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Obi N, Fukuda T, Nakayama N, Ervin J, Bando Y, Nishimura T, Nagatoishi S, Tsumoto K, Kawamura T. Development of drug discovery screening system by molecular interaction kinetics-mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2018; 32:665-671. [PMID: 29441684 DOI: 10.1002/rcm.8083] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 02/01/2018] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
RATIONALE Drug discovery studies invariably require qualitative and quantitative analyses of target compounds at every stage of drug discovery. We have developed a system combining molecular interaction analysis and mass spectrometry (LC-MS) using the principle of nanopore optical interferometry (nPOI) called molecular interaction kinetics-mass spectrometry (MIK-MS). Since nPOI has high binding capacity, the bond-dissociated compound can be directly detected using LC-MS. In this study, we use carbonic anhydrase II (CAII) as a ligand and apply six small compounds as analytes and report the affinity analysis using MIK-MS. METHODS CAII was immobilized onto a COOH sensor chip using standard amine coupling. A reference surface was prepared by activating and subsequently blocking the surface under identical conditions. An amount of 50 μL of mix solution was injected over the reference channel and sample channel for CAII immobilization. The solutions eluting from the sensor chip were collected from the waste-line of the SKi Pro system every 30 s. Reconstructed elution samples were then injected into the LC-MS/MS system. RESULTS A mixture containing furosemide, acetazolamide, 4-sulfamoylbenzoic acid, 5-(dimethylamino)-1-naphthalene sulfonamide (DNSA), sulfanilamide and sulpiride (15 μM each) was injected into the CAII-immobilized sensor chip, and the fractions eluted from the SKi Pro system were collected and subjected to selected reaction monitoring LC-MS characterization. Specific results were obtained for acetazolamide, DNSA, furosemide and sulpiride. The results suggest that the association-dissociation curve of a mixed sample can be obtained by one-time MIK-MS analysis. CONCLUSIONS Six small-molecule binders of CAII were analyzed quantitatively using nPOI and MIK-MS, and the results were compared to published surface plasmon resonance (SPR) results. The nPOI and SPR results show good agreement, confirming the reliability of the analysis. Time-dependent binding results may be obtained by our MS sensorgram approach. Drugs that meet medical needs in a short period are required; this nPOI-LC-MS system is considered an important tool for rapid drug discovery.
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Affiliation(s)
| | | | - Noboru Nakayama
- Biosys Technologies Inc., Tokyo, Japan
- Translational Medicine Informatics, St Marianna University School of Medicine, Research & Development, Biosys Technologies Inc., Tokyo, Japan
| | - John Ervin
- Silicon Kinetics Inc., San Diego, CA, USA
| | | | - Toshihide Nishimura
- Biosys Technologies Inc., Tokyo, Japan
- Translational Medicine Informatics, St Marianna University School of Medicine, Research & Development, Biosys Technologies Inc., Tokyo, Japan
| | | | - Kouhei Tsumoto
- School of Engineering, The University of Tokyo, Tokyo, Japan
| | - Takeshi Kawamura
- Proteomics Laboratory, Isotope Science Center, The University of Tokyo, Tokyo, Japan
- Laboratories for Systems Biology and Medicine (LSBM), Research Center for Advanced Science and Technology (RCAST), The University of Tokyo, Tokyo, Japan
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Anders U, Schaefer JV, Hibti FE, Frydman C, Suckau D, Plückthun A, Zenobi R. SPRi-MALDI MS: characterization and identification of a kinase from cell lysate by specific interaction with different designed ankyrin repeat proteins. Anal Bioanal Chem 2016; 409:1827-1836. [DOI: 10.1007/s00216-016-0127-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2016] [Revised: 11/22/2016] [Accepted: 11/29/2016] [Indexed: 01/24/2023]
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3
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Ahmed FE. Mining the oncoproteome and studying molecular interactions for biomarker development by 2DE, ChIP and SPR technologies. Expert Rev Proteomics 2014; 5:469-96. [DOI: 10.1586/14789450.5.3.469] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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4
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Ivanov AS, Ershov PV, Poverennaya EV, Lisitsa AV, Archakov AI. [Protocols of proteins interactomics: molecular fishing on optical chips and magnetic nanoparticles]. BIOMEDITSINSKAIA KHIMIIA 2013; 59:171-182. [PMID: 23789344 DOI: 10.18097/pbmc20135902171] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Now it is absolutely clear, that the majority of proteins in living systems function due to interaction with each other in stable or dynamic proteins complexes. Therefore necessity of deeper studies of proteins functions causes expansion of protein-protein interaction research. In the present review the brief description and comparative estimation of experimental methods and protocols of protein interactomics, based on technology of molecular fishing on an optical chips and paramagnetic nanoparticles is given.
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5
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Immuno-MALDI-MS in human plasma and on-chip biomarker characterizations at the femtomole level. SENSORS 2012. [PMID: 23202203 PMCID: PMC3522956 DOI: 10.3390/s121115119] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Immuno-SPR-MS is the combination of immuno-sensors in biochip format with mass spectrometry. This association of instrumentation allows the detection and the quantification of proteins of interest by SPR and their molecular characterization by additional MS analysis. However, two major bottlenecks must be overcome for a wide diffusion of the SPR-MS analytical platform: (i) To warrant all the potentialities of MS, an enzymatic digestion step must be developed taking into account the spot formats on the biochip and (ii) the biological relevancy of such an analytical solution requires that biosensing must be performed in complex media. In this study, we developed a procedure for the detection and the characterization at ∼1 μg/mL of the LAG3 protein spiked in human plasma. The analytical performances of this new method was established, particularly its specificity (S/N > 9) and sensitivity (100% of LAG3 identification with high significant mascot score >68 at the femtomole level). The collective and automated on-chip MALDI-MS imaging and analysis based on peptidic fragments opens numerous applications in the fields of proteomics and diagnosis.
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6
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Ershov P, Mezentsev Y, Gnedenko O, Mukha D, Yantsevich A, Britikov V, Kaluzhskiy L, Yablokov E, Molnar A, Ivanov A, Lisitsa A, Gilep A, Usanov S, Archakov A. Protein interactomics based on direct molecular fishing on paramagnetic particles: experimental simulation and SPR validation. Proteomics 2012; 12:3295-8. [PMID: 23001861 DOI: 10.1002/pmic.201200135] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2012] [Revised: 07/04/2012] [Accepted: 08/14/2012] [Indexed: 11/10/2022]
Abstract
We describe an experimental approach for direct molecular fishing of prey protein on the surface of two types of paramagnetic particles (PMP) having different size and composition. Human microsomal cytochrome b(5) (b(5)) and its known partner human cytochrome P450 3A5 (CYP3A5) were used as bait and prey proteins, respectively. For assessing the level of unspecific binding of background proteins, α-fetoprotein (aFP) was used. SPR measurements were applied for quantitative analysis of trapped proteins (CYP3A5 and aFP) after fishing on PMP. It was shown that the described approach of molecular fishing on micro-PMP provides enough prey proteins for LC-MS/MS identification and SPR validation, so this approach can be used for discovery of new protein-protein interactions in the framework of Human Proteome Project.
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Affiliation(s)
- Pavel Ershov
- Orechovich Institute of Biomedical Chemistry of RAMS, Moscow, Russia
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7
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Surface plasmon resonance imaging in arrays coupled with mass spectrometry (SUPRA–MS): proof of concept of on-chip characterization of a potential breast cancer marker in human plasma. Anal Bioanal Chem 2012; 404:423-32. [DOI: 10.1007/s00216-012-6130-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 05/19/2012] [Accepted: 05/20/2012] [Indexed: 01/20/2023]
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8
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Ivanov AS, Ershov PV, Mezentsev YV, Poverennaya EV, Lisitsa AV, Archakov AI. Protocols of protein interactomics: Molecular fishing on optical chips and magnetic nanoparticles. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2012. [DOI: 10.1134/s1990750812020072] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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9
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Abstract
Surface plasmon resonance (SPR) is a well-established label-free technique to detect mass changes near an SPR surface. For 20 years the benefits of SPR have been proven in biomolecular interaction analysis, including measurements of affinity and kinetics. The emergence of proteomics and a need for high throughput analysis drives the development of SPR systems capable of analyzing microarrays. The use of SPR imaging (also known as SPR microscopy) makes it possible to use multiplexed arrays to follow binding reactions. As SPR only analyzes the binding process, but not the identity of captured molecules on the SPR surface, technologies have been developed to integrate SPR with mass spectrometric (MS) analysis. Such approaches involve the recovery of analytes from the SPR surface and subsequent MALDI-TOF MS analysis, or LC-MS/MS after tryptic digestion of recovered proteins. An approach compatible with SPR arrays is on-chip MALDI-TOF MS, from arrayed spots on an SPR surface. This review describes some exciting developments in the application of SPR to proteomics, using instruments which are on the market already, or are expected to be available in the years to come.
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Affiliation(s)
- Nico J de Mol
- Department of Pharmaceutical Sciences, Utrecht University, Utrecht, The Netherlands.
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10
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Madeira A, Vikeved E, Nilsson A, Sjögren B, Andrén PE, Svenningsson P. Identification of protein-protein interactions by surface plasmon resonance followed by mass spectrometry. CURRENT PROTOCOLS IN PROTEIN SCIENCE 2011; Chapter 19:Unit19.21. [PMID: 21842469 DOI: 10.1002/0471140864.ps1921s65] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Elucidation of the function and meaning of the protein networks can be useful in the understanding of many pathological processes and the identification of new therapeutic targets. This unit describes an approach to discover protein-protein interactions by coupling surface plasmon resonance to mass spectrometry. Briefly, a protein is covalently bound to a sensor chip, which is then exposed to brain extracts injected over the surface via a microfluidic system. This allows the monitoring in real-time of the interactions between the immobilized ligand and the extracts. Interacting proteins from the extracts are then recovered, trypsinized, and identified using mass spectrometry. The data obtained are searched against a sequence database using the Mascot software. To exclude nonspecific interactors, control experiments using blank sensor chips, and/or randomized peptides, are performed. The protocol presented here does not require specific labeling or modification of proteins and can be performed in <4 days.
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11
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Ivanov AS, Zgoda VG, Archakov AI. Technologies of protein interactomics: A review. RUSSIAN JOURNAL OF BIOORGANIC CHEMISTRY 2011; 37:8-21. [DOI: 10.1134/s1068162011010092] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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12
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Situ C, Mooney MH, Elliott CT, Buijs J. Advances in surface plasmon resonance biosensor technology towards high-throughput, food-safety analysis. Trends Analyt Chem 2010. [DOI: 10.1016/j.trac.2010.09.003] [Citation(s) in RCA: 134] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Xu Y, Takai M, Ishihara K. Phospholipid Polymer Biointerfaces for Lab-on-a-Chip Devices. Ann Biomed Eng 2010; 38:1938-53. [DOI: 10.1007/s10439-010-0025-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2009] [Accepted: 03/22/2010] [Indexed: 01/09/2023]
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14
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Borch J, Roepstorff P. SPR/MS: recovery from sensorchips for protein identification by MALDI-TOF mass spectrometry. Methods Mol Biol 2010; 627:269-281. [PMID: 20217629 DOI: 10.1007/978-1-60761-670-2_19] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Surface plasmon resonance is widely used to study binding interactions with proteins, potentially yielding information on kinetics, thermodynamics and active concentrations. However, the technology cannot identify the involved interaction partners. Mass spectrometry, on the other hand, can be used for specific identification of proteins in amounts comparable to the levels that can be captured on a Biacore SPR sensorchip. Here we present protocols for capturing, washing and eluting proteins from Biacore instruments as well as for robust sample preparation for sensitive mass spectrometric identification.
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Affiliation(s)
- Jonas Borch
- Institute for Biochemistry and Molecular Biology, University of Southern Denmark, Odense M, Denmark
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15
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Abstract
The combination of surface plasmon resonance (SPR) and mass spectrometry (MS) creates a comprehensive protein investigation approach wherein SPR is employed for protein quantification and MS is utilized to structurally characterize the proteins. In such, MS utterly complements the SPR detection and reveals intrinsic protein structural modifications that go unregistered via the SPR detection. Protein complexes and non-specific binding can also be delineated via the SPR-MS approach. Described here are the protocols and know-how for successful and reproducible integration of SPR and MS. The individual steps of the entire SPR-MS process are illustrated via an example showing analysis of myoglobin from human plasma.
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16
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Bellon S, Buchmann W, Gonnet F, Jarroux N, Anger-Leroy M, Guillonneau F, Daniel R. Hyphenation of Surface Plasmon Resonance Imaging to Matrix-Assisted Laser Desorption Ionization Mass Spectrometry by On-Chip Mass Spectrometry and Tandem Mass Spectrometry Analysis. Anal Chem 2009; 81:7695-702. [DOI: 10.1021/ac901140m] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- S. Bellon
- CNRS, UMR8587, Université d’Evry-Val-d’Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, 91025 Evry, France, Université d’Evry-Val-d’Essonne, Laboratoire Matériaux Polymères aux Interfaces, 91025 Evry, France, GENOPTICS Bio Interactions-HORIBA Scientific, 91401 Orsay, France, and Université Paris Descartes, Plate-Forme Protéomique Paris 5, 75014 Paris, France
| | - W. Buchmann
- CNRS, UMR8587, Université d’Evry-Val-d’Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, 91025 Evry, France, Université d’Evry-Val-d’Essonne, Laboratoire Matériaux Polymères aux Interfaces, 91025 Evry, France, GENOPTICS Bio Interactions-HORIBA Scientific, 91401 Orsay, France, and Université Paris Descartes, Plate-Forme Protéomique Paris 5, 75014 Paris, France
| | - F. Gonnet
- CNRS, UMR8587, Université d’Evry-Val-d’Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, 91025 Evry, France, Université d’Evry-Val-d’Essonne, Laboratoire Matériaux Polymères aux Interfaces, 91025 Evry, France, GENOPTICS Bio Interactions-HORIBA Scientific, 91401 Orsay, France, and Université Paris Descartes, Plate-Forme Protéomique Paris 5, 75014 Paris, France
| | - N. Jarroux
- CNRS, UMR8587, Université d’Evry-Val-d’Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, 91025 Evry, France, Université d’Evry-Val-d’Essonne, Laboratoire Matériaux Polymères aux Interfaces, 91025 Evry, France, GENOPTICS Bio Interactions-HORIBA Scientific, 91401 Orsay, France, and Université Paris Descartes, Plate-Forme Protéomique Paris 5, 75014 Paris, France
| | - M. Anger-Leroy
- CNRS, UMR8587, Université d’Evry-Val-d’Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, 91025 Evry, France, Université d’Evry-Val-d’Essonne, Laboratoire Matériaux Polymères aux Interfaces, 91025 Evry, France, GENOPTICS Bio Interactions-HORIBA Scientific, 91401 Orsay, France, and Université Paris Descartes, Plate-Forme Protéomique Paris 5, 75014 Paris, France
| | - F. Guillonneau
- CNRS, UMR8587, Université d’Evry-Val-d’Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, 91025 Evry, France, Université d’Evry-Val-d’Essonne, Laboratoire Matériaux Polymères aux Interfaces, 91025 Evry, France, GENOPTICS Bio Interactions-HORIBA Scientific, 91401 Orsay, France, and Université Paris Descartes, Plate-Forme Protéomique Paris 5, 75014 Paris, France
| | - R. Daniel
- CNRS, UMR8587, Université d’Evry-Val-d’Essonne, Laboratoire Analyse et Modélisation pour la Biologie et l’Environnement, 91025 Evry, France, Université d’Evry-Val-d’Essonne, Laboratoire Matériaux Polymères aux Interfaces, 91025 Evry, France, GENOPTICS Bio Interactions-HORIBA Scientific, 91401 Orsay, France, and Université Paris Descartes, Plate-Forme Protéomique Paris 5, 75014 Paris, France
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17
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Madeira A, Öhman E, Nilsson A, Sjögren B, Andrén PE, Svenningsson P. Coupling surface plasmon resonance to mass spectrometry to discover novel protein–protein interactions. Nat Protoc 2009; 4:1023-37. [DOI: 10.1038/nprot.2009.84] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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18
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Towards Surface Plasmon Resonance biosensing combined with bioaffinity-assisted nano HILIC Liquid Chromatography / Time-of-flight Mass Spectrometry identification of Paralytic Shellfish Poisons. Trends Analyt Chem 2009. [DOI: 10.1016/j.trac.2009.04.008] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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19
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Ravanat C, Wurtz V, Ohlmann P, Fichter M, Cazenave JP, VanDorsselaer A, Lanza F, Gachet C. Use of tandem Biacore–mass spectrometry to identify platelet membrane targets of novel monoclonal antibodies. Anal Biochem 2009; 386:237-43. [DOI: 10.1016/j.ab.2008.12.010] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2008] [Accepted: 12/09/2008] [Indexed: 11/29/2022]
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20
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Visser NFC, Heck AJR. Surface plasmon resonance mass spectrometry in proteomics. Expert Rev Proteomics 2008; 5:425-33. [PMID: 18532910 DOI: 10.1586/14789450.5.3.425] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Due to the enormous complexity of the proteome, focus in proteomics shifts more and more from the study of the complete proteome to the targeted analysis of part of the proteome. The isolation of this specific part of the proteome generally includes an affinity-based enrichment. Surface plasmon resonance (SPR), a label-free technique able to follow enrichment in real-time and in a semiquantitative manner, is an emerging tool for targeted affinity enrichment. Furthermore, in combination with mass spectrometry (MS), SPR can be used to both selectively enrich for and identify proteins from a complex sample. Here we illustrate the use of SPR-MS to solve proteomics-based research questions, describing applications that use very different types of immobilized components: such as small (drug or messenger) molecules, peptides, DNA and proteins. We evaluate the current possibilities and limitations and discuss the future developments of the SPR-MS technique.
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Affiliation(s)
- Natasja F C Visser
- Bijvoet Center for Biomolecular Research & Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands.
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21
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Boireau W, Rouleau A, Lucchi G, Ducoroy P. Revisited BIA-MS combination: entire "on-a-chip" processing leading to the proteins identification at low femtomole to sub-femtomole levels. Biosens Bioelectron 2008; 24:1121-7. [PMID: 18829299 DOI: 10.1016/j.bios.2008.06.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2008] [Revised: 06/13/2008] [Accepted: 06/16/2008] [Indexed: 10/21/2022]
Abstract
We present the results of a study in which biomolecular interaction analysis (BIA, Biacoretrade mark 2000) was combined with mass spectrometry (MS) using entire "on-a-chip" procedure. Most BIA-MS studies included an elution step of the analyte prior MS analysis. Here, we report a low-cost approach combining Biacore analysis with homemade chips and MS in situ identification onto the chips without elution step. First experiments have been made with rat serum albumin to determine the sensitivity and validation of the concept has been obtained with an antibody/antigen couple. Our "on-a-chip" procedure allowed complete analysis by MS/MS(2) of the biochip leading to protein identifications at low femtomole to sub-femtomole levels. Using this technique, identification of protein complexes were routinely obtained giving the opportunity to the "on-a-chip" processing to complete the BIA-MS approach in the discovery and analysis of protein complexes.
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Affiliation(s)
- W Boireau
- Institut FEMTO-ST, Université de Franche Comté, Clinical-Innovation Proteomic Platform, 32 Av de I'Observatoire, CNRS, 25044 Besançon, France
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22
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Combination of a SAW-biosensor with MALDI mass spectrometric analysis. Biosens Bioelectron 2008; 23:1496-502. [DOI: 10.1016/j.bios.2008.01.013] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2007] [Accepted: 01/03/2008] [Indexed: 11/21/2022]
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23
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Visser NFC, Scholten A, van den Heuvel RHH, Heck AJR. Surface-plasmon-resonance-based chemical proteomics: efficient specific extraction and semiquantitative identification of cyclic nucleotide-binding proteins from cellular lysates by using a combination of surface plasmon resonance, sequential elution and liquid chromatography-tandem mass spectrometry. Chembiochem 2008; 8:298-305. [PMID: 17206730 DOI: 10.1002/cbic.200600449] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Chemical proteomics is a powerful methodology for identifying the cellular targets of small molecules, however, it is biased towards abundant proteins. Therefore, quantitative strategies are needed to distinguish between specific and nonspecific interactions. Here, we explore the potential of the combination of surface plasmon resonance (SPR) coupled to liquid chromatography-tandem mass spectrometry (LC-MS/MS) as an alternative approach in chemical proteomics. We coupled cGMP molecules to the SPR chip, and monitored the binding and dissociation of proteins from a human lysate by using sequential elution steps and SPR. The eluted proteins were subsequently identified by LC-MS/MS. Our approach enabled the efficient and selective extraction of low-abundant cyclic-nucleotide-binding proteins such as cGMP-dependent protein kinase, and a quantitative assessment of the less- and nonspecific competitive binding proteins. The data show that SPR-based chemical proteomics is a promising alternative for the efficient specific extraction and quantitative identification of small-molecule-binding proteins from complex mixtures.
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Affiliation(s)
- Natasja F C Visser
- Department of Biomolecular Mass Spectrometry, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Sorbonnelaan 16, 3584 CA Utrecht, The Netherlands
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24
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Nice EC, Rothacker J, Weinstock J, Lim L, Catimel B. Use of multidimensional separation protocols for the purification of trace components in complex biological samples for proteomics analysis. J Chromatogr A 2007; 1168:190-210; discussion 189. [PMID: 17597136 DOI: 10.1016/j.chroma.2007.06.015] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2007] [Revised: 06/06/2007] [Accepted: 06/07/2007] [Indexed: 01/09/2023]
Abstract
The routine detection of low abundance components in complex samples for detailed proteomics analysis continues to be a challenge. Whilst the potential of multidimensional chromatographic fractionation for this purpose has been proposed for some years, and was used effectively for the purification to homogeneity of trace components in bulk biological samples for N-terminal sequence analysis, its practical application in the proteomics arena is still limited. This article reviews some of the recent data using these approaches, including the use of microaffinity purification as part of multidimensional protocols for downstream proteomics analysis.
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Affiliation(s)
- E C Nice
- Protein Biosensing and Epithelial Laboratories, Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, P.O. Royal Melbourne Hospital, Parkville, Vic. 3050, Australia.
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Gloerich J, Wevers RA, Smeitink JAM, van Engelen BG, van den Heuvel LP. Proteomics approaches to study genetic and metabolic disorders. J Proteome Res 2007; 6:506-12. [PMID: 17269707 DOI: 10.1021/pr060487w] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Several proteomics approaches to study different aspects of genetic and metabolic diseases are presented. The choice of technique is strongly dependent on the biological question to be addressed and the availability and amount of sample. In general, there are three approaches that may be used to study genetic and metabolic diseases: protein profiling of complex biological samples, identification of affected proteins, or a functional proteomics approach to study protein interactions and function.
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Affiliation(s)
- Jolein Gloerich
- Laboratory for Pediatrics and Neurology, Nijmegen Centre for Mitochondrial Disorders, Department of Pediatrics, Neuromuscular Center Nijmegen, 6500 HB Nijmegen, The Netherlands
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Abstract
Biologists often claim that they follow a rational design strategy when their research is based on molecular knowledge of biological systems. This claim implies that their knowledge of the innumerable causal connections present in biological systems is sufficient to allow them to deduce and predict the outcome of their experimental interventions. The design metaphor is shown to originate in human intentionality and in the anthropomorphic fallacy of interpreting objects, events, and the behavior of all living organisms in terms of goals and purposes. Instead of presenting rational design as an effective research strategy, it would be preferable to acknowledge that advances in biomedicine are nearly always derived from empirical observations based on trial and error experimentation. The claim that rational design is an effective research strategy was tested in the case of current attempts to develop synthetic vaccines, in particular against human immunodeficiency virus. It was concluded that in this field of biomedicine, trial and error experimentation is more likely to succeed than a rational design approach. Current developments in systems biology may give us eventually a better understanding of the immune system and this may enable us in the future to develop improved vaccines.
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Affiliation(s)
- Marc H V Van Regenmortel
- Ecole Supérieure de Biotechnologie de Strasbourg, Centre de la Recherche Scientifique, Illkirch, France.
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Nedelkov D. Mass spectrometry-based immunoassays for the next phase of clinical applications. Expert Rev Proteomics 2007; 3:631-40. [PMID: 17181477 DOI: 10.1586/14789450.3.6.631] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent applications of affinity mass spectrometry into clinical laboratories brought a renewed interest in immunoaffinity mass spectrometry as a more specific affinity method capable of selectively targeting and studying protein biomarkers. In mass spectrometry-based immunoassays, proteins are affinity retrieved from biological samples via surface-immobilized antibodies, and are then detected via mass spectrometric analysis. The assays benefit from dual specificity, which is brought about by the affinity of the antibody and the protein mass readout. The mass spectrometry aspect of the assays enables single-step detection of protein isoforms and their individual quantification. This review offers a comprehensive review of mass spectrometry-based immunoassays, from historical perspectives in the development of the immunoaffinity mass spectrometry, to current applications of the assays in clinical and population proteomic endeavors. Described in more detail are two types of mass spectrometry-based immunoassays, one of which incorporates surface plasmon resonance detection for protein quantification. All mass spectrometry-based immunoassays offer high-throughput targeted protein investigation, with clear implications in clinical research, encompassing biomarker discovery and validation, and in diagnostic settings as the next-generation immunoassays.
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Affiliation(s)
- Dobrin Nedelkov
- Intrinsic Bioprobes Inc., 2155 East Conference Drive, Suite 104, Tempe, AZ 85284, USA.
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28
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Phillips KS, Cheng Q. Recent advances in surface plasmon resonance based techniques for bioanalysis. Anal Bioanal Chem 2007; 387:1831-40. [PMID: 17203259 DOI: 10.1007/s00216-006-1052-7] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2006] [Revised: 11/22/2006] [Accepted: 11/28/2006] [Indexed: 02/06/2023]
Abstract
Surface plasmon resonance (SPR) is a powerful and versatile spectroscopic method for biomolecular interaction analysis (BIA) and has been well reviewed in previous years. This updated 2006 review of SPR, SPR spectroscopy, and SPR imaging explores cutting-edge technology with a focus on material, method, and instrument development. A number of recent SPR developments and interesting applications for bioanalysis are provided. Three focus topics are discussed in more detail to exemplify recent progress. They include surface plasmon fluorescence spectroscopy, nanoscale glassification of SPR substrates, and enzymatic amplification in SPR imaging. Through these examples it is clear to us that the development of SPR-based methods continues to grow, while the applications continue to diversify. Major trends appear to be present in the development of combined techniques, use of new materials, and development of new methodologies. Together, these works constitute a major thrust that could eventually make SPR a common tool for surface interaction analysis and biosensing. The future outlook for SPR and SPR-associated BIA studies, in our opinion, is very bright. Surface plasmon resonance (SPR) is a powerful and versatile spectroscopic method for biomolecular interaction analysis (BIA) and has been well reviewed in previous years. This updated 2006 review of SPR, SPR spectroscopy, and SPR imaging explores cutting-edge technology with a focus on material, method, and instrument development. A number of recent SPR developments and interesting applications for bioanalysis are provided. Three focus topics are discussed in more detail to exemplify recent progress. They include surface plasmon fluorescence spectroscopy, nanoscale glassification of SPR substrates, and enzymatic amplification in SPR imaging. Through these examples it is clear to us that the development of SPR-based methods continues to grow, while the applications continue to diversify. Major trends appear to be present in the development of combined techniques, use of new materials, and development of new methodologies. Together, these works constitute a major thrust that could eventually make SPR a common tool for surface interaction analysis and biosensing. The future outlook for SPR and SPR-associated BIA studies, in our opinion, is very bright.
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Affiliation(s)
- K Scott Phillips
- Department of Chemistry, University of California, Riverside, CA 92521, USA
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29
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Rich RL, Myszka DG. Survey of the year 2006 commercial optical biosensor literature. J Mol Recognit 2007; 20:300-66. [DOI: 10.1002/jmr.862] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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