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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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2
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Exploring the structure and dynamics of macromolecular complexes by native mass spectrometry. J Proteomics 2020; 222:103799. [DOI: 10.1016/j.jprot.2020.103799] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Revised: 03/23/2020] [Accepted: 04/25/2020] [Indexed: 12/15/2022]
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3
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Liang Y, Zhang L, Zhang Y. Well-Defined Materials for High-Performance Chromatographic Separation. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2019; 12:451-473. [PMID: 30939031 DOI: 10.1146/annurev-anchem-061318-114854] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Chromatographic separation has been widely applied in various fields, such as chemical engineering, precision medicine, energy, and biology. Because chromatographic separation is based on differential partitioning between the mobile phase and stationary phase and affected by band dispersion and mass transfer resistance from these two phases, the materials used as the stationary phase play a decisive role in separation performance. In this review, we discuss the design of separation materials to achieve the separation with high efficiency and high resolution and highlight the well-defined materials with uniform pore structure and unique properties. The achievements, recent developments, challenges, and future trends of such materials are discussed. Furthermore, the surface functionalization of separation ma-terials for further improvement of separation performance is reviewed. Finally, future research directions and the challenges of chromatographic separation are presented.
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Affiliation(s)
- Yu Liang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China;
| | - Lihua Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China;
| | - Yukui Zhang
- CAS Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China;
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4
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Regl C, Wohlschlager T, Esser-Skala W, Wagner I, Samonig M, Holzmann J, Huber CG. Dilute-and-shoot analysis of therapeutic monoclonal antibody variants in fermentation broth: a method capability study. MAbs 2019; 11:569-582. [PMID: 30668249 PMCID: PMC6512939 DOI: 10.1080/19420862.2018.1563034] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Monoclonal antibodies (mAbs) are widely applied as highly specific and efficient therapeutic agents for various medical conditions, including cancer, inflammatory and autoimmune diseases. As protein production in cellular systems inherently generates a multitude of molecular variants, manufacturing of mAbs requires stringent control in order to ensure safety and efficacy of the drugs. Moreover, monitoring of mAb variants in the course of the fermentation process may allow instant tuning of process parameters to maintain optimal cell culture conditions. Here, we describe a fast and robust workflow for the characterization of mAb variants in fermentation broth. Sample preparation is minimal in that the fermentation broth is shortly centrifuged before dilution and HPLC-MS analysis in a short 15-min gradient run. In a single analysis, N-glycosylation and truncation variants of the expressed mAb are identified at the intact protein level. Simultaneously, absolute quantification of mAb content in fermentation broth is achieved. The whole workflow features excellent robustness as well as retention time and peak area stability. Additional enzymatic removal of N-glycans enables determination of mAb glycation levels, which are subsequently considered in relative N-glycoform quantification to correct for isobaric galactosylation. Several molecular attributes of the expressed therapeutic protein may thus be continuously monitored to ensure the desired product profile. Application of the described workflow in an industrial environment may therefore substantially enhance in-process control in mAb production, as well as targeted biosimilar development.
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Affiliation(s)
- Christof Regl
- a Department of Biosciences, Bioanalytical Research Labs , University of Salzburg , Salzburg , Austria.,b Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Salzburg , Austria
| | - Therese Wohlschlager
- a Department of Biosciences, Bioanalytical Research Labs , University of Salzburg , Salzburg , Austria.,b Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Salzburg , Austria
| | - Wolfgang Esser-Skala
- a Department of Biosciences, Bioanalytical Research Labs , University of Salzburg , Salzburg , Austria.,b Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Salzburg , Austria
| | - Iris Wagner
- a Department of Biosciences, Bioanalytical Research Labs , University of Salzburg , Salzburg , Austria.,b Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Salzburg , Austria
| | - Martin Samonig
- a Department of Biosciences, Bioanalytical Research Labs , University of Salzburg , Salzburg , Austria.,b Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Salzburg , Austria.,c Thermo Fisher Scientific GmbH , Germering , Germany
| | - Johann Holzmann
- b Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Salzburg , Austria.,d Technical Development Biosimilars , Global Drug Development, Novartis, Sandoz GmbH , Kundl , Austria
| | - Christian G Huber
- a Department of Biosciences, Bioanalytical Research Labs , University of Salzburg , Salzburg , Austria.,b Christian Doppler Laboratory for Innovative Tools for Biosimilar Characterization , University of Salzburg , Salzburg , Austria
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5
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Lakshmanan R, Loo JA. Top-Down Protein Identification using a Time-of-Flight Mass Spectrometer and Data Independent Acquisition. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2019; 435:136-144. [PMID: 31105465 PMCID: PMC6519736 DOI: 10.1016/j.ijms.2018.10.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Top-down mass spectrometry and direct dissociation of gas phase intact proteins have been demonstrated to be a powerful platform for identifying proteins from complex mixtures and for elucidating post-translational modifications (PTMs). Fragmentation of proteins in the atmospheric pressure/vacuum interface of the electrospray ionization mass spectrometer is an effective dissociation technique that can be utilized for on-line HPLC top-down analysis. We demonstrate the capability to perform intact protein identifications in a single-stage time-of- flight (TOF) mass spectrometer in a data independent (DIA) acquisition fashion by rapidly switching the in-source dissociation (ISD) energy during protein elution from a liquid chromatography (LC) column. The intact protein and product ion masses obtained at low and high ISD energies, respectively, were measured using a TOF mass analyzer. By coupling on-line protein separations to dissociation in the atmospheric pressure/vacuum interface region of the mass spectrometer, we identified proteins in simple complexity mixtures, including subunits from the human 20S proteasome complex, and PTMs such as phosphorylation and N-terminal acetylation events. This proof-of-principle study demonstrates that a data-independent pseudo- MS/MS method could be a relatively in-expensive platform for top-down MS.
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Affiliation(s)
- Rajeswari Lakshmanan
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095
| | - Joseph A. Loo
- Department of Chemistry and Biochemistry, University of California-Los Angeles, Los Angeles, CA 90095
- Department of Biological Chemistry, David Geffen School of Medicine at UCLA, Molecular Biology Institute, and UCLA/DOE Institute for Genomics and Proteomics, University of California-Los Angeles, Los Angeles, CA 90095
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6
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Development and validation of a (RP)UHPLC-UV-(HESI/Orbitrap)MS method for the identification and quantification of mixtures of intact therapeutical monoclonal antibodies using a monolithic column. J Pharm Biomed Anal 2018; 159:437-448. [DOI: 10.1016/j.jpba.2018.07.013] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 07/09/2018] [Accepted: 07/11/2018] [Indexed: 11/16/2022]
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7
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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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8
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Wasik AA, Schiller HB. Functional proteomics of cellular mechanosensing mechanisms. Semin Cell Dev Biol 2017; 71:118-128. [DOI: 10.1016/j.semcdb.2017.06.019] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Revised: 06/23/2017] [Accepted: 06/25/2017] [Indexed: 10/19/2022]
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9
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Plymire DA, Wing CE, Robinson DE, Patrie SM. Continuous Elution Proteoform Identification of Myelin Basic Protein by Superficially Porous Reversed-Phase Liquid Chromatography and Fourier Transform Mass Spectrometry. Anal Chem 2017; 89:12030-12038. [PMID: 29016107 DOI: 10.1021/acs.analchem.7b02426] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Myelin basic protein (MBP) plays an important structural and functional role in the neuronal myelin sheath. Translated MBP exhibits extreme microheterogeneity with numerous alternative splice variants (ASVs) and post-translational modifications (PTMs) reportedly tied to central nervous system maturation, myelin stability, and the pathobiology of various de- and dys-myelinating disorders. Conventional bioanalytical tools cannot efficiently examine ASV and PTM events simultaneously, which limits understanding of the role of MBP microheterogeneity in human physiology and disease. To address this need, we report on a top-down proteomics pipeline that combines superficially porous reversed-phase liquid chromatography (SPLC), Fourier transform mass spectrometry (FTMS), data-independent acquisition (DIA) with nozzle-skimmer dissociation (NSD), and aligned data processing resources to rapidly characterize abundant MBP proteoforms within murine tissue. The three-tier proteoform identification and characterization workflow resolved four known MBP ASVs and hundreds of differentially modified states from a single 90 min SPLC-FTMS run on ∼0.5 μg of material. This included 323 proteoforms for the 14.1 kDa ASV alone. We also identified two novel ASVs from an alternative transcriptional start site (ATSS) of the MBP gene as well as a never before characterized S-acylation event linking palmitic acid, oleic acid, and stearic acid at C78 of the 17.125 kDa ASV.
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Affiliation(s)
- Daniel A Plymire
- Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Casey E Wing
- Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Dana E Robinson
- Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
| | - Steven M Patrie
- Department of Chemistry, Northwestern University , 2145 Sheridan Road, Evanston, Illinois 60208, United States.,Department of Pathology, UT Southwestern Medical Center , 5323 Harry Hines Boulevard, Dallas, Texas 75390, United States
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10
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Tholey A, Becker A. Top-down proteomics for the analysis of proteolytic events - Methods, applications and perspectives. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2017; 1864:2191-2199. [PMID: 28711385 DOI: 10.1016/j.bbamcr.2017.07.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/07/2017] [Accepted: 07/09/2017] [Indexed: 02/06/2023]
Abstract
Mass spectrometry based proteomics is an indispensable tool for almost all research areas relevant for the understanding of proteolytic processing, ranging from the identification of substrates, products and cleavage sites up to the analysis of structural features influencing protease activity. The majority of methods for these studies are based on bottom-up proteomics performing analysis at peptide level. As this approach is characterized by a number of pitfalls, e.g. loss of molecular information, there is an ongoing effort to establish top-down proteomics, performing separation and MS analysis both at intact protein level. We briefly introduce major approaches of bottom-up proteomics used in the field of protease research and highlight the shortcomings of these methods. We then discuss the present state-of-the-art of top-down proteomics. Together with the discussion of known challenges we show the potential of this approach and present a number of successful applications of top-down proteomics in protease research. This article is part of a Special Issue entitled: Proteolysis as a Regulatory Event in Pathophysiology edited by Stefan Rose-John.
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Affiliation(s)
- Andreas Tholey
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany.
| | - Alexander Becker
- Systematic Proteome Research & Bioanalytics, Institute for Experimental Medicine, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
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11
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Shen Y, Tolić N, Piehowski PD, Shukla AK, Kim S, Zhao R, Qu Y, Robinson E, Smith RD, Paša-Tolić L. High-resolution ultrahigh-pressure long column reversed-phase liquid chromatography for top-down proteomics. J Chromatogr A 2017; 1498:99-110. [DOI: 10.1016/j.chroma.2017.01.008] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 11/29/2016] [Accepted: 01/03/2017] [Indexed: 11/17/2022]
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12
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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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13
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Astefanei A, Dapic I, Camenzuli M. Different Stationary Phase Selectivities and Morphologies for Intact Protein Separations. Chromatographia 2016; 80:665-687. [PMID: 28529348 PMCID: PMC5413533 DOI: 10.1007/s10337-016-3168-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/17/2016] [Accepted: 09/06/2016] [Indexed: 12/18/2022]
Abstract
The central dogma of biology proposed that one gene encodes for one protein. We now know that this does not reflect reality. The human body has approximately 20,000 protein-encoding genes; each of these genes can encode more than one protein. Proteins expressed from a single gene can vary in terms of their post-translational modifications, which often regulate their function within the body. Understanding the proteins within our bodies is a key step in understanding the cause, and perhaps the solution, to disease. This is one of the application areas of proteomics, which is defined as the study of all proteins expressed within an organism at a given point in time. The human proteome is incredibly complex. The complexity of biological samples requires a combination of technologies to achieve high resolution and high sensitivity analysis. Despite the significant advances in mass spectrometry, separation techniques are still essential in this field. Liquid chromatography is an indispensable tool by which low-abundant proteins in complex samples can be enriched and separated. However, advances in chromatography are not as readily adapted in proteomics compared to advances in mass spectrometry. Biologists in this field still favour reversed-phase chromatography with fully porous particles. The purpose of this review is to highlight alternative selectivities and stationary phase morphologies that show potential for application in top-down proteomics; the study of intact proteins.
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Affiliation(s)
- A. Astefanei
- Centre for Analytical Science in Amsterdam (CASA), Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - I. Dapic
- Centre for Analytical Science in Amsterdam (CASA), Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - M. Camenzuli
- Centre for Analytical Science in Amsterdam (CASA), Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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14
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Tucher J, Koudelka T, Schlenk J, Tholey A. From top-down to bottom-up: Time-dependent monitoring of proteolytic protein degradation by LC-MS. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1015-1016:111-120. [DOI: 10.1016/j.jchromb.2016.02.021] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 02/11/2016] [Accepted: 02/14/2016] [Indexed: 10/22/2022]
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15
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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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16
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Boeri Erba E, Petosa C. The emerging role of native mass spectrometry in characterizing the structure and dynamics of macromolecular complexes. Protein Sci 2015; 24:1176-92. [PMID: 25676284 DOI: 10.1002/pro.2661] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Revised: 02/06/2015] [Accepted: 02/06/2015] [Indexed: 12/31/2022]
Abstract
Mass spectrometry (MS) is a powerful tool for determining the mass of biomolecules with high accuracy and sensitivity. MS performed under so-called "native conditions" (native MS) can be used to determine the mass of biomolecules that associate noncovalently. Here we review the application of native MS to the study of protein-ligand interactions and its emerging role in elucidating the structure of macromolecular assemblies, including soluble and membrane protein complexes. Moreover, we discuss strategies aimed at determining the stoichiometry and topology of subunits by inducing partial dissociation of the holo-complex. We also survey recent developments in "native top-down MS", an approach based on Fourier Transform MS, whereby covalent bonds are broken without disrupting non-covalent interactions. Given recent progress, native MS is anticipated to play an increasingly important role for researchers interested in the structure of macromolecular complexes.
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Affiliation(s)
- Elisabetta Boeri Erba
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
| | - Carlo Petosa
- Université Grenoble Alpes, Institut de Biologie Structurale (IBS), 71 Avenue des Martyrs, F-38044, Grenoble, France.,Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), DSV, IBS, F-38044, Grenoble, France.,Centre National de la Recherche Scientifique (CNRS), IBS, F-38044, Grenoble, France
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17
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Wang D, Wynne C, Gu F, Becker C, Zhao J, Mueller HM, Li H, Shameem M, Liu YH. Characterization of Drug-Product-Related Impurities and Variants of a Therapeutic Monoclonal Antibody by Higher Energy C-Trap Dissociation Mass Spectrometry. Anal Chem 2015; 87:914-21. [DOI: 10.1021/ac503158g] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Deyun Wang
- Eurofins-Lancaster Laboratories Inc., 2425
New Holland Pike, Lancaster, Pennsylvania 17601, United States
| | - Colin Wynne
- Eurofins-Lancaster Laboratories Inc., 2425
New Holland Pike, Lancaster, Pennsylvania 17601, United States
| | - Flora Gu
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Chris Becker
- Protein Metrics Inc., 1622 San
Carlos Avenue, Suite C, San Carlos, California 94070, United States
| | - Jia Zhao
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Hans-Martin Mueller
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Huijuan Li
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Mohammed Shameem
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
| | - Yan-Hui Liu
- Protein
Mass Spectrometry, Sterile Product and Analytical Development, Bioprocess
Development, Merck Research Laboratories, 2000 Galloping Hill Road, Kenilworth, New Jersey 07033, United States
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18
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Boeri Erba E. Investigating macromolecular complexes using top-down mass spectrometry. Proteomics 2014; 14:1259-70. [PMID: 24723549 DOI: 10.1002/pmic.201300333] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2013] [Revised: 04/03/2014] [Accepted: 04/08/2014] [Indexed: 12/25/2022]
Abstract
MS has emerged as an important tool to investigate noncovalent interactions between proteins and various ligands (e.g. other proteins, small molecules, or drugs). In particular, ESI under so-called "native conditions" (a.k.a. "native MS") has considerably expanded the scope of such investigations. For instance, ESI quadrupole time of flight (Q-TOF) instruments have been used to probe the precise stoichiometry of protein assemblies, the interactions between subunits and the position of subunits within the complex (i.e. defining core and peripheral subunits). This review highlights several illustrative native Q-TOF-based investigations and recent seminal contributions of top-down MS (i.e. Fourier transform (FT) MS) to the characterization of noncovalent complexes. Combined top-down and native MS, recently demonstrated in "high-mass modified" orbitrap mass spectrometers, and further improvements needed for the enhanced investigation of biologically significant noncovalent interactions by MS will be discussed.
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Affiliation(s)
- Elisabetta Boeri Erba
- Institute of Structural Biology (Institut de Biologie Structurale), Centre National de la Recherche Scientifique (CNRS), University of Grenoble Alpes (Université de Grenoble Alpes), Commissariat à l'Énergie Atomique et aux Énergies Alternatives (CEA), DSV, Grenoble, France
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19
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Lakshmanan R, Wolff JJ, Alvarado R, Loo JA. Top-down protein identification of proteasome proteins with nanoLC-FT-ICR-MS employing data-independent fragmentation methods. Proteomics 2014; 14:1271-82. [PMID: 24478249 DOI: 10.1002/pmic.201300339] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Revised: 11/24/2013] [Accepted: 11/27/2013] [Indexed: 11/10/2022]
Abstract
A comparison of different data-independent fragmentation methods combined with LC coupled to high-resolution FT-ICR-MS/MS is presented for top-down MS of protein mixtures. Proteins composing the 20S and 19S proteasome complexes and their PTMs were identified using a 15 T FT-ICR mass spectrometer. The data-independent fragmentation modes with LC timescales allowed for higher duty-cycle measurements that better suit online LC-FT-ICR-MS. Protein top-down dissociation was effected by funnel-skimmer collisionally activated dissociation (FS-CAD) and CASI (continuous accumulation of selected ions)-CAD. The N-termini for 9 of the 14 20S proteasome proteins were found to be modified, and the α3 protein was found to be phosphorylated; these results are consistent with previous reports. Mass-measurement accuracy with the LC-FT-ICR system for the 20- to 30-kDa 20S proteasome proteins was 1 ppm. The intact mass of the 100-kDa Rpn1 subunit from the 19S proteasome complex regulatory particle was measured with a deviation of 17 ppm. The CASI-CAD technique is a complementary tool for intact-protein fragmentation and is an effective addition to the growing inventory of dissociation methods that are compatible with online protein separation coupled to FT-ICR-MS.
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Affiliation(s)
- Rajeswari Lakshmanan
- Department of Chemistry and Biochemistry, Molecular Biology Institute, University of California-Los Angeles, Los Angeles, CA, USA
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20
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Reinmuth-Selzle K, Ackaert C, Kampf CJ, Samonig M, Shiraiwa M, Kofler S, Yang H, Gadermaier G, Brandstetter H, Huber CG, Duschl A, Oostingh GJ, Pöschl U. Nitration of the birch pollen allergen Bet v 1.0101: efficiency and site-selectivity of liquid and gaseous nitrating agents. J Proteome Res 2014; 13:1570-7. [PMID: 24517313 PMCID: PMC3950889 DOI: 10.1021/pr401078h] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
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Nitration
of the major birch pollen allergen Bet v 1 alters the
immune responses toward this protein, but the underlying chemical
mechanisms are not yet understood. Here we address the efficiency
and site-selectivity of the nitration reaction of recombinant protein
samples of Bet v 1.0101 with different nitrating agents relevant for
laboratory investigations (tetranitromethane, TNM), for physiological
processes (peroxynitrite, ONOO–), and for the health
effects of environmental pollutants (nitrogen dioxide and ozone, O3/NO2). We determined the total tyrosine nitration
degrees (ND) and the NDs of individual tyrosine residues (NDY). High-performance liquid chromatography coupled to diode array
detection and HPLC coupled to high-resolution mass spectrometry analysis
of intact proteins, HPLC coupled to tandem mass spectrometry analysis
of tryptic peptides, and amino acid analysis of hydrolyzed samples
were performed. The preferred reaction sites were tyrosine residues
at the following positions in the polypeptide chain: Y83 and Y81 for
TNM, Y150 for ONOO–, and Y83 and Y158 for O3/NO2. The tyrosine residues Y83 and Y81 are located
in a hydrophobic cavity, while Y150 and Y158 are located in solvent-accessible
and flexible structures of the C-terminal region. The heterogeneous
reaction with O3/NO2 was found to be strongly
dependent on the phase state of the protein. Nitration rates were
about one order of magnitude higher for aqueous protein solutions
(∼20% per day) than for protein filter samples (∼2%
per day). Overall, our findings show that the kinetics and site-selectivity
of nitration strongly depend on the nitrating agent and reaction conditions,
which may also affect the biological function and adverse health effects
of the nitrated protein.
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Affiliation(s)
- Kathrin Reinmuth-Selzle
- Multiphase Chemistry and Biogeochemistry Departments, Max Planck Institute for Chemistry , Hahn-Meitner Weg 1, 55128 Mainz, Germany
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21
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Efficient separations of intact proteins using slip-flow with nano-liquid chromatography-mass spectrometry. Anal Chem 2014; 86:1592-8. [PMID: 24383398 PMCID: PMC3982985 DOI: 10.1021/ac403233d] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
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A capillary with a pulled tip, densely
packed with silica particles
of 0.47 μm in diameter, is shown to provide higher peak capacity
and sensitivity in the separation of intact proteins by reversed-phase
liquid chromatography–mass spectrometry (LC–MS). For
a C18 bonded phase, slip flow gave a 10-fold flow enhancement to allow
for stable nanospray with a 4-cm column length. Model proteins were
studied: ribonuclease A, trypsin inhibitor, and carbonic anhydrase,
where the latter had impurities of superoxide dismutase and ubiquitin.
The proteins were well separated at room temperature with negligible
peak tailing. The peak capacity for ubiquitin was 195 for a 10-min
gradient and 315 for a 40-min gradient based on Gaussian fitting of
the entire peak, rather than extrapolating the full-width at half-maximum.
Separation of a cell lysate with a 60 min gradient showed extremely
high peak capacities of 750 and above for a peptide and relatively
homogeneous proteins. Clean, low noise mass spectra for each model
protein were obtained. The physical widths of the peaks were an order
of magnitude narrower than those of conventional columns, giving increased
sensitivity. All proteins except ubiquitin exhibited significant heterogeneity
apparently due to multiple proteoforms, as indicated by both peak
shapes and mass spectra. The chromatograms exhibited excellent reproducibility
in retention time, with relative standard deviations of 0.09 to 0.34%.
The results indicate that submicrometer particles are promising for
improving the separation dimension of LC in top-down proteomics.
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22
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On-line solid phase extraction–liquid chromatography, with emphasis on modern bioanalysis and miniaturized systems. J Pharm Biomed Anal 2014; 87:120-9. [DOI: 10.1016/j.jpba.2013.05.006] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2013] [Revised: 05/06/2013] [Accepted: 05/07/2013] [Indexed: 11/24/2022]
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23
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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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24
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Acevedo N, Mohr J, Zakzuk J, Samonig M, Briza P, Erler A, Pomés A, Huber CG, Ferreira F, Caraballo L. Proteomic and immunochemical characterization of glutathione transferase as a new allergen of the nematode Ascaris lumbricoides. PLoS One 2013; 8:e78353. [PMID: 24223794 PMCID: PMC3817249 DOI: 10.1371/journal.pone.0078353] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 09/20/2013] [Indexed: 12/04/2022] Open
Abstract
Helminth infections and allergy have evolutionary and clinical links. Infection with the nematode Ascaris lumbricoides induces IgE against several molecules including invertebrate pan-allergens. These antibodies influence the pathogenesis and diagnosis of allergy; therefore, studying parasitic and non-parasitic allergens is essential to understand both helminth immunity and allergy. Glutathione transferases (GSTs) from cockroach and house dust mites are clinically relevant allergens and comparative studies between them and the GST from A. lumbricoides (GSTA) are necessary to evaluate their allergenicity. We sought to analyze the allergenic potential of GSTA in connection with the IgE response to non-parasitic GSTs. IgE to purified GSTs from Ascaris (nGSTA and rGSTA), house dust mites (rDer p 8, nBlo t 8 and rBlo t 8), and cockroach (rBla g 5) was measured by ELISA in subjects from Cartagena, Colombia. Also, multidimensional proteomic approaches were used to study the extract of A. lumbricoides and investigate the existence of GST isoforms. We found that among asthmatics, the strength of IgE levels to GSTA was significantly higher than to mite and cockroach GSTs, and there was a strong positive correlation between IgE levels to these molecules. Specific IgE to GSTA was found in 13.2% of controls and 19.5% of asthmatics. In addition nGSTA induced wheal and flare in skin of sensitized asthmatics indicating that it might be of clinical relevance for some patients. Frequency and IgE levels to GSTA were higher in childhood and declined with age. At least six GST isoforms in A. lumbricoides bind human IgE. Four isoforms were the most abundant and several amino acid substitutions were found, mainly on the N-terminal domain. In conclusion, a new allergenic component of Ascaris has been discovered; it could have clinical impact in allergic patients and influence the diagnosis of mite and cockroach allergy in tropical environments.
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Affiliation(s)
- Nathalie Acevedo
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
- Foundation for the Development of Medical and Biological Sciences, Cartagena, Colombia
| | - Jens Mohr
- Department of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Salzburg, Austria
| | - Josefina Zakzuk
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
- Foundation for the Development of Medical and Biological Sciences, Cartagena, Colombia
| | - Martin Samonig
- Department of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Salzburg, Austria
| | - Peter Briza
- Department of Molecular Biology, Division of Allergy and Immunology, University of Salzburg, Salzburg, Austria
| | - Anja Erler
- Department of Molecular Biology, Division of Allergy and Immunology, University of Salzburg, Salzburg, Austria
| | - Anna Pomés
- Indoor Biotechnologies Inc., Charlottesville, Virginia, United States of America
| | - Christian G. Huber
- Department of Molecular Biology, Division of Chemistry and Bioanalytics, University of Salzburg, Salzburg, Austria
| | - Fatima Ferreira
- Department of Molecular Biology, Division of Allergy and Immunology, University of Salzburg, Salzburg, Austria
| | - Luis Caraballo
- Institute for Immunological Research, University of Cartagena, Cartagena, Colombia
- Foundation for the Development of Medical and Biological Sciences, Cartagena, Colombia
- * E-mail:
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25
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Separation of intact proteins by using polyhedral oligomeric silsesquioxane based hybrid monolithic capillary columns. J Chromatogr A 2013; 1317:138-47. [DOI: 10.1016/j.chroma.2013.09.004] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2013] [Revised: 09/02/2013] [Accepted: 09/02/2013] [Indexed: 12/22/2022]
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26
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Schey KL, Anderson DM, Rose KL. Spatially-directed protein identification from tissue sections by top-down LC-MS/MS with electron transfer dissociation. Anal Chem 2013; 85:6767-74. [PMID: 23718750 DOI: 10.1021/ac400832w] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
MALDI imaging mass spectrometry (MALDI-IMS) has become a powerful tool for localizing both small molecules and intact proteins in a wide variety of tissue samples in both normal and diseased states. Identification of imaged signals in MALDI-IMS remains a bottleneck in the analysis and limits the interpretation of underlying biology of tissue specimens. In this work, spatially directed tissue microextraction of intact proteins followed by LC-MS/MS with electron transfer dissociation (ETD) was used to identify proteins from specific locations in three tissue types; ocular lens, brain, and kidney. Detection limits were such that a 1 μL extraction volume was sufficient to deliver proteins to the LC-MS/MS instrumentation with sufficient sensitivity to detect 50-100 proteins in a single experiment. Additionally, multiple modified proteins were identified; including truncated lens proteins that would be difficult to assign to an imaged mass using a bottom-up approach. Protein separation and identification are expected to improve with advances in intact protein fractionation/chromatography and advances in interpretation algorithms leading to increased depth of proteome coverage from distinct tissue locations.
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Affiliation(s)
- Kevin L Schey
- Department of Biochemistry and Mass Spectrometry Research Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232, USA.
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27
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Mao Y, Valeja SG, Rouse JC, Hendrickson CL, Marshall AG. Top-Down Structural Analysis of an Intact Monoclonal Antibody by Electron Capture Dissociation-Fourier Transform Ion Cyclotron Resonance-Mass Spectrometry. Anal Chem 2013; 85:4239-46. [DOI: 10.1021/ac303525n] [Citation(s) in RCA: 92] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Yuan Mao
- Department of Chemistry
and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32303, United States
| | - Santosh G. Valeja
- Department of Chemistry
and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32303, United States
| | - Jason C. Rouse
- Analytical Research & Development, BioTherapeutics Pharmaceutical Sciences, Pfizer, Inc., One Burtt Road, Andover, Massachusetts 01810, United States
| | - Christopher L. Hendrickson
- Department of Chemistry
and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32303, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive,
Tallahassee Florida 32310-4005, United States
| | - Alan G. Marshall
- Department of Chemistry
and Biochemistry, Florida State University, 95 Chieftain Way, Tallahassee, Florida 32303, United States
- National High Magnetic Field Laboratory, Florida State University, 1800 East Paul Dirac Drive,
Tallahassee Florida 32310-4005, United States
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28
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Pioch M, Bunz SC, Neusüss C. Capillary electrophoresis/mass spectrometry relevant to pharmaceutical and biotechnological applications. Electrophoresis 2012; 33:1517-30. [PMID: 22736352 DOI: 10.1002/elps.201200030] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Advanced analytical techniques play a crucial role in the pharmaceutical and biotechnological field. In this context, capillary electrophoresis/mass spectrometry (CE/MS) has attracted attention due to efficient and selective separation in combination with powerful detection allowing identification and detailed characterization. Method developments and applications of CE/MS have been focused on questions not easily accessible by liquid chromatography/mass spectrometry (LC/MS) as the analysis of intact proteins, carbohydrates, and various small molecules, including peptides. Here, recent approaches and applications of CE/MS relevant to (bio)pharmaceuticals are reviewed and discussed to show actual developments and future prospects. Based on other reviews on related subjects covering large parts of previous works, the paper is focused on general ideas and contributions of the last 2 years; for the analysis of glycans, the period is extended back to 2006.
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Affiliation(s)
- Markus Pioch
- Chemistry Department, Aalen University, Aalen, Germany
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29
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Taichrib A, Pioch M, Neusüß C. Toward a screening method for the analysis of small intact proteins by CE-ESI-TOF MS. Electrophoresis 2012; 33:1356-66. [DOI: 10.1002/elps.201100620] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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30
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Perfusion reversed-phase high-performance liquid chromatography for protein separation from detergent-containing solutions: An alternative to gel-based approaches. Anal Biochem 2012; 424:97-107. [DOI: 10.1016/j.ab.2012.02.021] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2011] [Revised: 02/15/2012] [Accepted: 02/16/2012] [Indexed: 11/19/2022]
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31
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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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32
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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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33
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Roth MJ, Plymire DA, Chang AN, Kim J, Maresh EM, Larson SE, Patrie SM. Sensitive and Reproducible Intact Mass Analysis of Complex Protein Mixtures with Superficially Porous Capillary Reversed-Phase Liquid Chromatography Mass Spectrometry. Anal Chem 2011; 83:9586-92. [DOI: 10.1021/ac202339x] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Michael J. Roth
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
| | - Daniel A. Plymire
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
| | - Audrey N. Chang
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
| | - Jaekuk Kim
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
| | - Erica M. Maresh
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
| | - Shane E. Larson
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
| | - Steven M. Patrie
- UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-9185, United States
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34
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High-resolution separations of protein isoforms with liquid chromatography time-of-flight mass spectrometry using polymer monolithic capillary columns. J Chromatogr A 2011; 1218:5504-11. [DOI: 10.1016/j.chroma.2011.06.049] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2011] [Revised: 05/16/2011] [Accepted: 06/10/2011] [Indexed: 11/22/2022]
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35
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Moore JB, Weeks ME. Proteomics and systems biology: current and future applications in the nutritional sciences. Adv Nutr 2011; 2:355-64. [PMID: 22332076 PMCID: PMC3125684 DOI: 10.3945/an.111.000554] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
In the last decade, advances in genomics, proteomics, and metabolomics have yielded large-scale datasets that have driven an interest in global analyses, with the objective of understanding biological systems as a whole. Systems biology integrates computational modeling and experimental biology to predict and characterize the dynamic properties of biological systems, which are viewed as complex signaling networks. Whereas the systems analysis of disease-perturbed networks holds promise for identification of drug targets for therapy, equally the identified critical network nodes may be targeted through nutritional intervention in either a preventative or therapeutic fashion. As such, in the context of the nutritional sciences, it is envisioned that systems analysis of normal and nutrient-perturbed signaling networks in combination with knowledge of underlying genetic polymorphisms will lead to a future in which the health of individuals will be improved through predictive and preventative nutrition. Although high-throughput transcriptomic microarray data were initially most readily available and amenable to systems analysis, recent technological and methodological advances in MS have contributed to a linear increase in proteomic investigations. It is now commonplace for combined proteomic technologies to generate complex, multi-faceted datasets, and these will be the keystone of future systems biology research. This review will define systems biology, outline current proteomic methodologies, highlight successful applications of proteomics in nutrition research, and discuss the challenges for future applications of systems biology approaches in the nutritional sciences.
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Affiliation(s)
- J. Bernadette Moore
- Nutritional Sciences Division, Faculty of Health and Medical Sciences, University of Surrey, Guildford, Surrey, GU2 7XH, UK,To whom correspondence should be addressed. E-mail:
| | - Mark E. Weeks
- Veterinary Laboratories Agency, New Haw, KT15 3NB, UK
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36
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Capriotti AL, Cavaliere C, Foglia P, Samperi R, Laganà A. Intact protein separation by chromatographic and/or electrophoretic techniques for top-down proteomics. J Chromatogr A 2011; 1218:8760-76. [PMID: 21689823 DOI: 10.1016/j.chroma.2011.05.094] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/13/2011] [Accepted: 05/28/2011] [Indexed: 12/26/2022]
Abstract
Mass spectrometry used in combination with a wide variety of separation methods is the principal methodology for proteomics. In bottom-up approach, proteins are cleaved with a specific proteolytic enzyme, followed by peptide separation and MS identification. In top-down approach intact proteins are introduced into the mass spectrometer. The ions generated by electrospray ionization are then subjected to gas-phase separation, fragmentation, fragment separation, and automated interpretation of mass spectrometric and chromatographic data yielding both the molecular weight of the intact protein and the protein fragmentation pattern. This approach requires high accuracy mass measurement analysers capable of separating the multi-charged isotopic cluster of proteins, such as hybrid ion trap-Fourier transform instruments (LTQ-FTICR, LTQ-Orbitrap). Front-end separation technologies tailored for proteins are of primary importance to implement top-down proteomics. This review intends to provide the state of art of protein chromatographic and electrophoretic separation methods suitable for MS coupling, and to illustrate both monodimensional and multidimensional approaches used for LC-MS top-down proteomics. In addition, some recent progresses in protein chromatography that may provide an alternative to those currently employed are also discussed.
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Affiliation(s)
- Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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37
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Tipton JD, Tran JC, Catherman AD, Ahlf DR, Durbin KR, Kelleher NL. Analysis of intact protein isoforms by mass spectrometry. J Biol Chem 2011; 286:25451-8. [PMID: 21632550 DOI: 10.1074/jbc.r111.239442] [Citation(s) in RCA: 84] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The diverse proteome of an organism arises from such events as single nucleotide substitutions at the DNA level, different RNA processing, and dynamic enzymatic post-translational modifications. This minireview focuses on the measurement of intact proteins to describe the diversity found in proteomes. The field of biological mass spectrometry has steadily advanced, enabling improvements in the characterization of single proteins to proteins derived from cells or tissues. In this minireview, we discuss the basic technology for "top-down" intact protein analysis. Furthermore, examples of studies involved with the qualitative and quantitative analysis of full-length polypeptides are provided.
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Affiliation(s)
- Jeremiah D Tipton
- Departmen of Chemistry, Northwestern University, Evanston, Illinois 60208, USA
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Ning Z, Zhou H, Wang F, Abu-Farha M, Figeys D. Analytical Aspects of Proteomics: 2009–2010. Anal Chem 2011; 83:4407-26. [DOI: 10.1021/ac200857t] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
| | - Hu Zhou
- Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai, China 201203
| | - Fangjun Wang
- Key Lab of Separation Sciences for Analytical Chemistry, National Chromatographic Research and Analysis Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China 116023
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Protein- versus peptide fractionation in the first dimension of two-dimensional high-performance liquid chromatography-matrix-assisted laser desorption/ionization tandem mass spectrometry for qualitative proteome analysis of tissue samples. J Chromatogr A 2010; 1217:6159-68. [PMID: 20810122 DOI: 10.1016/j.chroma.2010.07.044] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Revised: 07/08/2010] [Accepted: 07/14/2010] [Indexed: 11/21/2022]
Abstract
The availability of robust and highly efficient separation methods represents a major requirement for proteome analysis. This study investigated the characteristics of two different gel-free proteomic approaches to the fractionation of proteolytic peptides and intact proteins, respectively, in a first separation dimension. Separation and mass spectrometric detection by matrix-assisted laser desorption/ionization tandem mass spectrometry (MALDI-MS/MS) were performed at the peptide level in both methods. Bottom-up analysis (BU) was carried out employing well established peptide fractionation in the first separation dimension by strong cation-exchange chromatography (SCX), followed by ion-pair reversed-phase chromatography (IP-RPC) in the second dimension. In the semi-top-down approach (STD), which involved intact protein fractionation in the first dimension, the separation mode in both dimensions was IP-RPC utilizing monolithic columns. Application of the two approaches to the proteome analysis of proteins extracted from a tumor tissue revealed that the BU method identified more proteins (1245 in BU versus 920 in STD) while STD analysis offered higher sequence coverage (14.8% in BU versus 17.5% in STD on average). The identification of more basic and larger proteins was slightly favored in the BU approach, most probably due to higher losses of these proteins during intact protein handling and separation in the STD method. A significant degree of complementarity was revealed by an approximately 33% overlap between one BU and STD replicate, while 33% each of the protein identifications were unique to both methods. In the STD method, peptides obtained upon digestion of the proteins contained in fractions of the first separation dimension covered a broad elution window in the second-dimension separation, which demonstrates a high degree of "pseudo-orthogonality" of protein and peptide separation by IP-RPC in both separation dimensions.
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