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Hallez F, Combès A, Desoubries C, Bossée A, Pichon V. Development of an immobilized-trypsin reactor coupled to liquid chromatography and tandem mass spectrometry for the analysis of human hemoglobin adducts with sulfur mustard. J Chromatogr B Analyt Technol Biomed Life Sci 2021; 1186:123031. [PMID: 34781109 DOI: 10.1016/j.jchromb.2021.123031] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 11/03/2021] [Accepted: 11/07/2021] [Indexed: 11/24/2022]
Abstract
Sulfur mustard reacts with blood proteins, such as hemoglobin, to form stable adducts that can be used as long-lived biomarkers of exposure. These adducts can be analyzed by liquid chromatography coupled to tandem mass-spectrometry (LC-MS/MS) after an enzymatic digestion step. The objective of this study was to develop trypsin-based immobilized enzyme reactors (IMERs) in order to obtain a faster digestion of hemoglobin than the conventional in-solution digestion. Trypsin IMERs were synthetized by grafting the enzyme on a CNBr-Sepharose gel and the influence of several parameters on the digestion yields, such as the transfer volume between the injection loop and the IMER, the temperature and the digestion time was studied. The repeatability of the digestion on three laboratory-made IMERs was demonstrated for pure hemoglobin and hemoglobin previously exposed to different concentrations of sulfur mustard (RSD inferior to 13% and 21% respectively) and was better than that obtained for in-solution digestions (RSD inferior to 28% and up to 53% respectively). A preferential adduction of sulfur mustard on the histidine residues of hemoglobin was confirmed, for both in-solution and IMER digestion results. On a quantitative point of view, the performances of in-solution and IMER digestions were similar, with the theoretical possibility to detect peptides resulting from the in vitro incubation of hemoglobin in pure water with sulfur mustard at 7.5 ng⋅mL-1. However, digestion on IMER proved to be more repeatable and 32 times faster than in-solution digestion, and a given IMER could be reused at least 60 times.
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Affiliation(s)
- Florine Hallez
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), Chemistry, Biology and Innovation (CBI), ESPCI Paris, PSL University, CNRS, 10 rue Vauquelin, 75005 Paris, France
| | - Audrey Combès
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), Chemistry, Biology and Innovation (CBI), ESPCI Paris, PSL University, CNRS, 10 rue Vauquelin, 75005 Paris, France
| | - Charlotte Desoubries
- DGA, CBRN Defence, Analytical Chemistry Department, 5 rue Lavoisier, 91710 Vert-le-Petit, France
| | - Anne Bossée
- DGA, CBRN Defence, Analytical Chemistry Department, 5 rue Lavoisier, 91710 Vert-le-Petit, France
| | - Valérie Pichon
- Department of Analytical, Bioanalytical Sciences and Miniaturization (LSABM), Chemistry, Biology and Innovation (CBI), ESPCI Paris, PSL University, CNRS, 10 rue Vauquelin, 75005 Paris, France; Sorbonne Université, Campus UPMC, 4 Place Jussieu, 75005 Paris, France.
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2
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Ye X, Tang J, Mao Y, Lu X, Yang Y, Chen W, Zhang X, Xu R, Tian R. Integrated proteomics sample preparation and fractionation: Method development and applications. Trends Analyt Chem 2019. [DOI: 10.1016/j.trac.2019.115667] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
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3
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Ranade AV, Mukhtarov R, An Liu KJ, Behrner MA, Sun B. Characterization of Sample Loss Caused by Competitive Adsorption of Proteins in Vials Using Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:4224-4232. [PMID: 30813715 DOI: 10.1021/acs.langmuir.8b04281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Sample loss caused by competitive protein adsorption on solid surfaces from complex samples remains to be a major hurdle in sensitive analyses of proteins. No label-free techniques can easily quantify individual proteins adsorbed on irregular surfaces of Eppendorf vials or Falcon tubes, which are commonly used to contain complex biological samples. Multiplexed characterization of such adsorption by different proteins is technically challenging. Herein, we developed a direct protein analysis based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis for the characterization of sample loss occurred on the curved surface with limited area. Using this simple and easily accessible method, we discovered the effect of ethylenediaminetetraacetic acid on surface adsorption of different milk proteins, specifically an augmented loss of milk proteins in low-binding sample vials. In this study, we also identified severe biases of silver staining and established proteomics-based mapping of protein distribution in biological samples for absolute quantification of competitive protein adsorption on irregular surfaces.
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4
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Naldi M, Tramarin A, Bartolini M. Immobilized enzyme-based analytical tools in the -omics era: Recent advances. J Pharm Biomed Anal 2018; 160:222-237. [DOI: 10.1016/j.jpba.2018.07.051] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2018] [Revised: 07/26/2018] [Accepted: 07/30/2018] [Indexed: 02/01/2023]
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5
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Lee MCG, Sun B. Quantitation of nonspecific protein adsorption at solid–liquid interfaces for single-cell proteomics. CAN J CHEM 2018. [DOI: 10.1139/cjc-2017-0304] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Protein nonspecific adsorption that occurred at the solid–liquid interface has been subjected to intense physical and chemical characterizations due to its crucial role in a wide range of applications, including food and pharmaceutical industries, medical implants, biosensing, and so on. Protein-adsorption caused sample loss has largely hindered the studies of single-cell proteomics; the prevention of such loss requires the understanding of protein–surface adsorption at the proteome level, in which the competitive adsorption of thousands and millions of proteins with vast dynamic range occurs. To this end, we feel the necessity to review current methodologies on their potentials to characterize — more specifically to quantify — the proteome-wide adsorption. We hope this effort can help advancing single-cell proteomics and trace proteomics.
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Affiliation(s)
| | - Bingyun Sun
- Department of Chemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
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6
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Sielaff M, Kuharev J, Bohn T, Hahlbrock J, Bopp T, Tenzer S, Distler U. Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range. J Proteome Res 2017; 16:4060-4072. [DOI: 10.1021/acs.jproteome.7b00433] [Citation(s) in RCA: 145] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Malte Sielaff
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Jörg Kuharev
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Toszka Bohn
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Jennifer Hahlbrock
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Tobias Bopp
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Stefan Tenzer
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
| | - Ute Distler
- Institute
for Immunology, University Medical Center of the Johannes Gutenberg University Mainz, Langenbeckstr. 1, 55131 Mainz, Germany
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7
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Sun B, Kovatch JR, Badiong A, Merbouh N. Optimization and Modeling of Quadrupole Orbitrap Parameters for Sensitive Analysis toward Single-Cell Proteomics. J Proteome Res 2017; 16:3711-3721. [PMID: 28825293 DOI: 10.1021/acs.jproteome.7b00416] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Single-cell proteomics represents a field of extremely sensitive proteomic analysis, owing to the minute amount of yet complex proteins in a single cell. Without amplification potential as of nucleic acids, single-cell mass spectrometry (MS) analysis demands special instrumentation running with optimized parameters to maximize the sensitivity and throughput for comprehensive proteomic discovery. To facilitate such analysis, we here investigated two factors critical to peptide sequencing and protein detection in shotgun proteomics, i.e. precursor ion isolation window (IW) and maximum precursor ion injection time (ITmax), on an ultrahigh-field quadrupole Orbitrap (Q-Exactive HF). Counterintuitive to the frequently used proteomic parameters for bulk samples (>100 ng), our experimental data and subsequent modeling suggested a universally optimal IW of 4.0 Th for sample quantity ranging from 100 ng to 1 ng, and a sample-quantity dependent ITmax of more than 250 ms for 1-ng samples. Compared with the benchmark condition of IW = 2.0 Th and ITmax = 50 ms, our optimization generated up to 300% increase to the detected protein groups for 1-ng samples. The additionally identified proteins allowed deeper penetration of proteome for better revealing crucial cellular functions such as signaling and cell adhesion. We hope this effort can prompt single-cell and trace proteomic analysis and enable a rational selection of MS parameters.
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Affiliation(s)
- Bingyun Sun
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Faculty of Health Science, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada
| | - Jessica Rae Kovatch
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Faculty of Health Science, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada
| | - Albert Badiong
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Faculty of Health Science, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada
| | - Nabyl Merbouh
- Department of Chemistry, ‡Department of Molecular Biology and Biochemistry, and §Faculty of Health Science, Simon Fraser University , Burnaby, British Columbia V5A 1S6, Canada
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8
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Gao J, Zhong S, Zhou Y, He H, Peng S, Zhu Z, Liu X, Zheng J, Xu B, Zhou H. Comparative Evaluation of Small Molecular Additives and Their Effects on Peptide/Protein Identification. Anal Chem 2017; 89:5784-5792. [PMID: 28530406 DOI: 10.1021/acs.analchem.6b04886] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Detergents and salts are widely used in lysis buffers to enhance protein extraction from biological samples, facilitating in-depth proteomic analysis. However, these detergents and salt additives must be efficiently removed from the digested samples prior to LC-MS/MS analysis to obtain high-quality mass spectra. Although filter-aided sample preparation (FASP), acetone precipitation (AP), followed by in-solution digestion, and strong cation exchange-based centrifugal proteomic reactors (CPRs) are commonly used for proteomic sample processing, little is known about their efficiencies at removing detergents and salt additives. In this study, we (i) developed an integrative workflow for the quantification of small molecular additives in proteomic samples, developing a multiple reaction monitoring (MRM)-based LC-MS approach for the quantification of six additives (i.e., Tris, urea, CHAPS, SDS, SDC, and Triton X-100) and (ii) systematically evaluated the relationships between the level of additive remaining in samples following sample processing and the number of peptides/proteins identified by mass spectrometry. Although FASP outperformed the other two methods, the results were complementary in terms of peptide/protein identification, as well as the GRAVY index and amino acid distributions. This is the first systematic and quantitative study of the effect of detergents and salt additives on protein identification. This MRM-based approach can be used for an unbiased evaluation of the performance of new sample preparation methods. Data are available via ProteomeXchange under identifier PXD005405.
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Affiliation(s)
- Jing Gao
- Department of Chemistry, College of Sciences, Shanghai University , Shanghai, China 200444.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Shaoyun Zhong
- Department of Chemistry, College of Sciences, Shanghai University , Shanghai, China 200444.,Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Yanting Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203.,Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai, China 200237
| | - Han He
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Shuying Peng
- Thermo Fisher Scientific (China) Co., Ltd. , No. 6 Building, 27 Xinjinqiao Road, Shanghai, China 201206
| | - Zhenyun Zhu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Xing Liu
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203
| | - Jing Zheng
- Shanghai Key Laboratory of New Drug Design, School of Pharmacy, East China University of Science and Technology , 130 Meilong Road, Shanghai, China 200237
| | - Bin Xu
- Department of Chemistry, College of Sciences, Shanghai University , Shanghai, China 200444
| | - Hu Zhou
- Department of Analytical Chemistry and CAS Key Laboratory of Receptor Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences , 555 Zuchongzhi Road, Shanghai, China 201203.,University of Chinese Academy of Sciences , Beijing, China 100049.,E-institute of Shanghai Municipal Education Committee, Shanghai University of Traditional Chinese Medicine , 1200 Cai Lun Road, Shanghai, China 201203
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9
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Beck S, Michalski A, Raether O, Lubeck M, Kaspar S, Goedecke N, Baessmann C, Hornburg D, Meier F, Paron I, Kulak NA, Cox J, Mann M. The Impact II, a Very High-Resolution Quadrupole Time-of-Flight Instrument (QTOF) for Deep Shotgun Proteomics. Mol Cell Proteomics 2015; 14:2014-29. [PMID: 25991688 PMCID: PMC4587313 DOI: 10.1074/mcp.m114.047407] [Citation(s) in RCA: 120] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Indexed: 11/06/2022] Open
Abstract
Hybrid quadrupole time-of-flight (QTOF) mass spectrometry is one of the two major principles used in proteomics. Although based on simple fundamentals, it has over the last decades greatly evolved in terms of achievable resolution, mass accuracy, and dynamic range. The Bruker impact platform of QTOF instruments takes advantage of these developments and here we develop and evaluate the impact II for shotgun proteomics applications. Adaption of our heated liquid chromatography system achieved very narrow peptide elution peaks. The impact II is equipped with a new collision cell with both axial and radial ion ejection, more than doubling ion extraction at high tandem MS frequencies. The new reflectron and detector improve resolving power compared with the previous model up to 80%, i.e. to 40,000 at m/z 1222. We analyzed the ion current from the inlet capillary and found very high transmission (>80%) up to the collision cell. Simulation and measurement indicated 60% transfer into the flight tube. We adapted MaxQuant for QTOF data, improving absolute average mass deviations to better than 1.45 ppm. More than 4800 proteins can be identified in a single run of HeLa digest in a 90 min gradient. The workflow achieved high technical reproducibility (R2 > 0.99) and accurate fold change determination in spike-in experiments in complex mixtures. Using label-free quantification we rapidly quantified haploid against diploid yeast and characterized overall proteome differences in mouse cell lines originating from different tissues. Finally, after high pH reversed-phase fractionation we identified 9515 proteins in a triplicate measurement of HeLa peptide mixture and 11,257 proteins in single measurements of cerebellum—the highest proteome coverage reported with a QTOF instrument so far.
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Affiliation(s)
- Scarlet Beck
- From the ‡Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | | | - Oliver Raether
- §Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | - Markus Lubeck
- §Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | | | - Niels Goedecke
- §Bruker Daltonik GmbH, Fahrenheitstr. 4, 28359 Bremen, Germany
| | | | - Daniel Hornburg
- From the ‡Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Florian Meier
- From the ‡Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Igor Paron
- From the ‡Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Nils A Kulak
- From the ‡Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Juergen Cox
- ¶Computational Systems Biochemistry, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Matthias Mann
- From the ‡Proteomics and Signal Transduction, Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany;
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10
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Krisp C, Yang H, van Soest R, Molloy MP. Online Peptide fractionation using a multiphasic microfluidic liquid chromatography chip improves reproducibility and detection limits for quantitation in discovery and targeted proteomics. Mol Cell Proteomics 2015; 14:1708-19. [PMID: 25850434 DOI: 10.1074/mcp.m114.046425] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2014] [Indexed: 12/19/2022] Open
Abstract
Comprehensive proteomic profiling of biological specimens usually requires multidimensional chromatographic peptide fractionation prior to mass spectrometry. However, this approach can suffer from poor reproducibility because of the lack of standardization and automation of the entire workflow, thus compromising performance of quantitative proteomic investigations. To address these variables we developed an online peptide fractionation system comprising a multiphasic liquid chromatography (LC) chip that integrates reversed phase and strong cation exchange chromatography upstream of the mass spectrometer (MS). We showed superiority of this system for standardizing discovery and targeted proteomic workflows using cancer cell lysates and nondepleted human plasma. Five-step multiphase chip LC MS/MS acquisition showed clear advantages over analyses of unfractionated samples by identifying more peptides, consuming less sample and often improving the lower limits of quantitation, all in highly reproducible, automated, online configuration. We further showed that multiphase chip LC fractionation provided a facile means to detect many N- and C-terminal peptides (including acetylated N terminus) that are challenging to identify in complex tryptic peptide matrices because of less favorable ionization characteristics. Given as much as 95% of peptides were detected in only a single salt fraction from cell lysates we exploited this high reproducibility and coupled it with multiple reaction monitoring on a high-resolution MS instrument (MRM-HR). This approach increased target analyte peak area and improved lower limits of quantitation without negatively influencing variance or bias. Further, we showed a strategy to use multiphase LC chip fractionation LC-MS/MS for ion library generation to integrate with SWATH(TM) data-independent acquisition quantitative workflows. All MS data are available via ProteomeXchange with identifier PXD001464.
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Affiliation(s)
- Christoph Krisp
- From the ‡Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, 2109, Sydney, Australia
| | - Hao Yang
- §Eksigent, part of AB SCIEX, 94065, Redwood City, California
| | - Remco van Soest
- §Eksigent, part of AB SCIEX, 94065, Redwood City, California
| | - Mark P Molloy
- From the ‡Australian Proteome Analysis Facility (APAF), Department of Chemistry and Biomolecular Sciences, Macquarie University, 2109, Sydney, Australia;
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11
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Pooladi M, Abad SKR, Hashemi M. Proteomics analysis of human brain glial cell proteome by 2D gel. Indian J Cancer 2015; 51:159-62. [PMID: 25104200 DOI: 10.4103/0019-509x.138271] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Proteomics is increasingly employed in both neurological and oncological research, and applied widely in every area of neuroscience research including brain cancer. Astrocytomas are the most common glioma and can occur in most parts of the brain and occasionally in the spinal cord. Patients with high-grade astrocytomas have a life expectancy of <1 year even after surgery, chemotherapy, and radiotherapy. MATERIALS AND METHODS We extracted proteins from tumors and normal brain tissues and then evaluated the protein purity by Bradford test and spectrophotometry method. In this study, we separated proteins by the two-dimensional (2DG) gel electrophoresis method, and the spots were analyzed and compared using statistical data. RESULTS On each analytical 2D gel, an average of 800 spots was observed. In this study, 164 spots exhibited up-regulation of expression level, whereas the remaining 179 spots decreased in astrocytoma tumor relative to normal tissue. RESULTS demonstrate that functional clustering and principal component analysis (PCA) has considerable merits in aiding the interpretation of proteomic data. Proteomics is a powerful tool in identifying multiple proteins that are altered following a neuropharmacological intervention in a disease of the central nervous system (CNS). CONCLUSION 2-D gel and cluster analysis have important roles in the diagnostic management of astrocytoma patients, providing insight into tumor biology. The application of proteomics to CNS research has invariably been very successful in yielding large amounts of data.
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Affiliation(s)
| | | | - M Hashemi
- Department of Genetics, Tehran Medical Branch, Islamic Azad University, Tehran, Iran
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12
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Wiśniewski JR, Hein MY, Cox J, Mann M. A "proteomic ruler" for protein copy number and concentration estimation without spike-in standards. Mol Cell Proteomics 2014; 13:3497-506. [PMID: 25225357 PMCID: PMC4256500 DOI: 10.1074/mcp.m113.037309] [Citation(s) in RCA: 563] [Impact Index Per Article: 56.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Revised: 09/08/2014] [Indexed: 12/12/2022] Open
Abstract
Absolute protein quantification using mass spectrometry (MS)-based proteomics delivers protein concentrations or copy numbers per cell. Existing methodologies typically require a combination of isotope-labeled spike-in references, cell counting, and protein concentration measurements. Here we present a novel method that delivers similar quantitative results directly from deep eukaryotic proteome datasets without any additional experimental steps. We show that the MS signal of histones can be used as a "proteomic ruler" because it is proportional to the amount of DNA in the sample, which in turn depends on the number of cells. As a result, our proteomic ruler approach adds an absolute scale to the MS readout and allows estimation of the copy numbers of individual proteins per cell. We compare our protein quantifications with values derived via the use of stable isotope labeling by amino acids in cell culture and protein epitope signature tags in a method that combines spike-in protein fragment standards with precise isotope label quantification. The proteomic ruler approach yields quantitative readouts that are in remarkably good agreement with results from the precision method. We attribute this surprising result to the fact that the proteomic ruler approach omits error-prone steps such as cell counting or protein concentration measurements. The proteomic ruler approach is readily applicable to any deep eukaryotic proteome dataset-even in retrospective analysis-and we demonstrate its usefulness with a series of mouse organ proteomes.
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Affiliation(s)
- Jacek R Wiśniewski
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Marco Y Hein
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Jürgen Cox
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Matthias Mann
- From the ‡Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
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13
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Mitulović G. New HPLC Techniques for Proteomics Analysis: A Short Overview of Latest Developments. J LIQ CHROMATOGR R T 2014. [DOI: 10.1080/10826076.2014.941266] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Goran Mitulović
- a Clinical Institute of Laboratory Medicine and Proteomics Core Facility , Medical University of Vienna , Wien , Austria
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14
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Zougman A, Selby PJ, Banks RE. Suspension trapping (STrap) sample preparation method for bottom-up proteomics analysis. Proteomics 2014; 14:1006-0. [PMID: 24678027 DOI: 10.1002/pmic.201300553] [Citation(s) in RCA: 254] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Revised: 01/16/2014] [Accepted: 02/11/2014] [Indexed: 01/28/2023]
Abstract
Despite recent developments in bottom-up proteomics, the need still exists in a fast, uncomplicated, and robust method for comprehensive sample processing especially when applied to low protein amounts. The suspension trapping method combines the advantage of efficient SDS-based protein extraction with rapid detergent removal, reactor-type protein digestion, and peptide cleanup. Proteins are solubilized in SDS. The sample is acidified and introduced into the suspension trapping tip incorporating the depth filter and hydrophobic compartments, filled with the neutral pH methanolic solution. The instantly formed fine protein suspension is trapped in the depth filter stack-this crucial step is aimed at separating the particulate matter in space. SDS and other contaminants are removed in the flow-through, and a protease is introduced. Following the digestion, the peptides are cleaned up using the tip's hydrophobic part. The methodology allows processing of protein loads down to the low microgram/submicrogram levels. The detergent removal takes about 5 min, whereas the tryptic proteolysis of a cellular lysate is complete in as little as 30 min. We have successfully utilized the method for analysis of cellular lysates, enriched membrane preparations, and immunoprecipitates. We expect that due to its robustness and simplicity, the method will become an essential proteomics tool.
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Affiliation(s)
- Alexandre Zougman
- Cancer Research UK Centre, Leeds Institute of Cancer and Pathology, St James's University Hospital, Leeds, UK
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15
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Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells. Nat Methods 2014; 11:319-24. [PMID: 24487582 DOI: 10.1038/nmeth.2834] [Citation(s) in RCA: 1166] [Impact Index Per Article: 116.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 12/20/2013] [Indexed: 12/13/2022]
Abstract
Mass spectrometry (MS)-based proteomics typically employs multistep sample-preparation workflows that are subject to sample contamination and loss. We report an in-StageTip method for performing sample processing, from cell lysis through elution of purified peptides, in a single, enclosed volume. This robust and scalable method largely eliminates contamination or loss. Peptides can be eluted in several fractions or in one step for single-run proteome analysis. In one day, we obtained the largest proteome coverage to date for budding and fission yeast, and found that protein copy numbers in these cells were highly correlated (R(2) = 0.78). Applying the in-StageTip method to quadruplicate measurements of a human cell line, we obtained copy-number estimates for 9,667 human proteins and observed excellent quantitative reproducibility between replicates (R(2) = 0.97). The in-StageTip method is straightforward and generally applicable in biological or clinical applications.
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16
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Cheng G, Chen P, Wang ZG, Sui XJ, Zhang JL, Ni JZ. Immobilization of trypsin onto multifunctional meso-/macroporous core-shell microspheres: A new platform for rapid enzymatic digestion. Anal Chim Acta 2014; 812:65-73. [DOI: 10.1016/j.aca.2013.12.035] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2013] [Revised: 12/16/2013] [Accepted: 12/24/2013] [Indexed: 10/25/2022]
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17
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HEO J. Spatial Distance Effect of Bienzymes on the Efficiency of Sequential Reactions in a Microfluidic Reactor Packed with Enzyme-immobilized Microbeads. ANAL SCI 2014; 30:991-7. [DOI: 10.2116/analsci.30.991] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Jinseok HEO
- Department of Chemistry, The State University of New York College at Buffalo
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18
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Hustoft HK, Brandtzaeg OK, Rogeberg M, Misaghian D, Torsetnes SB, Greibrokk T, Reubsaet L, Wilson SR, Lundanes E. Integrated enzyme reactor and high resolving chromatography in "sub-chip" dimensions for sensitive protein mass spectrometry. Sci Rep 2013; 3:3511. [PMID: 24336509 PMCID: PMC3863811 DOI: 10.1038/srep03511] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2013] [Accepted: 11/28/2013] [Indexed: 12/29/2022] Open
Abstract
Reliable, sensitive and automatable analytical methodology is of great value in e.g. cancer diagnostics. In this context, an on-line system for enzymatic cleavage of proteins, subsequent peptide separation by liquid chromatography (LC) with mass spectrometric detection has been developed using "sub-chip" columns (10-20 μm inner diameter, ID). The system could detect attomole amounts of isolated cancer biomarker progastrin-releasing peptide (ProGRP), in a more automatable fashion compared to previous methods. The workflow combines protein digestion using an 20 μm ID immobilized trypsin reactor with a polymeric layer of 2-hydroxyethyl methacrylate-vinyl azlactone (HEMA-VDM), desalting on a polystyrene-divinylbenzene (PS-DVB) monolithic trap column, and subsequent separation of resulting peptides on a 10 μm ID (PS-DVB) porous layer open tubular (PLOT) column. The high resolution of the PLOT columns was maintained in the on-line system, resulting in narrow chromatographic peaks of 3-5 seconds. The trypsin reactors provided repeatable performance and were compatible with long-term storage.
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Affiliation(s)
- Hanne Kolsrud Hustoft
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | | | - Magnus Rogeberg
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
- Department of Neurology, Akershus University Hospital, 1478 Lørenskog, Norway
| | - Dorna Misaghian
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Silje Bøen Torsetnes
- School of Pharmacy, University of Oslo, Post Box 1068 Blindern, NO-0316 Oslo, Norway
| | - Tyge Greibrokk
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Léon Reubsaet
- School of Pharmacy, University of Oslo, Post Box 1068 Blindern, NO-0316 Oslo, Norway
| | - Steven Ray Wilson
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
| | - Elsa Lundanes
- Department of Chemistry, University of Oslo, Post Box 1033 Blindern, NO-0315 Oslo, Norway
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19
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Vladisavljević GT, Khalid N, Neves MA, Kuroiwa T, Nakajima M, Uemura K, Ichikawa S, Kobayashi I. Industrial lab-on-a-chip: design, applications and scale-up for drug discovery and delivery. Adv Drug Deliv Rev 2013; 65:1626-63. [PMID: 23899864 DOI: 10.1016/j.addr.2013.07.017] [Citation(s) in RCA: 152] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2013] [Revised: 07/16/2013] [Accepted: 07/18/2013] [Indexed: 01/09/2023]
Abstract
Microfluidics is an emerging and promising interdisciplinary technology which offers powerful platforms for precise production of novel functional materials (e.g., emulsion droplets, microcapsules, and nanoparticles as drug delivery vehicles- and drug molecules) as well as high-throughput analyses (e.g., bioassays, detection, and diagnostics). In particular, multiphase microfluidics is a rapidly growing technology and has beneficial applications in various fields including biomedicals, chemicals, and foods. In this review, we first describe the fundamentals and latest developments in multiphase microfluidics for producing biocompatible materials that are precisely controlled in size, shape, internal morphology and composition. We next describe some microfluidic applications that synthesize drug molecules, handle biological substances and biological units, and imitate biological organs. We also highlight and discuss design, applications and scale up of droplet- and flow-based microfluidic devices used for drug discovery and delivery.
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20
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Martin JG, Rejtar T, Martin SA. Integrated microscale analysis system for targeted liquid chromatography mass spectrometry proteomics on limited amounts of enriched cell populations. Anal Chem 2013; 85:10680-5. [PMID: 24083476 DOI: 10.1021/ac401937c] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Limited samples, such as those that are in vivo sourced via biopsy, are closely representative of biological systems and contain valuable information for drug discovery. However, these precious samples are often heterogeneous and require cellular prefractionation prior to proteomic analysis to isolate specific subpopulations of interest. Enriched cells from in vivo samples are often very limited (<10(4) cells) and pose a significant challenge to proteomic nanoliquid chromatography mass spectrometry (nanoLCMS) sample preparation. To enable the streamlined analysis of these limited samples, we have developed an online cell enrichment, microscale sample preparation, nanoLCMS proteomics workflow by integrating fluorescence activated cell sorting (FACS), focused ultrasonication, microfluidics, immobilized trypsin digestion, and nanoLCMS. To assess the performance of the online FACS-Chip-LCMS workflow, 5000 fluorescent labeled cells were enriched from a 5% heterogeneous cell population and processed for LCMS proteomics in less than 2 h. Within these 5000 enriched cells, 30 peptides corresponding to 17 proteins spanning more than 4 orders of magnitude of cellular abundance were quantified using a QExactive MS. The results from the online FACS-Chip-LCMS workflow starting from 5000 enriched cells were directly compared to results from a traditional macroscale sample preparation workflow starting from 2.0 × 10(6) cells. The microscale FACS-Chip-LCMS workflow demonstrated high cellular enrichment efficiency and high peptide recovery across the wide dynamic range of targeted peptides. Overall the microscale FACS-Chip-LCMS workflow has shown effectiveness in efficiently preparing limited amounts of FACS enriched cells in an online manner for proteomic LCMS.
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Affiliation(s)
- Jeffrey G Martin
- Novartis Institutes for Biomedical Research , Cambridge, Massachusetts 02139, United States
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21
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Pham MD, Yu SSF, Han CC, Chan SI. Improved Mass Spectrometric Analysis of Membrane Proteins Based on Rapid and Versatile Sample Preparation on Nanodiamond Particles. Anal Chem 2013; 85:6748-55. [DOI: 10.1021/ac400713g] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Minh D. Pham
- Taiwan International Graduate Program (TIGP), Academia Sinica, Taipei 11529, Taiwan
- Department of Chemistry, National Tsing Hua University, Hsinchu 30013, Taiwan
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Steve S.-F. Yu
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chau-Chung Han
- Institute of Atomic and Molecular Sciences, Academia Sinica, Taipei 10617, Taiwan
| | - Sunney I. Chan
- Institute of Chemistry, Academia Sinica, Taipei 11529, Taiwan
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22
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Nge PN, Rogers CI, Woolley AT. Advances in microfluidic materials, functions, integration, and applications. Chem Rev 2013; 113:2550-83. [PMID: 23410114 PMCID: PMC3624029 DOI: 10.1021/cr300337x] [Citation(s) in RCA: 518] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Pamela N. Nge
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Chad I. Rogers
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
| | - Adam T. Woolley
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84602
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23
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Yamaguchi H, Miyazaki M. Enzyme-immobilized reactors for rapid and efficient sample preparation in MS-based proteomic studies. Proteomics 2013; 13:457-66. [DOI: 10.1002/pmic.201200272] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2012] [Revised: 11/03/2012] [Accepted: 11/14/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Hiroshi Yamaguchi
- Liberal Arts Education Center; Tokai University; Minamiaso Kumamoto Japan
| | - Masaya Miyazaki
- Measurement Solution Research Center; National Institute of Advanced Industrial Science and Technology; Tosu Saga Japan
- Interdisciplinary Graduate School of Engineering Science; Kyushu University; Kasuga Fukuoka Japan
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24
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LIU J, WANG FJ, ZHANG ZB, ZOU HF. Reversed Phase Monolithic Column Based Enzyme Reactor for Protein Analysis. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2013. [DOI: 10.1016/s1872-2040(13)60619-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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25
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Wang F, Wei X, Zhou H, Liu J, Figeys D, Zou H. Combination of online enzyme digestion with stable isotope labeling for high-throughput quantitative proteome analysis. Proteomics 2012; 12:3129-37. [DOI: 10.1002/pmic.201200162] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2012] [Revised: 07/15/2012] [Accepted: 08/14/2012] [Indexed: 12/31/2022]
Affiliation(s)
- Fangjun Wang
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
| | - Xiaoluan Wei
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
| | - Hu Zhou
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
- Shanghai Institute of Materia Medica; Chinese Academy of Sciences; Shanghai China
| | - Jing Liu
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
| | - Daniel Figeys
- Ottawa Institute of Systems Biology; University of Ottawa; Ottawa Canada
| | - Hanfa Zou
- CAS Key Lab of Separation Sciences for Analytical Chemistry; National Chromatographic Research and Analysis Center; Dalian Institute of Chemical Physics, Chinese Academy of Sciences; Dalian China
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26
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Calleri E, Ambrosini S, Temporini C, Massolini G. New monolithic chromatographic supports for macromolecules immobilization: Challenges and opportunities. J Pharm Biomed Anal 2012; 69:64-76. [DOI: 10.1016/j.jpba.2012.01.032] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2011] [Revised: 01/19/2012] [Accepted: 01/20/2012] [Indexed: 01/15/2023]
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27
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Krenkova J, Foret F. On-line CE/ESI/MS interfacing: recent developments and applications in proteomics. Proteomics 2012; 12:2978-90. [PMID: 22888067 DOI: 10.1002/pmic.201200140] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2012] [Revised: 05/17/2012] [Accepted: 06/12/2012] [Indexed: 12/13/2022]
Abstract
After shining as the ultimate separation - sequencing technique used for the successful completion of the Human Genome Project, in the early 2000s CE experienced lowered popularity among separation scientists. The renewed interest in recent years relates to the separation needs, especially in proteomics, metabolomics, and glycomics, where CE complements liquid chromatography techniques. This interest is further boosted by the regulators requiring additional separation techniques for characterization of newly developed pharmaceuticals. This paper gives a short overview of recent developments in the on-line interfacing of CE separation techniques with electrospray ionization/mass spectrometric analysis. Both the instrumentation and selected CE/ESI/MS applications including analyses of peptides, proteins, and glycans are discussed with the stress on research published in the past 3 years. Techniques related to the proteomic and glycomic analyses such as sample preconcentration, on-line protein digestion, and analyte derivatization prior CE/ESI/MS analysis are also included.
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Affiliation(s)
- Jana Krenkova
- Institute of Analytical Chemistry of the ASCR, Brno, Czech Republic.
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28
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Zhang Z, Wang F, Xu B, Qin H, Ye M, Zou H. Preparation of capillary hybrid monolithic column with sulfonate strong cation exchanger for proteome analysis. J Chromatogr A 2012; 1256:136-43. [DOI: 10.1016/j.chroma.2012.07.071] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2012] [Revised: 07/17/2012] [Accepted: 07/19/2012] [Indexed: 11/16/2022]
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29
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Çelebi B, Bayraktar A, Tuncel A. Synthesis of a monolithic, micro-immobilised enzyme reactor via click-chemistry. Anal Bioanal Chem 2012; 403:2655-63. [DOI: 10.1007/s00216-012-6075-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2011] [Revised: 04/19/2012] [Accepted: 04/21/2012] [Indexed: 10/28/2022]
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