sample quantities are not limited and sample cohorts are large. Examples include clinical analyses of body fluids, tissues, drug discovery and chemical biology investigations, plus systems biology projects across all kingdoms of life. When combined with rapid and sensitive MS, intelligent data acquisition, and informatics approaches, it will soon become possible to analyze large cohorts of more than 10,000 samples in a comprehensive and fully quantitative fashion.
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Affiliation(s)
- Yangyang Bian
- The College of Life Science, Northwest University, Xi'an, P.R. China
| | - Chunli Gao
- The College of Life Science, Northwest University, Xi'an, P.R. China
| | - Bernhard Kuster
- Chair of Proteomics and Bioanalytics, Technical University of Munich, Freising, Germany
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3
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Li T, Hentschel A, Ahrends R. Analytical comparison of absolute quantification strategies to investigate the Insulin signaling pathway in fat cells. Proteomics 2021; 22:e2100136. [PMID: 34964541 DOI: 10.1002/pmic.202100136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 11/08/2022]
Abstract
So far, mass spectrometry based targeted proteomics is the most sensitive approach to answer and address specific biological questions in an accurate and quantitative fashion. However, the data analysis design used for such quantification varies in the field leading to discrepancies in the reported values. In this study, different quantification strategies based on calibration curves were evaluated and compared. The best accuracy and coefficient of variation was achieved by ratio to ratio calibration curves. We applied the ratio to ratio quantification approach to analyze very low abundant insulin signaling proteins such as PIK3RA (0.10-0.93 fmol/μg), AKT1 (0.1-0.39 fmol/μg) and the Insulin receptor (0.22 -2.62 fmol/μg) in a fat cell model and demonstrated the adaptation of this pathway at different states of insulin sensitivity. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Tingting Li
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Otto-Hahn-Straße 6b, Dortmund, 44227, Germany
| | - Andreas Hentschel
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Otto-Hahn-Straße 6b, Dortmund, 44227, Germany
| | - Robert Ahrends
- Leibniz-Institut für Analytische Wissenschaften - ISAS - e. V., Otto-Hahn-Straße 6b, Dortmund, 44227, Germany.,Department of Analytical Chemistry, University of Vienna, Währinger Straße 38, Vienna, 1090, Austria
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4
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Nice EC. The separation sciences, the front end to proteomics: An historical perspective. Biomed Chromatogr 2020; 35:e4995. [DOI: 10.1002/bmc.4995] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Revised: 09/18/2020] [Accepted: 09/23/2020] [Indexed: 02/06/2023]
Affiliation(s)
- Edouard C. Nice
- Department of Biochemistry and Molecular Biology Monash University Clayton Victoria Australia
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5
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A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of this Field. Proteomes 2020; 8:proteomes8030014. [PMID: 32640657 PMCID: PMC7564415 DOI: 10.3390/proteomes8030014] [Citation(s) in RCA: 147] [Impact Index Per Article: 36.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Revised: 06/25/2020] [Accepted: 07/01/2020] [Indexed: 02/07/2023] Open
Abstract
Proteomics is the field of study that includes the analysis of proteins, from either a basic science prospective or a clinical one. Proteins can be investigated for their abundance, variety of proteoforms due to post-translational modifications (PTMs), and their stable or transient protein–protein interactions. This can be especially beneficial in the clinical setting when studying proteins involved in different diseases and conditions. Here, we aim to describe a bottom-up proteomics workflow from sample preparation to data analysis, including all of its benefits and pitfalls. We also describe potential improvements in this type of proteomics workflow for the future.
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6
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McPherson RL, Ong SE, Leung AKL. Ion-Pairing with Triethylammonium Acetate Improves Solid-Phase Extraction of ADP-Ribosylated Peptides. J Proteome Res 2020; 19:984-990. [PMID: 31859514 DOI: 10.1021/acs.jproteome.9b00696] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
ADP-ribosylation refers to the post-translational modification of protein substrates with monomers or polymers of the small molecule ADP-ribose. ADP-ribosylation is enzymatically regulated and plays roles in cellular processes including DNA repair, nucleic acid metabolism, cell death, cellular stress responses, and antiviral immunity. Recent advances in the field of ADP-ribosylation have led to the development of proteomics approaches to enrich and identify endogenous ADP-ribosylated peptides by liquid chromatography tandem mass spectrometry (LC-MS/MS). A number of these methods rely on reverse-phase solid-phase extraction as a critical step in preparing cellular peptides for further enrichment steps in proteomics workflows. The anionic ion-pairing reagent trifluoroacetic acid (TFA) is typically used during reverse-phase solid-phase extraction to promote retention of tryptic peptides. Here we report that TFA and other carboxylate ion-pairing reagents are inefficient for reverse-phase solid-phase extraction of ADP-ribosylated peptides. Substitution of TFA with cationic ion-pairing reagents, such as triethylammonium acetate (TEAA), improves recovery of ADP-ribosylated peptides. We further demonstrate that substitution of TFA with TEAA in a proteomics workflow specific for identifying ADP-ribosylated peptides increases identification rates of ADP-ribosylated peptides by LC-MS/MS.
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Affiliation(s)
- Robert Lyle McPherson
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health , Johns Hopkins University , Baltimore , Maryland 21205 , United States
| | - Shao-En Ong
- Department of Pharmacology , University of Washington , Seattle , Washington 98195 , United States
| | - Anthony K L Leung
- Department of Biochemistry and Molecular Biology, Bloomberg School of Public Health , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,Department of Molecular Biology and Genetics, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States.,Department of Oncology, School of Medicine , Johns Hopkins University , Baltimore , Maryland 21205 , United States
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7
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Fernández-Pumarega A, Dores-Sousa JL, Eeltink S. A comprehensive investigation of the peak capacity for the reversed-phase gradient liquid-chromatographic analysis of intact proteins using a polymer-monolithic capillary column. J Chromatogr A 2020; 1609:460462. [DOI: 10.1016/j.chroma.2019.460462] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 08/13/2019] [Accepted: 08/16/2019] [Indexed: 12/31/2022]
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8
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Yang J, He S, Liu A, Chen J, Dong Y. Preparation of a poly(1, 6-hexylene dimethacrylate) conventional size high performance liquid chromatographic monolithic column for separation of small molecules. Microchem J 2019. [DOI: 10.1016/j.microc.2019.02.032] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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9
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Aydoğan C, Gökaltun A, Denizli A, El‐Rassi Z. Organic polymer‐based monolithic capillary columns and their applications in food analysisψ. J Sep Sci 2019; 42:962-979. [DOI: 10.1002/jssc.201801051] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 12/13/2018] [Accepted: 12/18/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Cemil Aydoğan
- Department of Food EngineeringBingöl University Bingöl Turkey
| | - Aslıhan Gökaltun
- Department of Chemical EngineeringHacettepe University Ankara Turkey
| | - Adil Denizli
- Department of ChemistryHacettepe University Ankara Turkey
| | - Ziad El‐Rassi
- Department of ChemistryOklahoma State University Stillwater OK USA
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10
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Dores-Sousa JL, Fernández-Pumarega A, De Vos J, Lämmerhofer M, Desmet G, Eeltink S. Guidelines for tuning the macropore structure of monolithic columns for high-performance liquid chromatography. J Sep Sci 2018; 42:522-533. [DOI: 10.1002/jssc.201801092] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 10/31/2018] [Accepted: 10/31/2018] [Indexed: 11/12/2022]
Affiliation(s)
- José Luís Dores-Sousa
- Department of Chemical Engineering; Vrije Universiteit Brussel (VUB); Brussels Belgium
| | - Alejandro Fernández-Pumarega
- Departament de Química Analítica and Institut de Biomedicina (IBUB); Universitat de Barcelona, Facultat de Química; Barcelona Spain
| | - Jelle De Vos
- Department of Chemical Engineering; Vrije Universiteit Brussel (VUB); Brussels Belgium
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences, Pharmaceutical (Bio-)Analysis; University of Tübingen; Tübingen Germany
| | - Gert Desmet
- Department of Chemical Engineering; Vrije Universiteit Brussel (VUB); Brussels Belgium
| | - Sebastiaan Eeltink
- Department of Chemical Engineering; Vrije Universiteit Brussel (VUB); Brussels Belgium
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11
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Lynch KB, Ren J, Beckner MA, He C, Liu S. Monolith columns for liquid chromatographic separations of intact proteins: A review of recent advances and applications. Anal Chim Acta 2018; 1046:48-68. [PMID: 30482303 DOI: 10.1016/j.aca.2018.09.021] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 09/10/2018] [Accepted: 09/11/2018] [Indexed: 01/20/2023]
Abstract
In this article we survey 256 references (with an emphasis on the papers published in the past decade) on monolithic columns for intact protein separation. Protein enrichment and purification are included in the broadly defined separation. After a brief introduction, we describe the types of monolithic columns and modes of chromatographic separations employed for protein separations. While the majority of the work is still in the research and development phase, papers have been published toward utilizing monolithic columns for practical applications. We survey these papers as well in this review. Characteristics of selected methods along with their pros and cons will also be discussed.
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Affiliation(s)
- Kyle B Lynch
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Jiangtao Ren
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Matthew A Beckner
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States
| | - Chiyang He
- School of Chemistry and Chemical Engineering, Wuhan Textile University, 1 Textile Road, Wuhan, 430073, PR China
| | - Shaorong Liu
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, OK, 73019, United States.
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12
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Zhu Z, Chen H, Ren J, Lu JJ, Gu C, Lynch KB, Wu S, Wang Z, Cao C, Liu S. Two-dimensional chromatographic analysis using three second-dimension columns for continuous comprehensive analysis of intact proteins. Talanta 2018; 179:588-593. [DOI: 10.1016/j.talanta.2017.11.060] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2017] [Revised: 11/22/2017] [Accepted: 11/26/2017] [Indexed: 11/16/2022]
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13
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Andjelković U, Tufegdžić S, Popović M. Use of monolithic supports for high-throughput protein and peptide separation in proteomics. Electrophoresis 2017; 38:2851-2869. [DOI: 10.1002/elps.201700260] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Revised: 09/02/2017] [Accepted: 09/03/2017] [Indexed: 01/08/2023]
Affiliation(s)
- Uroš Andjelković
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
- Department of Biotechnology; University of Rijeka; Rijeka Croatia
| | - Srdjan Tufegdžić
- Department of Chemistry-Institute of Chemistry; Technology and Metallurgy; University of Belgrade; Belgrade Serbia
| | - Milica Popović
- Faculty of Chemistry; University of Belgrade; Belgrade Serbia
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14
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Capillary methacrylate-based monoliths by grafting from/to γ-ray polymerization on a tentacle-type reactive surface for the liquid chromatographic separations of small molecules and intact proteins. J Chromatogr A 2017; 1498:46-55. [DOI: 10.1016/j.chroma.2016.11.039] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2016] [Revised: 10/20/2016] [Accepted: 11/21/2016] [Indexed: 12/13/2022]
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15
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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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16
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Development and optimisation of a generic micro LC-ESI-MS method for the qualitative and quantitative determination of 30-mer toxic gliadin peptides in wheat flour for food analysis. Anal Bioanal Chem 2016; 409:989-997. [DOI: 10.1007/s00216-016-0013-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2016] [Revised: 09/01/2016] [Accepted: 10/06/2016] [Indexed: 01/06/2023]
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17
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Micro-liquid chromatography mass spectrometry for the analysis of antineoplastic drugs from wipe samples. Anal Bioanal Chem 2016; 408:8221-8229. [DOI: 10.1007/s00216-016-9932-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/22/2016] [Accepted: 09/07/2016] [Indexed: 12/11/2022]
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18
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Pröfrock D. Coupling Techniques and Orthogonal Combination of Mass Spectrometric Techniques. Metallomics 2016. [DOI: 10.1002/9783527694907.ch2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Daniel Pröfrock
- Helmholtz-Zentrum Geesthacht, Centre for Materials and Coastal Research; Department Marine Bioanalytical Chemistry, Institute of Coastal Research/Biogeochemistry in Coastal Seas; Max-Planck Str.1 21502 Geesthacht Germany
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19
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Zhang H, Ou J, Wei Y, Wang H, Liu Z, Zou H. A hybrid fluorous monolithic capillary column with integrated nanoelectrospray ionization emitter for determination of perfluoroalkyl acids by nano-liquid chromatography–nanoelectrospray ionization-mass spectrometry/mass spectrometry. J Chromatogr A 2016; 1440:66-73. [DOI: 10.1016/j.chroma.2016.02.025] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/05/2016] [Accepted: 02/07/2016] [Indexed: 10/22/2022]
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20
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Optimization of poly(methyl styrene-co-bis(p-vinylbenzyl)dimethylsilane)-based capillary monoliths for separation of low, medium, and high molecular-weight analytes. J Chromatogr A 2016; 1443:126-35. [DOI: 10.1016/j.chroma.2016.03.034] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 03/11/2016] [Accepted: 03/14/2016] [Indexed: 11/15/2022]
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21
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Moravcová D, Rantamäki AH, Duša F, Wiedmer SK. Monoliths in capillary electrochromatography and capillary liquid chromatography in conjunction with mass spectrometry. Electrophoresis 2016; 37:880-912. [PMID: 26800083 DOI: 10.1002/elps.201500520] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2015] [Revised: 12/18/2015] [Accepted: 12/21/2015] [Indexed: 12/29/2022]
Abstract
Here, we have reviewed separation studies utilizing monolithic capillary columns for separation of compounds preceding MS analysis. The review is divided in two parts according to the used separation method, namely CEC and capillary LC (cLC). Based on our overview, monolithic CEC-MS technique have been more focused on the syntheses of highly specialized and selective separation phase materials for fast and efficient separation of specific types of analytes. In contrast, monolithic cLC-MS is more widely used and is often employed, for instance, in the analysis of oligonucleotides, metabolites, and peptides and proteins in proteomic studies. While poly(styrene-divinylbenzene)-based and silica-based monolithic capillaries found their place in proteomic analyses, the other laboratory-synthesized monoliths still wait for their wider utilization in routine analyses. The development of new monolithic materials will most likely continue due to the demand of more efficient and rapid separation of increasingly complex samples.
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Affiliation(s)
- Dana Moravcová
- Institute of Analytical Chemistry of the CAS, v. v. i, Brno, Czech Republic
| | | | - Filip Duša
- Institute of Analytical Chemistry of the CAS, v. v. i, Brno, Czech Republic
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22
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Simone P, Pierri G, Foglia P, Gasparrini F, Mazzoccanti G, Capriotti AL, Ursini O, Ciogli A, Laganà A. Separation of intact proteins on γ-ray-induced polymethacrylate monolithic columns: A highly permeable stationary phase with high peak capacity for capillary high-performance liquid chromatography with high-resolution mass spectrometry. J Sep Sci 2015; 39:264-71. [PMID: 26530449 DOI: 10.1002/jssc.201500844] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2015] [Revised: 10/19/2015] [Accepted: 10/19/2015] [Indexed: 11/09/2022]
Abstract
Polymethacrylate-based monolithic capillary columns, prepared by γ-radiation-induced polymerization, were used to optimize the experimental conditions (nature of the organic modifiers, the content of trifluoroacetic acid and the column temperature) in the separation of nine standard proteins with different hydrophobicities and a wide range of molecular weights. Because of the excellent permeability of the monolithic columns, an ion-pair reversed-phase capillary liquid chromatography with high-resolution mass spectrometry method has been developed by coupling the column directly to the mass spectrometer without a flow-split and using a standard electrospray interface. Additionally, the high working flow and concomitant high efficiency of these columns allowed us to employ a longer column (up to 50 cm) and achieve a peak capacity value superior to 1000. This work is motivated by the need to develop new materials for high-resolution chromatographic separation that combine chemical stability at elevated temperatures (up to 75°C) and a broad pH range, with a high peak capacity value. The advantage of the γ-ray-induced monolithic column lies in the batch-to-batch reproducibility and long-term high-temperature stability. Their proven high loading capacity, recovery, good selectivity and high permeability, moreover, compared well with that of a commercially available poly(styrene-divinylbenzene) monolithic column, which confirms that such monolithic supports might facilitate analysis in proteomics.
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Affiliation(s)
- Patrizia Simone
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
| | - Giuseppe Pierri
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
| | - Patrizia Foglia
- Dipartimento di Chimica, Sapienza Università di Roma, Roma, Italy
| | | | - Giulia Mazzoccanti
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
| | | | - Ornella Ursini
- Istituto di Metodologie Chimiche, Area della Ricerca di Roma del CNR, Monterotondo Stazione, Roma, Italy
| | - Alessia Ciogli
- Dipartimento di Chimica e Tecnologie del Farmaco, Sapienza Università di Roma, Roma, Italy
| | - Aldo Laganà
- Dipartimento di Chimica, Sapienza Università di Roma, Roma, Italy
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Abstract
In proteomics, nano-LC is arguably the most common tool for separating peptides/proteins prior to MS. The main advantage of nano-LC is enhanced sensitivity, as compounds enter the MS in more concentrated bands. This is particularly relevant for determining low abundant compounds in limited samples. Nano-LC columns can produce peak capacities of 1000 or more, and very narrow columns can be used to perform proteomics of 1000 cells or less. Also, nano-LC can be coupled with online add-ons such as selective trap columns or enzymatic reactors, for faster and more automated analysis. Nano-LC is today an established tool for research laboratories; but can nano-LC-based systems soon be ready for more routine settings, such as in clinics?
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Abstract
Recent findings have elucidated numerous novel biological functions for oligonucleotides. Current standard methods for the study of oligonucleotides (i.e., hybridization and PCR) are not fully equipped to deal with the experimental needs arising from these new discoveries. More importantly, as the intracellular capacity of oligonucleotides is being harnessed for biomedical applications, alternative bioanalytical techniques become indispensable in order to comply with ever-increasing regulatory requirements. Owing to its ability to detect oligonucleotides independent of their sequence, LC-MS is emerging as the analytical method of choice for oligonucleotides. In this article, the current applications of LC-MS in the analysis of oligonucleotides, with an emphasis on RNA therapeutics and biomarkers, will be examined. In addition, the theoretical framework of oligonucleotide ESI is carefully inspected with the purpose of identifying the contributing factors to MS signal intensity.
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25
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Dietz L, Sickmann A. Mass Spectrometry-Based Proteomics for Relative Protein Quantification and Biomarker Identification in Primary Human Hepatocytes. Methods Mol Biol 2015; 1250:251-65. [PMID: 26272148 DOI: 10.1007/978-1-4939-2074-7_18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Liquid chromatography-tandem mass spectrometry-based proteomics is a highly sensitive and effective tool to identify and quantify potential biomarkers in repeated dose toxicity studies using primary cell culture systems. In this respect, 8-plex isobaric tag for relative and absolute quantification labeling is the method of choice for relative quantification. After cell lysis and tryptic protein digestion, an individual isobaric tag is added to the amine groups of arginine and lysine. Then, up to eight differentially labeled samples are mixed and analyzed together in a mass spectrometry experiment. During peptide fragmentation in the mass spectrometer, the individual tag intensity of each identified peptide could be detected, reflecting the peptide intensities in the eight samples. The identified peptides are matched to their specific protein using specific search engines and finally to eight individual relative protein quantities. The two-dimensional fractionation of complex peptide mixtures minimizes the possibility of co-fragmentation of peptides from different origin in the mass spectrometer, which leads to a higher number of peptide search matches and therefore to better identification and quantification results.
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Affiliation(s)
- Lisa Dietz
- Leibniz-Institut für Analytische Wissenschaften-ISAS-e.V., Bunsen-Kirchhoff-Str. 11, 44139, Dortmund, Germany
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Becher D, Bernhardt J, Fuchs S, Riedel K. Metaproteomics to unravel major microbial players in leaf litter and soil environments: challenges and perspectives. Proteomics 2014; 13:2895-909. [PMID: 23894095 DOI: 10.1002/pmic.201300095] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 05/03/2013] [Accepted: 05/13/2013] [Indexed: 11/06/2022]
Abstract
Soil- and litter-borne microorganisms vitally contribute to biogeochemical cycles. However, changes in environmental parameters but also human interferences may alter species composition and elicit alterations in microbial activities. Soil and litter metaproteomics, implying the assignment of soil and litter proteins to specific phylogenetic and functional groups, has a great potential to provide essential new insights into the impact of microbial diversity on soil ecosystem functioning. This article will illuminate challenges and perspectives of current soil and litter metaproteomics research, starting with an introduction to an appropriate experimental design and state-of-the-art proteomics methodologies. This will be followed by a summary of important studies aimed at (i) the discovery of the major biotic drivers of leaf litter decomposition, (ii) metaproteomics analyses of rhizosphere-inhabiting microbes, and (iii) global approaches to study bioremediation processes. The review will be closed by a brief outlook on future developments and some concluding remarks, which should assist the reader to develop successful concepts for soil and litter metaproteomics studies.
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Affiliation(s)
- Dörte Becher
- Ernst-Moritz-Arndt-University of Greifswald, Institute of Microbiology, Greifswald, Germany
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27
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Qu J, Young R, Page BJ, Shen X, Tata N, Li J, Duan X, Fallavollita JA, Canty JM. Reproducible ion-current-based approach for 24-plex comparison of the tissue proteomes of hibernating versus normal myocardium in swine models. J Proteome Res 2014; 13:2571-84. [PMID: 24697261 PMCID: PMC4015685 DOI: 10.1021/pr5000472] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Hibernating
myocardium is an adaptive response to repetitive myocardial
ischemia that is clinically common, but the mechanism of adaptation
is poorly understood. Here we compared the proteomes of hibernating
versus normal myocardium in a porcine model with 24 biological replicates.
Using the ion-current-based proteomic strategy optimized in this study
to expand upon previous proteomic work, we identified differentially
expressed proteins in new molecular pathways of cardiovascular interest.
The methodological strategy includes efficient extraction with detergent
cocktail; precipitation/digestion procedure with high, quantitative
peptide recovery; reproducible nano-LC/MS analysis on a long, heated
column packed with small particles; and quantification based on ion-current
peak areas. Under the optimized conditions, high efficiency and reproducibility
were achieved for each step, which enabled a reliable comparison of
24 the myocardial samples. To achieve confident discovery of differentially
regulated proteins in hibernating myocardium, we used highly stringent
criteria to define “quantifiable proteins”. These included
the filtering criteria of low peptide FDR and S/N > 10 for peptide
ion currents, and each protein was quantified independently from ≥2
distinct peptides. For a broad methodological validation, the quantitative
results were compared with a parallel, well-validated 2D-DIGE analysis
of the same model. Excellent agreement between the two orthogonal
methods was observed (R = 0.74), and the ion-current-based
method quantified almost one order of magnitude more proteins. In
hibernating myocardium, 225 significantly altered proteins were discovered
with a low false-discovery rate (∼3%). These proteins are involved
in biological processes including metabolism, apoptosis, stress response,
contraction, cytoskeleton, transcription, and translation. This provides
compelling evidence that hibernating myocardium adapts to chronic
ischemia. The major metabolic mechanisms include a down-regulation
of mitochondrial respiration and an increase in glycolysis. Meanwhile,
cardioprotective and cytoskeletal proteins are increased, while cardiomyocyte
contractile proteins are reduced. These intrinsic adaptations to regional
ischemia maintain long-term cardiomyocyte viability at the expense
of contractile function.
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Affiliation(s)
- Jun Qu
- Department of Pharmaceutical Sciences, ‡Department of Biochemistry, §Department of Medicine, ∥Department of Physiology and Biophysics, ⊥The Center for Research in Cardiovascular Medicine, and #Center for Excellence in Bioinformatics and Life Sciences, State University of New York at Buffalo , Buffalo, New York 14214, United States
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Whitelegge J, Halgand F, Souda P, Zabrouskov V. Top-down mass spectrometry of integral membrane proteins. Expert Rev Proteomics 2014; 3:585-96. [PMID: 17181473 DOI: 10.1586/14789450.3.6.585] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Top-down mass spectrometry focuses on intact proteins, thereby avoiding loss of information accompanying 'shotgun' protocols that reduce the proteome to a collection of peptides. A suite of liquid-chromatography technologies has been developed for purification of intact integral membrane proteins in aqueous/organic solvent mixtures compatible with biological 'soft-ionization' mass spectrometry, preserving covalent structure into the gas phase. Multiply charged protein ions are fragmented in the gas phase, using either collision-activated or electron-capture dissociation, thus yielding complex spectra of sequence-dependent product ions that collectively define the original native covalent state of an intact protein. Top down offers a more detail-orientated approach to post-transcriptional and post-translational diversity allowing an enhanced insight beyond genomic translation, which has now extended into the bilayer proteome.
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Affiliation(s)
- Julian Whitelegge
- University of California, Pasarow Mass Spectrometry Laboratory, Jane and Terry Semel Institute for Neuroscience and Human Behavior, David Geffen School of Medicine, Los Angeles, CA 90024, USA.
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29
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Xiao Z, Wang L, Liu Y, Wang Q, Zhang B. A “plug-and-use” approach towards facile fabrication of capillary columns for high performance nanoflow liquid chromatography. J Chromatogr A 2014; 1325:109-14. [DOI: 10.1016/j.chroma.2013.12.002] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2013] [Revised: 11/28/2013] [Accepted: 12/01/2013] [Indexed: 11/27/2022]
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Highly crosslinked polymeric monoliths with various C6 functional groups for reversed-phase capillary liquid chromatography of small molecules. J Chromatogr A 2013; 1321:80-7. [DOI: 10.1016/j.chroma.2013.10.071] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 10/18/2013] [Accepted: 10/22/2013] [Indexed: 02/06/2023]
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31
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Kofler S, Ackaert C, Samonig M, Asam C, Briza P, Horejs-Hoeck J, Cabrele C, Ferreira F, Duschl A, Huber C, Brandstetter H. Stabilization of the dimeric birch pollen allergen Bet v 1 impacts its immunological properties. J Biol Chem 2013; 289:540-51. [PMID: 24253036 PMCID: PMC3879576 DOI: 10.1074/jbc.m113.518795] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Many allergens share several biophysical characteristics, including the capability to undergo oligomerization. The dimerization mechanism in Bet v 1 and its allergenic properties are so far poorly understood. Here, we report crystal structures of dimeric Bet v 1, revealing a noncanonical incorporation of cysteine at position 5 instead of genetically encoded tyrosine. Cysteine polysulfide bridging stabilized different dimeric assemblies, depending on the polysulfide linker length. These dimers represent quaternary arrangements that are frequently observed in related proteins, reflecting their prevalence in unmodified Bet v 1. These conclusions were corroborated by characteristic immunologic properties of monomeric and dimeric allergen variants. Hereby, residue 5 could be identified as an allergenic hot spot in Bet v 1. The presented results refine fundamental principles in protein chemistry and emphasize the importance of protein modifications in understanding the molecular basis of allergenicity.
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Affiliation(s)
- Stefan Kofler
- From the Structural Biology Group, Department of Molecular Biology
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32
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Jandera P. Advances in the development of organic polymer monolithic columns and their applications in food analysis—A review. J Chromatogr A 2013; 1313:37-53. [DOI: 10.1016/j.chroma.2013.08.010] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Revised: 07/29/2013] [Accepted: 08/03/2013] [Indexed: 01/04/2023]
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Comments on the Implementation of a Simple Peak Capacity Optimization Procedure and Comparison of Poly(styrene–divinylbenzene) and RP-18 Silica Monolithic Capillary Columns of 5-cm for the Analysis of Protein Digests. Chromatographia 2013. [DOI: 10.1007/s10337-013-2550-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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34
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Liu K, Aggarwal P, Lawson JS, Tolley HD, Lee ML. Organic monoliths for high-performance reversed-phase liquid chromatography. J Sep Sci 2013; 36:2767-81. [DOI: 10.1002/jssc.201300431] [Citation(s) in RCA: 54] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 05/31/2013] [Accepted: 05/31/2013] [Indexed: 11/09/2022]
Affiliation(s)
- Kun Liu
- Department of Chemistry and Biochemistry; Brigham Young University; Provo UT USA
| | - Pankaj Aggarwal
- Department of Chemistry and Biochemistry; Brigham Young University; Provo UT USA
| | - John S. Lawson
- Department of Statistics; Brigham Young University; Provo UT USA
| | - H. Dennis Tolley
- Department of Statistics; Brigham Young University; Provo UT USA
| | - Milton L. Lee
- Department of Chemistry and Biochemistry; Brigham Young University; Provo UT USA
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35
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Zhang Z, Wang F, Dong J, Lin H, Ou J, Zou H. A “one step” approach for preparation of an octadecyl–silica hybrid monolithic column via a non-hydrolytic sol–gel (NHSG) method. RSC Adv 2013. [DOI: 10.1039/c3ra42003e] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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36
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Beck F, Burkhart JM, Geiger J, Zahedi RP, Sickmann A. Robust workflow for iTRAQ-based peptide and protein quantification. Methods Mol Biol 2012; 893:101-13. [PMID: 22665297 DOI: 10.1007/978-1-61779-885-6_8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/20/2023]
Abstract
Quantitative proteomics has become a routinely used technique to globally compare protein content and expression profiles of biological samples, for instance after differential stimulation. In this context, chemical stable isotope-based labeling techniques, such as ICAT and iTRAQ, have been successfully applied in a large variety of studies. Since iTRAQ labels are isobaric, quantitation is conducted on the MS/MS level. Consequently, up to eight samples can be multiplexed and quantified in a single experiment without increasing sample complexity. Here, we present a robust workflow to conduct iTRAQ quantification of biological samples such as human platelets, which comprises (a) an adequate sample preparation procedure, (b) an optimized tryptic digestion protocol, (c) SPE desalting and subsequent peptide labeling using a 4-plex iTRAQ labeling kit, and (d) fractionation of the obtained peptide mixture by strong cation exchange chromatography.
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Affiliation(s)
- Florian Beck
- Leibniz-Institut für Analytische Wissenschaften, ISAS-e.V., Dortmund, Germany
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37
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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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38
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Shu S, Kobayashi H, Okubo M, Sabarudin A, Butsugan M, Umemura T. Chemical anchoring of lauryl methacrylate-based reversed phase monolith to 1/16″ o.d. polyetheretherketone tubing. J Chromatogr A 2012; 1242:59-66. [DOI: 10.1016/j.chroma.2012.04.030] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2012] [Revised: 04/09/2012] [Accepted: 04/10/2012] [Indexed: 10/28/2022]
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39
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Li Y, Aggarwal P, Tolley H, Lee M. Organic Monolith Column Technology for Capillary Liquid Chromatography. ADVANCES IN CHROMATOGRAPHY 2012; 50:237-80. [DOI: 10.1201/b11636-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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40
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Fekete S, Veuthey JL, Guillarme D. New trends in reversed-phase liquid chromatographic separations of therapeutic peptides and proteins: theory and applications. J Pharm Biomed Anal 2012; 69:9-27. [PMID: 22475515 DOI: 10.1016/j.jpba.2012.03.024] [Citation(s) in RCA: 101] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2012] [Revised: 03/12/2012] [Accepted: 03/13/2012] [Indexed: 12/22/2022]
Abstract
In the pharmaceutical field, there is considerable interest in the use of peptides and proteins for therapeutic purposes. There are various ways to characterize such complex samples, but during the last few years, a significant number of technological developments have been brought to the field of RPLC and RPLC-MS. Thus, the present review focuses first on the basics of RPLC for peptides and proteins, including the inherent problems, some possible solutions and some directions for developing a new RPLC method that is dedicated to biomolecules. Then the latest advances in RPLC, such as wide-pore core-shell particles, fully porous sub-2 μm particles, organic monoliths, porous layer open tubular columns and elevated temperature, are described and critically discussed in terms of both kinetic efficiency and selectivity. Numerous applications with real samples are presented that confirm the relevance of these different strategies. Finally, one of the key advantages of RPLC for peptides and proteins over other historical approaches is its inherent compatibility with MS using both MALDI and ESI sources.
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Affiliation(s)
- Szabolcs Fekete
- School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Bd d'Yvoy 20, 1211 Geneva 4, Switzerland.
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41
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Zhang Z, Lin H, Ou J, Qin H, Wu R, Dong J, Zou H. Preparation of phenyl-silica hybrid monolithic column with ?one-pot? process for capillary liquid chromatography. J Chromatogr A 2012; 1228:263-9. [DOI: 10.1016/j.chroma.2011.07.048] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Revised: 07/08/2011] [Accepted: 07/14/2011] [Indexed: 10/18/2022]
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42
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Highly crosslinked polymeric monoliths for reversed-phase capillary liquid chromatography of small molecules. J Chromatogr A 2012; 1227:96-104. [DOI: 10.1016/j.chroma.2011.12.081] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 12/14/2011] [Accepted: 12/17/2011] [Indexed: 11/19/2022]
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43
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Donato P, Cacciola F, Mondello L, Dugo P. Comprehensive chromatographic separations in proteomics. J Chromatogr A 2011; 1218:8777-90. [DOI: 10.1016/j.chroma.2011.05.070] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2011] [Revised: 05/11/2011] [Accepted: 05/21/2011] [Indexed: 01/22/2023]
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44
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45
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46
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Preparation and characterization of lauryl methacrylate-based monolithic microbore column for reversed-phase liquid chromatography. J Chromatogr A 2011; 1218:5228-34. [DOI: 10.1016/j.chroma.2011.05.104] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2011] [Revised: 05/27/2011] [Accepted: 05/31/2011] [Indexed: 11/24/2022]
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47
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van de Meent MHM, Eeltink S, de Jong GJ. Potential of poly(styrene-co-divinylbenzene) monolithic columns for the LC-MS analysis of protein digests. Anal Bioanal Chem 2011; 399:1845-52. [PMID: 21184056 PMCID: PMC3026671 DOI: 10.1007/s00216-010-4578-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2010] [Revised: 12/01/2010] [Accepted: 12/02/2010] [Indexed: 11/25/2022]
Abstract
Two polystyrene-based capillary monolithic columns of different length (50 and 250 mm) were used to evaluate the effects of column length on gradient separation of protein digests. A tryptic digest of a 9-protein mixture was used as a test sample. Peak capacities were determined from selected extracted ion chromatograms, and tandem mass spectrometry data were used for database matching using the MASCOT search engine. Peak capacities and protein identification scores were higher for the long column with all gradients. Peak capacities appear to approach a plateau for longer gradient times; maximum peak capacity was estimated to be 294 for the short column and 370 for the long column. Analyses with similar gradient slope produced a ratio of the peak capacities of 3.36 for the long and the short column, which is slightly higher than the expected value of the square root of the column length ratio. The use of a longer monolith improves peptide separation, as reflected by higher peak capacity, and also increases protein identification, as observed from higher identification scores and a larger number of identified peptides. Attention has also been paid to the peak production rate (PPR, peak capacity per unit time). For short analysis times, the short column produces a higher PPR, while for analysis times longer than 40 min, the PPR of the 250-mm column is higher.
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Affiliation(s)
- Michiel H M van de Meent
- Division of Biomedical Analysis, Department of Pharmaceutical Sciences, Utrecht University, P.O. Box 80082, 3508 TB Utrecht, The Netherlands.
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48
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Thangaraj B, Ryan CM, Souda P, Krause K, Faull KF, Weber APM, Fromme P, Whitelegge JP. Data-directed top-down Fourier-transform mass spectrometry of a large integral membrane protein complex: photosystem II from Galdieria sulphuraria. Proteomics 2011; 10:3644-56. [PMID: 20845333 DOI: 10.1002/pmic.201000190] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
High-resolution top-down MS was used to characterize eleven integral and five peripheral subunits of the 750 kDa photosystem II complex from the eukaryotic red alga, Galdieria sulphuraria. The primary separation used LC MS with concomitant fraction collection (LC-MS+), yielding around 40 intact mass tags at 100 ppm mass accuracy on a low-resolution ESI mass spectrometer, whose retention and mass were used to guide subsequent high-resolution top-down nano-electrospray FT ion-cyclotron resonance MS experiments (FT-MS). Both collisionally activated and electron capture dissociation were used to confirm the presence of eleven small subunits to mass accuracy within 5 ppm; PsbE, PsbF, PsbH, PsbI, PsbJ, PsbK, PsbL, PsbM, PsbT, PsbX and PsbZ. All subunits showed covalent modifications that fall into three classes including retention of initiating formyl-methionine, removal of methionine at the N-terminus with or without acetylation, and removal of a longer N-terminal peptide. Peripheral subunits identified by top-down analysis included oxygen-evolving complex subunits PsbO, PsbU, PsbV, as well as Psb28 (PsbW) and Psb27 ("PsbZ-like"). Top-down high-resolution MS provides the necessary precision, typically less than 5 ppm, for identification and characterization of polypeptide composition of these important membrane protein complexes.
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Affiliation(s)
- Balakumar Thangaraj
- Department of Chemistry and Biochemistry, Arizona State University, Tempe, AZ 90024, USA
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49
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Mohr J, Swart R, Samonig M, Böhm G, Huber CG. High-efficiency nano- and micro-HPLC--high-resolution Orbitrap-MS platform for top-down proteomics. Proteomics 2011; 10:3598-609. [PMID: 20859959 DOI: 10.1002/pmic.201000341] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
In terms of resolution, mass accuracy, and sensitivity, the Orbitrap represents one of the most potent mass analyzers available today. We here elucidate the potential of interfacing Orbitrap-MS to ion-pair RP HPLC for intact protein analysis. Using gradients of ACN and monolithic columns of 1.0 and 0.10 mm id, peak capacities between 120 and 130 were achievable within 20-25 min separation time. Compared with silica-based stationary phases, protein recovery and carryover from monolithic columns were found clearly superior. Intact proteins were detectable in a mass range covering 5.7-150 kDa with LODs in the low femtomol range. Compared with UV detection, MS detection with a scanning speed of 1.6 s per spectrum on average led to a 26% increase in chromatographic peak widths, whereas chromatographic patterns were mostly preserved in extracted ion chromatograms at an acquisition rate of 0.5 s per spectrum. Isotopic resolution of multiply charged ions was demonstrated for proteins up to 42 kDa. A micro-HPLC-Orbitrap-MS setup employing a 1.0 mm id column was utilized to characterize a 150 kDa recombinant monoclonal antibody. The applicability of nano-HPLC-Orbitrap-MS to the analysis of highly complex protein mixtures is demonstrated for the 70% ethanol extractable subproteome of wheat grains.
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Affiliation(s)
- Jens Mohr
- Department of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Salzburg, Austria
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50
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Detobel F, De Bruyne S, Vangelooven J, De Malsche W, Aerts T, Terryn H, Gardeniers H, Eeltink S, Desmet G. Fabrication and chromatographic performance of porous-shell pillar-array columns. Anal Chem 2011; 82:7208-17. [PMID: 20687586 DOI: 10.1021/ac100971a] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report on a new approach to obtain highly homogeneous silica-monolithic columns, applying a sol-gel fabrication process inside a rectangular pillar-array column (1 mm in width, 29 microm in height and 33.75 mm in length) having a cross-sectional area comparable to that of a 200 microm diameter circular capillary. Starting from a silicon-based pillar array and working under high phase-separation-tendency conditions (low poly(ethylene glycol) (PEG)-concentration), highly regular silica-based chromatographic systems with an external porosity in the order of 66-68% were obtained. The pillars, 2.4 microm in diameter, were typically clad with a 0.5 microm shell layer of silica, thus creating a 3.4 microm total outer pillar diameter and leaving a minimal through-pore size of 2.2 microm. After mesopore creation by hydrothermal treatment and column derivatization with octyldimethylchlorosilane, the monolithic column was used for chip-based liquid-chromatographic separations of coumarin dyes. Minimal plate heights ranging between 3.9 microm (nonretaining conditions) and 6 mum (for a retention factor of 6.5) were obtained, corresponding to domain-size-reduced plate heights ranging between 0.7 and 1.2. The column permeability was in the order of 1.3 x 10(13) m(2), lower than theoretically expected, but this is probably due to obstructions induced by the sol-gel process in the supply channels.
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Affiliation(s)
- Frederik Detobel
- Vrije Universiteit Brussel, Department of Chemical Engineering, Belgium
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