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Prokai L, Zaman K, Prokai-Tatrai K. Mass spectrometry-based retina proteomics. MASS SPECTROMETRY REVIEWS 2023; 42:1032-1062. [PMID: 35670041 PMCID: PMC9730434 DOI: 10.1002/mas.21786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 04/28/2022] [Accepted: 04/29/2022] [Indexed: 06/15/2023]
Abstract
A subfield of neuroproteomics, retina proteomics has experienced a transformative growth since its inception due to methodological advances in enabling chemical, biochemical, and molecular biology techniques. This review focuses on mass spectrometry's contributions to facilitate mammalian and avian retina proteomics to catalog and quantify retinal protein expressions, determine their posttranslational modifications, as well as its applications to study the proteome of the retina in the context of biology, health and diseases, and therapy developments.
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Affiliation(s)
- Laszlo Prokai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Khadiza Zaman
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Katalin Prokai-Tatrai
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
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2
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Römer J, Montealegre C, Schlecht J, Kiessig S, Moritz B, Neusüß C. Online mass spectrometry of CE (SDS)-separated proteins by two-dimensional capillary electrophoresis. Anal Bioanal Chem 2019; 411:7197-7206. [PMID: 31616969 DOI: 10.1007/s00216-019-02102-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 08/01/2019] [Accepted: 08/23/2019] [Indexed: 10/25/2022]
Abstract
Sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) is the fundamental technique for protein separation by size. Applying this technology in capillary format, gaining high separation efficiency in a more automated way, is a key technology for size separation of proteins in the biopharmaceutical industry. However, unequivocal identification by online mass spectrometry (MS) is impossible so far, due to strong interference in the electrospray process by SDS and other components of the SDS-MW separation gel buffer. Here, a heart-cut two-dimensional electrophoretic separation system applying an electrically isolated valve with an internal loop of 20 nL is presented. The peak of interest in the CE (SDS) separation is transferred to the CZE-MS, where electrospray-interfering substances of the SDS-MW gel are separated prior to online electrospray ionization mass spectrometry. An online SDS removal strategy for decomplexing the protein-SDS complex is implemented in the second dimension, consisting of the co-injection of organic solvent and cationic surfactant. This online CE (SDS)-CZE-MS system allows MS characterization of proteoforms separated in generic CE (SDS), gaining additional separation in the CZE and detailed MS information. In general, the system can be applied to all kinds of proteins separated by CE (SDS). Here, we present results of the CE (SDS)-CZE-MS system on the analysis of several biopharmaceutically relevant antibody impurities and fragments. Additionally, the versatile application spectrum of the system is demonstrated by the analysis of extracted proteins from soybean flour. The online hyphenation of CE (SDS) resolving power and MS identification capabilities will be a powerful tool for protein and mAb characterization. Graphical abstract Two-dimensional capillary electrophoresis system hyphenated with mass spectrometry for the characterization of CE (SDS)-separated proteins. As first dimension, a generic and high MS-interfering CE (SDS) separation is performed for size separation. After heart-cut transfer of the unknown CE (SDS) protein peak, via a four-port nanoliter valve to a volatile electrolyte system as second dimension, interference-free mass spectrometric data of separated mAb fragments and soybean proteins are obtained.
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Affiliation(s)
- Jennifer Römer
- Faculty of Chemistry, Aalen University, Beethovenstraße 1, 73430, Aalen, Germany
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitätsstraße 31, 93053, Regensburg, Germany
| | - Cristina Montealegre
- Faculty of Chemistry, Aalen University, Beethovenstraße 1, 73430, Aalen, Germany
| | - Johannes Schlecht
- Faculty of Chemistry, Aalen University, Beethovenstraße 1, 73430, Aalen, Germany
- F. Hoffmann-La Roche Ltd, Grenzacherstraße 124, 4070, Basel, Switzerland
| | - Steffen Kiessig
- F. Hoffmann-La Roche Ltd, Grenzacherstraße 124, 4070, Basel, Switzerland
| | - Bernd Moritz
- F. Hoffmann-La Roche Ltd, Grenzacherstraße 124, 4070, Basel, Switzerland
| | - Christian Neusüß
- Faculty of Chemistry, Aalen University, Beethovenstraße 1, 73430, Aalen, Germany.
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3
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Heink A, Davidson WS, Swertfeger DK, Lu LJ, Shah AS. A Comparison of Methods To Enhance Protein Detection of Lipoproteins by Mass Spectrometry. J Proteome Res 2015; 14:2943-50. [PMID: 26039899 PMCID: PMC4714602 DOI: 10.1021/acs.jproteome.5b00270] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We sought to develop a new method to more efficiently analyze lipid-bound proteins by mass spectrometry using a combination of a lipid removal agent (LRA) that selectively targets lipid-bound proteins and a mass spectrometry compatible detergent, anionic acid labile surfactant (AALS), that is capable of eluting proteins off the LRA. This method was compared to established methods that use the lipid removal agent alone and straight proteomic analysis of human plasma after organic solvent delipidation (OSD). Plasma from healthy individuals was separated by gel filtration chromatography and prepared for mass spectrometry analysis by each of the described methods. The addition of AALS to LRA increased the overall number of proteins detected in both the high and low density lipoprotein size range, the number of peptide counts for each protein, and the overall sequence coverage. Organic solvent delipidation detected the most proteins, though with some decrease in overall protein detection and sequence coverage due to the presence of nonlipid-bound proteins. The use of LRA allows for selection and analysis of lipid-bound proteins. The addition of a mass spectrometry compatible detergent improved detection of lipid-bound proteins from human plasma using LRA.
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Affiliation(s)
- Anna Heink
- Department of Pediatrics, Cincinnati Children’s Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, Ohio 45229-3039, United States
| | - W. Sean Davidson
- Center for Lipid and Arteriosclerosis Science, Department of Pathology and Laboratory Medicine, University of Cincinnati, 2120 East Galbraith Road, Cincinnati, Ohio 45237-0507, United States
| | - Debi K Swertfeger
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, Ohio 45229-3039, United States
| | - L. Jason Lu
- Division of Biomedical Informatics, Cincinnati Children’s Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, Ohio 45229-3039, United States
| | - Amy S Shah
- Department of Pediatrics, Cincinnati Children’s Hospital Research Foundation, 3333 Burnet Avenue, Cincinnati, Ohio 45229-3039, United States
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4
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Chung M, Kim D, Herr AE. Polymer sieving matrices in microanalytical electrophoresis. Analyst 2014; 139:5635-54. [DOI: 10.1039/c4an01179a] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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5
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Hahn AS, Kaufmann JK, Wies E, Naschberger E, Panteleev-Ivlev J, Schmidt K, Holzer A, Schmidt M, Chen J, König S, Ensser A, Myoung J, Brockmeyer NH, Stürzl M, Fleckenstein B, Neipel F. The ephrin receptor tyrosine kinase A2 is a cellular receptor for Kaposi's sarcoma–associated herpesvirus. Nat Med 2012; 18:961-6. [PMID: 22635007 DOI: 10.1038/nm.2805] [Citation(s) in RCA: 133] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2011] [Accepted: 04/17/2012] [Indexed: 12/12/2022]
Abstract
Kaposi's sarcoma-associated herpesvirus (KSHV) is the causative agent of Kaposi's sarcoma(1), a highly vascularized tumor originating from lymphatic endothelial cells, and of at least two different B cell malignancies(2,3). A dimeric complex formed by the envelope glycoproteins H and L (gH-gL) is required for entry of herpesviruses into host cells(4). We show that the ephrin receptor tyrosine kinase A2 (EphA2) is a cellular receptor for KSHV gH-gL. EphA2 co-precipitated with both gH-gL and KSHV virions. Infection of human epithelial cells with a GFP-expressing recombinant KSHV strain, as measured by FACS analysis, was increased upon overexpression of EphA2. Antibodies against EphA(2) and siRNAs directed against EphA2 inhibited infection of endothelial cells. Pretreatment of KSHV with soluble EphA2 resulted in inhibition of KSHV infection by up to 90%. This marked reduction of KSHV infection was seen with all the different epithelial and endothelial cells used in this study. Similarly, pretreating epithelial or endothelial cells with the soluble EphA2 ligand ephrinA4 impaired KSHV infection. Deletion of the gene encoding EphA2 essentially abolished KSHV infection of mouse endothelial cells. Binding of gH-gL to EphA2 triggered EphA2 phosphorylation and endocytosis, a major pathway of KSHV entry(5,6). Quantitative RT-PCR and in situ histochemistry revealed a close correlation between KSHV infection and EphA2 expression both in cultured cells derived from human Kaposi's sarcoma lesions or unaffected human lymphatic endothelium, and in situ in Kaposi's sarcoma specimens, respectively. Taken together, our results identify EphA2, a tyrosine kinase with known functions in neovascularization and oncogenesis, as an entry receptor for KSHV.
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Affiliation(s)
- Alexander S Hahn
- Virologisches Institut, Universitätsklinikum Erlangen, Erlangen, Germany
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6
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Stanley B, Lucy CA. Micellar electrokinetic chromatography with acid labile surfactant. J Chromatogr A 2012; 1226:55-60. [DOI: 10.1016/j.chroma.2011.09.065] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Revised: 09/23/2011] [Accepted: 09/23/2011] [Indexed: 01/12/2023]
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7
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Wu F, Sun D, Wang N, Gong Y, Li L. Comparison of surfactant-assisted shotgun methods using acid-labile surfactants and sodium dodecyl sulfate for membrane proteome analysis. Anal Chim Acta 2011; 698:36-43. [DOI: 10.1016/j.aca.2011.04.039] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2010] [Revised: 04/13/2011] [Accepted: 04/18/2011] [Indexed: 01/11/2023]
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8
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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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9
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Lesur A, Varesio E, Hopfgartner G. Accelerated tryptic digestion for the analysis of biopharmaceutical monoclonal antibodies in plasma by liquid chromatography with tandem mass spectrometric detection. J Chromatogr A 2009; 1217:57-64. [PMID: 19939394 DOI: 10.1016/j.chroma.2009.11.011] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2009] [Revised: 10/29/2009] [Accepted: 11/02/2009] [Indexed: 11/27/2022]
Abstract
Accelerated tryptic digestion of a therapeutic protein including microwave irradiation and thermal transfer by convection at 60 degrees C and 37 degrees C was investigated. An analytical setup was devised to follow the protein digestion rate using 1D gel electrophoresis and liquid chromatography coupled a triple quadrupole linear ion trap mass spectrometer. The formation kinetic of its tryptic peptides was monitored in the selected monitoring mode (LC-SRM/MS). Different digestion end points (e.g. 2, 5, 10, 15, 30 and 60min) as well as an overnight digestion were tested using a therapeutic human monoclonal antibody (mAb) with the goal of its LC-SRM/MS quantification in human plasma. The peptides from the human mAb were generated at different rates and were classified into three categories: (1) the fast forming peptides, (2) the slow forming peptides and (3) the peptides degrading over time. For many monitored peptides, a heating temperature of 37 degrees C with a 750rpm mixing applied for at least 30min provided equivalent results to microwave-assisted digestion and generally allowed the achievement of an equivalent peptide concentration as an overnight digestion carried out at 37 degrees C. The disappearance of the protein of the heavy and light chains can be monitored by 1D gel electrophoresis but was found not to be representative of the final tryptic peptide concentrations. For quantitative purposes a stable isotope labeled version ((13)C(4), (15)N(1)) of the therapeutic protein was used. The labeled protein as internal standard was found to be very efficient to compensate for incomplete digestion or losses during sample preparation.
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Affiliation(s)
- Antoine Lesur
- Life Sciences Mass Spectrometry, School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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10
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Norrgran J, Williams TL, Woolfitt AR, Solano MI, Pirkle JL, Barr JR. Optimization of digestion parameters for protein quantification. Anal Biochem 2009; 393:48-55. [DOI: 10.1016/j.ab.2009.05.050] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2009] [Revised: 05/27/2009] [Accepted: 05/29/2009] [Indexed: 11/30/2022]
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11
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Root BE, Zhang B, Barron AE. Size-based protein separations by microchip electrophoresis using an acid-labile surfactant as a replacement for SDS. Electrophoresis 2009; 30:2117-22. [DOI: 10.1002/elps.200800771] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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12
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Lam TC, Chun RKM, Li KK, To CH. Application of proteomic technology in eye research: a mini review. Clin Exp Optom 2008; 91:23-33. [PMID: 18045249 DOI: 10.1111/j.1444-0938.2007.00194.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Proteomics is a rapidly growing research area for the study of the protein cognate of genomic data. This review gives a brief overview of the modern proteomic technology. In addition to general applications of proteomics, we highlight its contribution to studying the physiology of different ocular tissues. We also summarise the published proteomic literature in the broad context of ophthalmic diseases, such as cataract, age-related maculopathy, diabetic retinopathy, glaucoma and myopia. The proteomic technology is a useful research tool and it will continue to advance our understanding of a variety of molecular processes in ocular tissues and diseases.
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Affiliation(s)
- Thomas C Lam
- Laboratory of Experimental Optometry, Centre for Myopia Research, School of Optometry, The Hong Kong Polytechnic University, Hong Kong SAR, China
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13
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Norris JL, Porter NA, Caprioli RM. Combination detergent/MALDI matrix: functional cleavable detergents for mass spectrometry. Anal Chem 2007; 77:5036-40. [PMID: 16053319 DOI: 10.1021/ac050460g] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This study reports the synthesis of the first functional cleavable detergent designed specifically for applications in mass spectrometry. Upon cleavage, two inert compounds and the MALDI matrix are formed, eliminating sources of potential interference originating from traditional cleavable detergents. Analysis of peptides demonstrates that MALDI matrix generated in situ results in MALDI spectra equivalent to those prepared using established protocols. Analysis of the membrane protein diacylglycerol kinase was accomplished using the combination detergent/MALDI matrix. Applications of the functional cleavable detergents to the profiling of whole cell lysates results in increased signal-to-noise ratios of many ions and the detection of additional proteins previously not observed.
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Affiliation(s)
- Jeremy L Norris
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37232-8575, USA
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14
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Liedtke T, Schwamborn JC, Schröer U, Thanos S. Elongation of axons during regeneration involves retinal crystallin beta b2 (crybb2). Mol Cell Proteomics 2007; 6:895-907. [PMID: 17264069 DOI: 10.1074/mcp.m600245-mcp200] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Adult retinal ganglion cells (RGCs) can regenerate their axons in vitro. Using proteomics, we discovered that the supernatants of cultured retinas contain isoforms of crystallins with crystallin beta b2 (crybb2) being clearly up-regulated in the regenerating retina. Immunohistochemistry revealed the expression of crybb within the retina, including in filopodial protrusions and axons of RGCs. Cloning and overexpression of crybb2 in RGCs and hippocampal neurons increased axonogenesis, which in turn could be blocked with antibodies against beta-crystallin. Conditioned medium from crybb2-transfected cell cultures also supported the growth of axons. Finally real time imaging of the uptake of green fluorescent protein-tagged crybb2 fusion protein showed that this protein becomes internalized. These data are the first to show that axonal regeneration is related to crybb2 movement. The results suggest that neuronal crystallins constitute a novel class of neurite-promoting factors that likely operate through an autocrine mechanism and that they could be used in neurodegenerative diseases.
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Affiliation(s)
- Thomas Liedtke
- Department of Experimental Ophthalmology, University of Münster, Germany
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15
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Zhou J, Zhou T, Cao R, Liu Z, Shen J, Chen P, Wang X, Liang S. Evaluation of the application of sodium deoxycholate to proteomic analysis of rat hippocampal plasma membrane. J Proteome Res 2006; 5:2547-53. [PMID: 17022626 DOI: 10.1021/pr060112a] [Citation(s) in RCA: 95] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Detergents have been widely used for the solubilization of membrane proteins and the improvement of their digestion. In this paper, we have evaluated the application of sodium deoxycholate (SDC) to the solubilization and digestion of rat hippocampal plasma membrane (PM) proteins. For in-solution digestion, rat hippocampal PM fraction from sucrose-density gradient centrifugation was solubilized by boiling in 1.0% SDC, and directly digested without dilution. During the in-gel digestion of the hippocampal PM proteins separated by SDS-PAGE, 0.1% SDC was added. Before analysis of peptide mixture by liquid chromatography and electrospray mass spectrometry, SDC in the tryptic digests was removed by centrifugation following acidification. Use of 1.0% SDC in solubilization and in-solution digestion of rat PM proteins had led to 77 PM or membrane-associated proteins identified, a more than 2-fold increase over that by use of SDS. The addition of 0.1% SDC to the in-gel digestion of SDS-PAGE-resolved membrane proteins remarkably enhanced the coverage of tryptic peptides and the number of hydrophobic membrane proteins identified. Being a cheaper and more tractable acid-insoluble detergent, SDC could be used at higher concentration in the solubilization and tryptic digestion of proteins including PM proteins with the purpose of enhancing the protein solubility and at the same time making no interference with trypsin activity and subsequent analyses.
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Affiliation(s)
- Jian Zhou
- College of Life Sciences, Hunan Normal University, Changsha, P.R. China
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16
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Ruth MC, Old WM, Emrick MA, Meyer-Arendt K, Aveline-Wolf LD, Pierce KG, Mendoza AM, Sevinsky JR, Hamady M, Knight RD, Resing KA, Ahn NG. Analysis of Membrane Proteins from Human Chronic Myelogenous Leukemia Cells: Comparison of Extraction Methods for Multidimensional LC−MS/MS. J Proteome Res 2006; 5:709-19. [PMID: 16512687 DOI: 10.1021/pr050313z] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An important strategy for "shotgun proteomics" profiling involves solution proteolysis of proteins, followed by peptide separation using multidimensional liquid chromatography and automated sequencing by mass spectrometry (LC-MS/MS). Several protocols for extracting and handling membrane proteins for shotgun proteomics experiments have been reported, but few direct comparisons of different protocols have been reported. We compare four methods for preparing membrane proteins from human cells, using acid labile surfactants (ALS), urea, and mixed organic-aqueous solvents. These methods were compared with respect to their efficiency of protein solubilization and proteolysis, peptide and protein recovery, membrane protein enrichment, and peptide coverage of transmembrane proteins. Overall, approximately 50-60% of proteins recovered were membrane-associated, identified from Gene Ontology annotations and transmembrane prediction software. Samples extracted with ALS, extracted with urea followed by dilution, or extracted with urea followed by desalting yielded comparable peptide recoveries and sequence coverage of transmembrane proteins. In contrast, suboptimal proteolysis was observed with organic solvent. Urea extraction followed by desalting may be a particularly useful approach, as it is less costly than ALS and yields satisfactory protein denaturation and proteolysis under conditions that minimize reactivity with urea-derived cyanate. Spectral counting was used to compare datasets of proteins from membrane samples with those of soluble proteins from K562 cells, and to estimate fold differences in protein abundances. Proteins most highly abundant in the membrane samples showed enrichment of integral membrane protein identifications, consistent with their isolation by differential centrifugation.
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Affiliation(s)
- Mariah C Ruth
- Yale University School of Medicine, New Haven, Connecticut 06510, USA
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17
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Abstract
Application of proteomics technologies in the investigation of biological systems creates new possibilities in the elucidation of biopathomechanisms and the discovery of novel drug targets and early disease markers. A proteomic analysis involves protein separation and protein identification as well as characterization of the post-translational modifications. Proteomics has been applied in the investigation of various disorders, like neurological diseases, and the application has resulted in the detection of a large number of differences in the levels and the modifications of proteins between healthy and diseased states. However, the current proteomics technologies are still under development and show certain limitations. In this article, we discuss the major drawbacks and pitfalls of proteomics we have observed in our laboratory and in particular during the application of proteomics technologies in the investigation of the brain.
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Affiliation(s)
- Spyros Garbis
- Academy of Athens, Foundation for Biomedical Research, Division of Biotechnology, Soranou Ephessius 4, 11527 Athens, Greece
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18
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Tummala R, Green-Church KB, Limbach PA. Interactions between sodium dodecyl sulfate micelles and peptides during matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) of proteolytic digests. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2005; 16:1438-1446. [PMID: 16006141 DOI: 10.1016/j.jasms.2005.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2004] [Revised: 04/08/2005] [Accepted: 04/08/2005] [Indexed: 05/03/2023]
Abstract
Although sodium dodecyl sulfate (SDS) is routinely used as a denaturing agent for proteins, its presence is highly detrimental on the analysis of peptides and proteins by mass spectrometry. It has been found, however, that when SDS is present in concentrations near to or above its critical micelle concentration (CMC), improvements in the matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) analysis of peptide mixtures or hydrophobic proteins are obtained. To elucidate possible explanations for such improvements, here we have undertaken a study examining the effect of SDS micelles on peptide mixtures. Fluorescently labeled peptides were used as probes to determine whether hydrophobic or hydrophilic peptides interact exclusively with SDS micelles. In addition, four globular proteins were digested with trypsin and then various amounts of SDS were added before MALDI mass spectrometry. To examine the role of mixture complexity on the mass spectral results, the tryptic digest of bovine serum albumin was also fractionated according to hydrophobicity before SDS treatment. Results from these experiments suggest that micelle-peptide interactions increase peptide-matrix cocrystallization irrespective of analyte hydrophobicity. As these studies were performed using the dried-droplet method of sample spotting, the presence of micelles is also hypothesized to reduce Marangoni effects during the crystallization process.
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Affiliation(s)
- Rama Tummala
- 429K Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, P.O. Box 210172, 45221-0172, Cincinnati, OH, USA
| | - Kari B Green-Church
- 429K Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, P.O. Box 210172, 45221-0172, Cincinnati, OH, USA
| | - Patrick A Limbach
- 429K Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, P.O. Box 210172, 45221-0172, Cincinnati, OH, USA.
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19
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Shieh IF, Lee CY, Shiea J. Eliminating the Interferences from TRIS Buffer and SDS in Protein Analysis by Fused-Droplet Electrospray Ionization Mass Spectrometry. J Proteome Res 2005; 4:606-12. [PMID: 15822941 DOI: 10.1021/pr049765m] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Multiply charged protein ions were detected from the solutions containing a high concentration of tris(hydroxymethyl) aminomethane buffer (TRIS) and sodium dodecyl sulfate (SDS) using fused-droplet electrospray ionization mass spectrometry (FD-ESI/MS). The sample aerosols were generated at ambient temperature with a pneumatic nebulizer commonly used to produce sample aerosols in an atmospheric pressure chemical ionization (APCI) source. The aerosols were carried by nitrogen gas to the tip of a capillary where charged methanol droplets had been continuously generated by electrospraying an acidic methanol solution. The neutral sample aerosols then fused with the charged methanol droplets and electrospray ionization proceeded from the newly formed fused droplets to generate multiply charged protein ions. Because of its low solubility in methanol, TRIS molecules (concentration as high as 1 M) were efficiently excluded from the newly formed droplets and the protein ion signals were detected and observed in the mass spectra. To remove the interferences from SDS, equal moles of positively charged cetyltrimethylammonium bromide (CTAB) was added into the SDS containing sample solution to form the dodecyl sulfate-cetyltrimethylammonium ion pair (DS-CTA). The DS-CTA ion pair has a low polarity and solubility in methanol and is excluded from the fused droplet. Protein ions were still detected from the solution containing 10(-2) M of SDS.
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Affiliation(s)
- I-Fan Shieh
- Department of Chemistry, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
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20
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Norris JL, Porter NA, Caprioli RM. Mass spectrometry of intracellular and membrane proteins using cleavable detergents. Anal Chem 2004; 75:6642-7. [PMID: 14640740 DOI: 10.1021/ac034802z] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Detergents have been used to enhance the solubility of hydrophobic biomolecules for decades. Despite the widespread use of detergents in biochemistry, the presence of these molecules often complicates further analysis by mass spectrometry. This study presents a solution to this problem by outlining a method utilizing a novel cleavable detergent, 3-[3-(1,1-bisalkyloxyethyl)pyridin-1-yl]propane-1-sulfonate (PPS). This detergent can be used to extract protein contained within the interior of the cell by disrupting cell membranes. Once the proteins are free from the cell, PPS also assists in protein solubilization by shielding the hydrophobic regions of the newly extracted protein from unfavorable interactions with water. The added advantage of PPS over conventional detergents such as sodium dodecyl sulfate or n-octylglucoside is that the detergent properties that interfere with MALDI mass spectrometry can be eliminated prior to analysis. PPS was found to improve sensitivity in MALDI analyses of both soluble proteins and membrane proteins without degrading spectral quality. The virtues of this strategy were applied to whole cell extracts. Analysis of these extracts resulted in an overall increase in both the number of peaks observed and overall signal intensity.
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Affiliation(s)
- Jeremy L Norris
- Mass Spectrometry Research Center, Department of Chemistry, Vanderbilt University, 465 21st Avenue South, Medical Research Building 3, Room 9160, Nashville, Tennessee 37232-8575, USA
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21
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Fountoulakis M. Application of proteomics technologies in the investigation of the brain. MASS SPECTROMETRY REVIEWS 2004; 23:231-258. [PMID: 15133836 DOI: 10.1002/mas.10075] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Approximately 30-50% of the genes in mammals are expressed in the nervous system. A differential expression of genes in distinct patterns is necessary for the generation of the large variety of neuronal phenotypes. Proteomic analysis of brain compartments may be useful to understand the complexity, to investigate disorders of the central nervous system, and to search for corresponding early markers. Up to now, proteomics has mainly studied the identity and levels of the abundant human, rat, and mouse brain proteins as well as changes of their levels and the modifications that result from various neurological disorders, like Alzheimer's disease and Down's syndrome in humans and in animal models of those diseases. The proteins, for which altered levels in these disorders have been observed, exert mainly neurotransmission, guidance, and signal-transduction functions, or are involved in detoxification, metabolism, and conformational changes. Some of those proteins may be potential drug targets. Further improvement of proteomics technologies to increase sensitivity and efficiency of detection of certain protein classes is necessary for a more detailed analysis of the brain proteome. In this review, a description of the proteomics technologies applied in the investigation of the brain, the major findings that resulted from their application, and the potential and limitations of the current technologies are discussed.
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Affiliation(s)
- Michael Fountoulakis
- F. Hoffmann-La Roche Ltd., Center for Medical Genomics, Building 93-444, 4070 Basel, Switzerland.
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22
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Arnold RJ, Hrncirova P, Annaiah K, Novotny MV. Fast Proteolytic Digestion Coupled with Organelle Enrichment for Proteomic Analysis of Rat Liver. J Proteome Res 2004; 3:653-7. [PMID: 15253449 DOI: 10.1021/pr034110r] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The use of an acid-labile surfactant as an alternative to urea denaturation allows for same-day proteolytic digestion and fast cleanup of cellular lysate samples. Homogenized rat liver tissue was separated into four fractions enriched in nuclei, mitochondria, microsomes (remaining organelles), and cytosol. Each subcellular fraction was then subjected to proteolytic digestion with trypsin for 2 h after denaturing with an acid-labile surfactant (ALS), separated by nanoflow reversed phase HPLC, and mass analyzed by tandem mass spectrometry in a 3-D ion trap. The results obtained from ALS denaturation for both organelle enrichment and whole cell lysate samples were comparable to those obtained from aliquots of the same samples treated by reduction, alkylation, and urea denaturation. Each method resulted in a similar number of peptides (694 for urea, 674 for ALS) and proteins (225 for urea, 229 for ALS) identified, with generally the same proteins (47% overlap) identified. As expected, organelle enrichment enabled the identification of more proteins (66% more with urea, 60% more with ALS) compared to a whole cell lysate. With organelle enrichment, the number of proteins with equal or increased sequence coverage went up by 73% with urea and 67% with ALS compared to the whole cell lysate. Additional information regarding the subcellular location of many proteins is obtained by organelle enrichment. While organelle enrichment is demonstrated with a bottom-up proteomics approach, it should be easily amenable to top-down proteomics approaches.
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Affiliation(s)
- Randy J Arnold
- Proteomics R&D Facility, Department of Chemistry, Indiana University, Bloomington, Indiana 47405, USA
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23
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Current Awareness on Comparative and Functional Genomics. Comp Funct Genomics 2003. [PMCID: PMC2447285 DOI: 10.1002/cfg.230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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