1
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Kachuk C, Doucette AA. The benefits (and misfortunes) of SDS in top-down proteomics. J Proteomics 2018; 175:75-86. [DOI: 10.1016/j.jprot.2017.03.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 01/19/2017] [Accepted: 03/03/2017] [Indexed: 12/18/2022]
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2
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Ma Z, Boye JI, Hu X. In vitro digestibility, protein composition and techno-functional properties of Saskatchewan grown yellow field peas (Pisum sativum L.) as affected by processing. Food Res Int 2017; 92:64-78. [PMID: 28290299 DOI: 10.1016/j.foodres.2016.12.012] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 11/18/2016] [Accepted: 12/22/2016] [Indexed: 11/17/2022]
Abstract
Saskatchewan grown yellow field pea was subjected to different processing conditions including dehulling, micronization, roasting, conventional/microwave cooking, germination, and combined germination and conventional cooking/roasting. Their nutritional and antinutritional compositions, functional properties, microstructure, thermal properties, in vitro protein and starch digestibility, and protein composition were studied. Processed field peas including conventional cooked yellow peas (CCYP), microwave cooked yellow peas (MCYP), germinated-conventional cooked yellow peas (GCCYP), and germinated-roasted yellow peas (GRYP) exhibited the significantly higher in vitro protein digestibility (IVPD), which was in accordance with their significantly lower trypsin inhibitor activity and tannin content. The SDS-PAGE and size exclusion HPLC profiles of untreated pea proteins and their hydrolysates also confirmed the IVPD result that these four treatments facilitated the hydrolysis of pea proteins to a greater extent. The CCYP, MCYP, GCCYP, and GRYP also exhibited significantly higher starch digestibility which was supported by their lower onset (To), peak (Tp), and conclusion (Tc) temperatures obtained from DSC thermogram, their lower pasting properties and starch damage results, as well as their distinguished amorphous flakes' configuration observed on the scanning electron microscopic image. LC/ESI-MS/MS analysis following in-gel digests of SDS-PAGE separated proteins allowed detailed compositional characterization of pea proteins. The present study would provide fundamental information to help to better understand the functionality of field peas as ingredients, and particularly in regards to agri-food industry to improve the process efficiency of field peas with enhanced nutritional and techno-functional qualities.
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Affiliation(s)
- Zhen Ma
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710062, China.
| | - Joyce I Boye
- Food Research and Development Centre, Agriculture and Agri-Food Canada, 3600 Casavant Blvd West, St. Hyacinthe, Quebec J2S 8E3, Canada
| | - Xinzhong Hu
- College of Food Engineering and Nutritional Science, Shaanxi Normal University, Xi'an, Shaanxi 710062, China
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3
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Zhang W, Yuan Z, Huang L, Kang J, Jiang R, Zhong H. Titanium Dioxide Photocatalytic Polymerization of Acrylamide for Gel Electrophoresis (TIPPAGE) of Proteins and Structural Identification by Mass Spectrometry. Sci Rep 2016; 6:20981. [PMID: 26865351 PMCID: PMC4750088 DOI: 10.1038/srep20981] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2015] [Accepted: 01/14/2016] [Indexed: 11/09/2022] Open
Abstract
Polyacrylamide gel electrophoresis (PAGE) coupled with mass spectrometry has been well established for separating, identifying and quantifying protein mixtures from cell lines, tissues or other biological samples. The copolymerization process of acrylamide and bis-acrylamide is the key to mastering this powerful technique. In general, this is a vinyl addition reaction initiated by free radical-generating reagents such as ammonium persulfate (APS) and tetramethylethylenediamine (TEMED) under basic pH and degassing experimental condition. We report herein a photocatalytic polymerization approach that is based on photo-generated hydroxyl radicals with nanoparticles of titanium dioxide. It was shown that the polymerization process is greatly accelerated in acidic condition when ultraviolet light shots on the gel solution containing TiO2 nanoparticles without degassing. This feature makes it very useful in preparing Triton X-100 acid urea (TAU) gel that has been developed for separating basic proteins such as histones and variants in acidic experimental condition. Additionally, the presence of titanium dioxide in the gel not only improves mechanistic property of gels but also changes the migration pattern of different proteins that have different affinities to titanium dioxide.
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Affiliation(s)
- Wenyang Zhang
- Mass Spectrometry Center for Structural Identification of Biological Molecules and Precision Medicine, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Zhiwei Yuan
- Mass Spectrometry Center for Structural Identification of Biological Molecules and Precision Medicine, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Lulu Huang
- Mass Spectrometry Center for Structural Identification of Biological Molecules and Precision Medicine, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Jie Kang
- Mass Spectrometry Center for Structural Identification of Biological Molecules and Precision Medicine, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Ruowei Jiang
- Mass Spectrometry Center for Structural Identification of Biological Molecules and Precision Medicine, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
| | - Hongying Zhong
- Mass Spectrometry Center for Structural Identification of Biological Molecules and Precision Medicine, Key Laboratory of Pesticides and Chemical Biology, Ministry of Education, College of Chemistry, Central China Normal University, Wuhan, Hubei 430079, P. R. China
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Dagley LF, Emili A, Purcell AW. Application of quantitative proteomics technologies to the biomarker discovery pipeline for multiple sclerosis. Proteomics Clin Appl 2014; 7:91-108. [PMID: 23112123 DOI: 10.1002/prca.201200104] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2012] [Revised: 10/04/2012] [Accepted: 10/11/2012] [Indexed: 11/08/2022]
Abstract
Multiple sclerosis is an inflammatory-mediated demyelinating disorder most prevalent in young Caucasian adults. The various clinical manifestations of the disease present several challenges in the clinic in terms of diagnosis, monitoring disease progression and response to treatment. Advances in MS-based proteomic technologies have revolutionized the field of biomarker research and paved the way for the identification and validation of disease-specific markers. This review focuses on the novel candidates discovered by the application of quantitative proteomics to relevant disease-affected tissues in both the human context and within the animal model of the disease known as experimental autoimmune encephalomyelitis. The role of targeted MS approaches for biomarker validation studies, such as multiple reaction monitoring will also be discussed.
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Affiliation(s)
- Laura F Dagley
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
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5
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Shen Y, Smith RD. Advanced nanoscale separations and mass spectrometry for sensitive high-throughput proteomics. Expert Rev Proteomics 2014; 2:431-47. [PMID: 16000088 DOI: 10.1586/14789450.2.3.431] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Recent developments in combined separations with mass spectrometry for sensitive and high-throughput proteomic analyses are reviewed herein. These developments primarily involve high-efficiency (separation peak capacities of approximately 10(3)) nanoscale liquid chromatography (flow rates extending down to approximately 20 nl/min at optimal liquid mobile-phase separation linear velocities through narrow packed capillaries) in combination with advanced mass spectrometry and in particular, high-sensitivity and high-resolution Fourier transform ion cyclotron resonance mass spectrometry. Such approaches enable analysis of low nanogram level proteomic samples (i.e., nanoscale proteomics) with individual protein identification sensitivity at the low zeptomole level. The resultant protein measurement dynamic range can approach 10(6) for nanogram-sized proteomic samples, while more abundant proteins can be detected from subpicogram-sized (total) proteome samples. These qualities provide the foundation for proteomics studies of single or small populations of cells. The instrumental robustness required for automation and providing high-quality routine performance nanoscale proteomic analyses is also discussed.
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Affiliation(s)
- Yufeng Shen
- Biological Science Division & Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, PO Box 999, Richland, WA 99352, USA.
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6
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Sun D, Wang N, Li L. Integrated SDS Removal and Peptide Separation by Strong-Cation Exchange Liquid Chromatography for SDS-Assisted Shotgun Proteome Analysis. J Proteome Res 2012; 11:818-28. [DOI: 10.1021/pr200676v] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Difei Sun
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Nan Wang
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
| | - Liang Li
- Department
of Chemistry, University of Alberta, Edmonton, Alberta T6G 2G2, Canada
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7
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Masuda T, Sugiyama N, Tomita M, Ishihama Y. Microscale Phosphoproteome Analysis of 10 000 Cells from Human Cancer Cell Lines. Anal Chem 2011; 83:7698-703. [DOI: 10.1021/ac201093g] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Takeshi Masuda
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Naoyuki Sugiyama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Masaru Tomita
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
| | - Yasushi Ishihama
- Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata, Japan
- Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto, Japan
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8
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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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9
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Fabrication of core-shell structured nanoparticle layer substrate for excitation of localized surface plasmon resonance and its optical response for DNA in aqueous conditions. Anal Chim Acta 2010; 661:200-5. [DOI: 10.1016/j.aca.2009.12.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2009] [Revised: 12/11/2009] [Accepted: 12/15/2009] [Indexed: 11/20/2022]
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10
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Bun Ching C, Zhang J, Sui J, Ning Chen W. Proteomics profile of cellular response to chiral drugs: Prospects for pharmaceutical applications. Proteomics 2009; 10:888-93. [DOI: 10.1002/pmic.200900094] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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11
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Electrokinetic sample extraction and enrichment: a new method for the isolation of analytes from sludge-type matrices. Anal Bioanal Chem 2009; 395:1831-41. [DOI: 10.1007/s00216-009-3059-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2009] [Revised: 07/13/2009] [Accepted: 08/11/2009] [Indexed: 11/26/2022]
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Matharoo-Ball B, Miles AK, Creaser CS, Ball G, Rees R. Serum biomarker profiling in cancer studies: a question of standardisation? Vet Comp Oncol 2009; 6:224-47. [PMID: 19178682 DOI: 10.1111/j.1476-5829.2008.00171.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Companion animals are exposed to similar environmental conditions and carcinogens as humans. In some animal cancers, there also appears to be the same genetic changes associated as in humans. However, little work has been carried out in cancer biomarker identification in animals. The recent dramatic advances in molecular medicine, genomics, proteomics and translational research will allow biomarker identification, which may provide the best strategies for veterinarians and clinicians to combat disease by early diagnosis and administration of effective treatments. Proteomics may have important applications in cancer diagnosis, prognosis and predictive clinical outcome that could directly change clinical practice by affecting critical elemen-ts of care and management. This review summarizes the advances in proteomics that has propelled us to this exciting age of clinical proteomics, and highlights the future work that is required for this to become a reality. In this review, we will discuss the available proteomic technologies and their limitations, and highlight the key areas of research and how they have been used to discover cancer biomarkers. The principles described here are equally applicable to human and animal disease, but implementation of 'omic' technologies requires stringent guidelines for collection of clinical material, the application of analytical techniques and interpretation of the data.
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Affiliation(s)
- B Matharoo-Ball
- The John Van Geest Cancer Research Centre, School of Science and Technology, Nottingham Trent University, Nottingham, UK
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Endo T, Kerman K, Nagatani N, Hiepa HM, Kim DK, Yonezawa Y, Nakano K, Tamiya E. Multiple Label-Free Detection of Antigen−Antibody Reaction Using Localized Surface Plasmon Resonance-Based Core−Shell Structured Nanoparticle Layer Nanochip. Anal Chem 2006; 78:6465-75. [PMID: 16970322 DOI: 10.1021/ac0608321] [Citation(s) in RCA: 207] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this research, a localized surface plasmon resonance (LSPR)-based bioanalysis method for developing multiarray optical nanochip suitable for screening bimolecular interactions is described. LSPR-based label-free monitoring enables to solve the problems of conventional methods that require large sample volumes and time-consuming labeling procedures. We developed a multiarray LSPR-based nanochip for the label-free detection of proteins. The multiarray format was constructed by a core-shell-structured nanoparticle layer, which provided 300 nanospots on the sensing surface. Antibodies were immobilized onto the nanospots using their interaction with Protein A. The concentrations of antigens were determined from the peak absorption intensity of the LSPR spectra. We demonstrated the capability of the array measurement using immunoglobulins (IgA, IgD, IgG, IgM), C-reactive protein, and fibrinogen. The detection limit of our label-free method was 100 pg/mL. Our nanochip is readily transferable to monitor the interactions of other biomolecules, such as whole cells or receptors, with a massively parallel detection capability in a highly miniaturized package. We anticipate that the direct label-free optical immunoassay of proteins reported here will revolutionize clinical diagnosis and accelerate the development of hand-held and user-friendly point-of-care devices.
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Affiliation(s)
- Tatsuro Endo
- Department of Mechano-Micro Engineering, Interdisciplinary Graduate School of Science and Engineering, Tokyo Institute of Technology, Midori-ku, Yokohama, 226-8502, Japan
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Visser NFC, Lingeman H, Li K, Irth H. Quantitative Transfer of In-Gel Digest Products to Liquid Chromatography-Electrospray Mass Spectrometry Using On-Line Coupled Extraction. Chromatographia 2005. [DOI: 10.1365/s10337-005-0532-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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15
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Cui JF, Liu YK, Pan BS, Song HY, Zhang Y, Sun RX, Chen J, Feng JT, Tang ZY, Yu YL, Shen HL, Yang PY. Differential proteomic analysis of human hepatocellular carcinoma cell line metastasis-associated proteins. J Cancer Res Clin Oncol 2004; 130:615-22. [PMID: 15243804 DOI: 10.1007/s00432-004-0576-5] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2003] [Accepted: 03/25/2004] [Indexed: 11/24/2022]
Abstract
PURPOSE The comparative study of differentially expression of protein profiles of hepatocellular carcinoma cell lines with various metastasic potential and screening key molecules related to hepatocellular carcinoma metastasis and recurrence. METHODS Using two-dimensional electrophoresis and liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS), we analyzed differentially displayed proteomics of human hepatocellular carcinoma cell lines Hep3B, MHCC97L, MHCC97H with different metastasic potential. RESULTS Approximate 1,000 protein spots were detected on silver-stained gel by ImageMaster (977+/-113 spots in Hep3B, 1092+/-40 in MHCC97L, and 889+/-14 in MHCC97H). Fifty distinct different protein spots were analyzed with online LC-ESI-MS/MS. Only 26 protein spots had a positive result, including annexin1, S100A4, and so on. In comparison with nonmetastasis Hep3B cell lines, there were 16 proteins overexpressed in MHCC97H and MHCC97L, 10 proteins underexpressed in MHCC97H and MHCC97L. Applying cell immunohistochemistry and RT-PCR, we further validated two interesting and different proteins, annexin1 and S100A4. CONCLUSION The protein profile of metastatic hepatocellular carcinoma cell lines displayed obvious differences compared with non-metastatic liver cancer cell lines. The results imply that various different proteins may lead to HCC metastasis together.
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Affiliation(s)
- Jie-Feng Cui
- Liver Cancer Institute, Zhongshan Hospital, Fudan University, 136 Yi Xue Yuan Road, 200032 Shanghai, China
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Abstract
An integrated gel protein identification technology is developed and demonstrated for the effective ( approximately 90% recovery), rapid (less than 5 min), and sensitive identification (as low as 1 ng gel protein loading) of gel-resolved proteins using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). This integrated technology involves on-line combination of electronic protein transfer with nanoscale proteolytic digestion in a capillary platform, enabling electrokinetic-based protein extraction and stacking, real-time proteolytic cleavage of extracted proteins, and direct deposition of protein digests onto MALDI targets. By revisiting the yeast two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) in similar isoelectric point and molecular mass ranges as studied by Gygi and co-workers (Gygi, S. P.; Corthals, G. L.; Zhang, Y.; Rochon, Y.; Aebersold, R. Proc. Natl. Acad. Sci. U.S.A. 2000, 97, 9390-9395), we are additionally able to identify a large number of low abundance proteins with codon adaptation index (CAI) values of <0.2 and increase the proteome coverage to nearly 50%. The CAI value distribution for identified yeast proteins now more closely approximates that predicted for the entire yeast proteome. We further note that the current single-capillary methodology can be easily expanded to a multiplexed capillary platform as a ultrahigh throughput and greatly effective tool for linking 2-D PAGE with MS, particularly for the analysis of low-abundance proteins.
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17
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She YM, Wang GQ, Loboda A, Ens W, Standing KG, Burczynski FJ. Sequencing of rat liver cytosolic proteins by matrix-assisted laser desorption ionization-quadrupole time-of-flight mass spectrometry following electrophoretic separation and extraction. Anal Biochem 2002; 310:137-47. [PMID: 12423631 DOI: 10.1016/s0003-2697(02)00321-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
A new technique is described that enables the direct determination of the complete or partial amino acid sequence of cytosolic proteins separated by gel electrophoresis and allows for the further observation of disease- or drug-induced posttranslational modifications. The procedure uses a two-phase extraction strategy (ethyl acetate/ammonium bicarbonate) for the efficient separation of proteins/peptides from an electrophoretic matrix and subsequent sequence analysis by matrix-assisted laser desorption ionization-quadrupole time-of-flight mass spectrometry. The method was tested using hepatocyte cytosolic proteins and compared to a complementary approach using direct solvent extraction from in-gel digests. Although the latter procedure identified the proteins, it did not enable complete amino acid sequence determination. In contrast, high sequence coverage was obtained using the peptide extraction procedure, without any apparent dependence on protein size. The technique minimized the chemically inconsistent modifications generated from in-gel digestion, thus aiding mass spectrometric interpretation and valid protein sequence identification.
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Affiliation(s)
- Yi-Min She
- Department of Physics and Astronomy, Faculty of Science, University of Manitoba, Man, R3T 2N2, Winnipeg, Canada
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18
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Abstract
In the last few years there has been an increased effort to develop technologies capable of identifying and quantifying large numbers of proteins expressed within a cell system (i.e., the proteome). The complexity of the mixtures being analyzed has made the development of effective fractionation and separation methods a critical component of this effort. This review highlights many of the protein and peptide fractionation and separation methods, such as electrophoresis and high-performance liquid chromatography (HPLC), which have experienced significant development over the past forty years. Modern instrumental strategies for the resolution of cell proteins, based on separations employing a single high-resolution or multidimensional approach, and the relative merits of each, will be discussed. The focus of this manuscript will be on the development of multidimensional separations such as two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), HPLC/HPLC, and HPLC-capillary electrophoresis and their application to the characterization of complex proteome mixtures.
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Affiliation(s)
- Haleem J Issaq
- Analytical Chemistry Laboratory, SAIC Frederick NCI-Frederick, Frederick, MD 21702, USA.
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19
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Shen Y, Zhao R, Berger SJ, Anderson GA, Rodriguez N, Smith RD. High-efficiency nanoscale liquid chromatography coupled on-line with mass spectrometry using nanoelectrospray ionization for proteomics. Anal Chem 2002; 74:4235-49. [PMID: 12199598 DOI: 10.1021/ac0202280] [Citation(s) in RCA: 220] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We describe high-efficiency (peak capacities of approximately 10(3)) nanoscale (using column inner diameters down to 15 microm) liquid chromatography (nanoLC)/low flow rate electrospray (nanoESI) mass spectrometry (MS) for the sensitive analysis of complex global cellular protein enzymatic digests (i.e., proteomics). Using a liquid slurry packing method with carefully selected packing solvents, 87-cm-length capillaries having inner diameters of 14.9-74.5 microm were successfully packed with 3-microm C18-bonded porous (300-A pores) silica particles at a pressure of 18,000 psi. With a mobile-phase delivery pressure of 10,000 psi, these packed capillaries provided mobile-phase flow rates as low as approximately 20 nL/min at LC linear velocities of approximately 0.2 cm/s, which is near optimal for separation efficiency. To maintain chromatographic efficiency, unions with internal channel diameters as small as 10 microm were specially produced for connecting packed capillaries to replaceable nanoESI emitters having orifice diameters of 2-10 microm (depending on the packed capillary dimensions). Coupled on-line with a hybrid-quadrupole time-of-flight MS through the nanoESI interface, the nanoLC separations provided peak capacities of approximately 10(3) for proteome proteolytic polypeptide mixtures when a positive feedback switching valve was used for quantitatively introducing samples. Over a relatively large range of sample loadings (e.g., 5-100 ng, and 50-500 ng of cellular proteolytic peptides for 14.9- and 29.7-microm-i.d. packed capillaries, respectively), the nanoLC/nanoESI MS response for low-abundance components of the complex mixtures was found to increase linearly with sample loading. The nanoLC/nanoESI-MS sensitivity also increased linearly with decreasing flow rate (or approximately inversely proportional to the square of the capillary inner diameter) in the flow range of 20-400 nL/min. Thus, except at the lower loadings, decreasing the separation capillary inner diameter has an effect equivalent to increasing sample loading, which is important for sample-limited proteomic applications. No significant effects on recovery of eluting polypeptides were observed using porous C18 particles with surface pores of 300-A versus nonporous particles. Tandem MS analyses were also demonstrated using the high-efficiency nanoLC separations. Chromatographic elution time, MS response intensity, and mass measurement accuracy was examined between runs with a single column (with a single nanoESI emitter), between different columns (same and different inner diameters with different nanoESI emitters), and for different samples (various concentrations of cellular proteolytic peptides) and demonstrated robust and reproducible sensitive analyses for complex proteomic samples.
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Affiliation(s)
- Yufeng Shen
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99352, USA
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20
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Cooper JW, Gao J, Lee CS. Gel protein capillary extraction apparatus. electronic protein transfer. Anal Chem 2002; 74:1182-6. [PMID: 11924982 DOI: 10.1021/ac0110000] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A gel protein capillary extraction apparatus is developed and demonstrated for its rapid and effective transfer of SDS-protein complexes from polyacrylamide gel to a fused-silica capillary. The small dimensions of capillary columns permit the application of high voltages for achieving rapid and effective transfer of gel proteins. Furthermore, the fused-silica capillaries are internally coated with polyacrylamide for the elimination of electroosmotic pumping and protein adsorption onto the capillary wall. The extracted proteins are present in a highly concentrated solution plug as the result of field amplification and sample stacking during the extraction process. Three model proteins, including cytochrome c (14 kDa), ovalbumin (45 kDa), and beta-galactosidase (116 kDa), are visualized using coomassie blue staining and electrophoretically extracted from the gels with protein loading as low as 50 ng. The SDS-cytochrome c complexes extracted from a 50-ng protein loading are concentrated in a 30-nL solution plug inside the capillary with an estimated concentration of 0. 1 mg/mL or 10(-5) M. The capillary format allows the straightforward integration of a miniaturized trypsin-membrane reactor for on-line proteolytic digestion and ESI-MS analysis for protein/peptide identification.
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Affiliation(s)
- Jonathan W Cooper
- Department of Chemistry and Biochemistry, University of Maryland, College Park 20742, USA
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21
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Nordhoff E, Egelhofer V, Giavalisco P, Eickhoff H, Horn M, Przewieslik T, Theiss D, Schneider U, Lehrach H, Gobom J. Large-gel two-dimensional electrophoresis-matrix assisted laser desorption/ionization-time of flight-mass spectrometry: an analytical challenge for studying complex protein mixtures. Electrophoresis 2001; 22:2844-55. [PMID: 11565779 DOI: 10.1002/1522-2683(200108)22:14<2844::aid-elps2844>3.0.co;2-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The large-gel two-dimensional electrophoresis (2-DE) technique, developed by Klose and co-workers over the past 25 years, provides the resolving power necessary to separate crude proteome extracts of higher eukaryotes. Matrix assisted laser desorption/ionization-time of flight-mass spectrometry (MALDI-TOF-MS) provides the sample throughput necessary to identify thousands of different protein species in an adequate time period. Spot excision, in situ proteolysis, and extraction of the cleavage products from the gel matrix, peptide purification and concentration as well as the mass spectrometric sample preparation are the crucial steps that interface the two analytical techniques. Today, these routines and not the mass spectrometric instrumentation determine how many protein digests can be analyzed per day per instrument. The present paper focuses on this analytical interface and reports on an integrated protocol and technology developed in our laboratory. Automated identification of proteins in sequence databases by mass spectrometric peptide mapping requires a powerful search engine that makes full use of the information contained in the experimental data, and scores the search results accordingly. This challenge is heading a second part of the paper.
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Affiliation(s)
- E Nordhoff
- Department Lehrach, Max-Planck-Institute for Molecular Genetics, Berlin, Germany.
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Current literature in mass spectrometry. JOURNAL OF MASS SPECTROMETRY : JMS 2000; 35:1474-1485. [PMID: 11180639 DOI: 10.1002/1096-9888(200012)35:12<1474::aid-jms985>3.0.co;2-u] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
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