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Xu T, Han L, George Thompson AM, Sun L. An improved capillary isoelectric focusing-mass spectrometry method for high-resolution characterization of monoclonal antibody charge variants. ANALYTICAL METHODS : ADVANCING METHODS AND APPLICATIONS 2022; 14:383-393. [PMID: 34939625 DOI: 10.1039/d1ay01556g] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Routine and high-resolution characterization of monoclonal antibody (mAb) charge variants is vital for controlling mAb quality as therapeutics. Capillary isoelectric focusing-mass spectrometry (cIEF-MS) has emerged as a powerful tool for characterizing mAb charge variants because it can achieve high-resolution separation and highly sensitive detection of proteins. It provides much better identification of charge variants than the traditionally used cIEF-UV method. However, further improvement of cIEF-MS regarding stability and separation resolution is needed. Here, we improved the stability and enhanced separation resolution of automated cIEF-MS by bettering the quality of capillary neutral coating, reducing catholyte pH to 10 for cIEF-MS for the first time, and systematically optimizing the cIEF separation conditions. The improved cIEF-MS method was applied to characterize charge variants of three previously well characterized mAbs (NISTmAb, cetuximab, trastuzumab) and one tool mAb (mAb1). The charge variants of the studied mAbs were well resolved, and the majority of post-translational modifications (PTMs) found in those mAbs agreed with the literature. cIEF-MS analyses of mAb1 were capable of discovering ten charge variants with various interesting PTMs, such as PGK amidation, incomplete C-terminal lysine clipping, glycosylation, and deamination. cIEF-MS was successfully used for accurately determining the isoelectric points (pIs) of mAb1 charge variants via analyzing the pI markers and spiking in a standard protein (cytochrome c) to samples for migration time normalization, which is beneficial for evaluating pI-related pharmacokinetic properties. Our cIEF-MS agreed with and, in some cases (i.e., cetuximab and mAb1), outperformed cIEF-UV for detecting mAb charge variants.
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Affiliation(s)
- Tian Xu
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
| | - Linjie Han
- New Biological Entities (NBE), Analytical R&D, AbbVie Inc., 1 Waukegan Rd, North Chicago, IL, 60064, USA
| | - Alayna M George Thompson
- New Biological Entities (NBE), Analytical R&D, AbbVie Inc., 1 Waukegan Rd, North Chicago, IL, 60064, USA
| | - Liangliang Sun
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, MI 48824, USA.
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2
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Proteomic Profiling of Emiliania huxleyi Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry. Molecules 2020; 25:molecules25133028. [PMID: 32630776 PMCID: PMC7411631 DOI: 10.3390/molecules25133028] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Revised: 06/30/2020] [Accepted: 06/30/2020] [Indexed: 12/31/2022] Open
Abstract
Emiliania huxleyi is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of Emiliania huxleyi have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) system consisting of strong cation exchange, high- and low-pH reversed-phase liquid chromatography was established for in-depth proteomic profiling of Emiliania huxleyi. From tryptic proteome digest, 70 fractions were generated and analyzed using liquid chromatography-tandem mass spectrometry. In total, more than 84,000 unique peptides and 10,000 proteins groups were identified with a false discovery rate of ≤0.01. The physicochemical properties of the identified peptides were evaluated. Using ClueGO, approximately 700 gene ontology terms and 15 pathways were defined from the identified protein groups with p-value ≤0.05, covering a wide range of biological processes, cellular components, and molecular functions. Many biological processes associated with CO2 fixation, photosynthesis, biosynthesis, and metabolic process were identified. Various molecular functions relating to protein binding and enzyme activities were also found. The 3D-LC strategy is a powerful approach for comparative proteomic studies on Emiliania huxleyi to reveal changes in its protein level and related mechanism.
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3
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Lu B, Maharbiz MM. Ion concentration polarization (ICP) of proteins at silicon micropillar nanogaps. PLoS One 2019; 14:e0223732. [PMID: 31682605 PMCID: PMC6827887 DOI: 10.1371/journal.pone.0223732] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 09/26/2019] [Indexed: 01/21/2023] Open
Abstract
Fast detection of low-abundance protein remains a challenge because detection speed is limited by analyte transport to the detection site of a biosensor. In this paper, we demonstrate a scalable fabrication process for producing vertical nanogaps between micropillars which enable ion concentration polarization (ICP) enrichment for fast analyte detection. Compared to horizontal nanochannels, massively paralleled vertical nanogaps not only provide comparable electrokinetics, but also significantly reduce fluid resistance, enabling microbead-based assays. The channels on the device are straightforward to fabricate and scalable using conventional lithography tools. The device is capable of enriching protein molecules by >1000 fold in 10 min. We demonstrate fast detection of IL6 down to 7.4 pg/ml with only a 10 min enrichment period followed by a 5 min incubation. This is a 162-fold enhancement in sensitivity compared to that without enrichment. Our results demonstrate the possibility of using silicon/silica based vertical nanogaps to mimic the function of polymer membranes for the purpose of protein enrichment.
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Affiliation(s)
- Bochao Lu
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California–Berkeley, Berkeley, California, United States of America
| | - Michel M. Maharbiz
- UC Berkeley-UCSF Graduate Program in Bioengineering, University of California–Berkeley, Berkeley, California, United States of America
- Electrical Engineering and Computer Science Department, University of California–Berkeley, Berkeley, California, United States of America
- Chan Zuckerberg Biohub, San Francisco, California, United States of America
- * E-mail:
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4
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Beutner A, Herl T, Matysik FM. Selectivity enhancement in capillary electrophoresis by means of two-dimensional separation or dual detection concepts. Anal Chim Acta 2018; 1057:18-35. [PMID: 30832915 DOI: 10.1016/j.aca.2018.11.042] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2018] [Revised: 11/01/2018] [Accepted: 11/19/2018] [Indexed: 12/18/2022]
Abstract
For the identification and quantification of analytes in complex samples, highly selective analytical strategies are required. The selectivity of single separation techniques such as gas chromatography (GC), liquid chromatography (LC), or capillary electrophoresis (CE) with common detection principles can be enhanced by hyphenating orthogonal separation techniques but also by using complementary detection systems. In this review, two-dimensional systems containing CE in at least one dimension are reviewed, namely LC-CE or 2D CE systems. Particular attention is paid to the aspect of selectivity enhancement due to the orthogonality of the different separation mechanisms. As an alternative concept, dual detection approaches are reviewed using the common detectors of CE such as UV/VIS, laser-induced fluorescence, capacitively coupled contactless conductivity (C4D), electrochemical detection, and mass spectrometry. Special emphasis is given to dual detection systems implementing the highly flexible C4D as one detection component. Selectivity enhancement can be achieved in case of complementarity of the different detection techniques.
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Affiliation(s)
- Andrea Beutner
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany
| | - Thomas Herl
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany
| | - Frank-Michael Matysik
- Institute of Analytical Chemistry, Chemo- and Biosensors, University of Regensburg, Universitaetsstrasse 31, 93053, Regensburg, Germany.
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5
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Mo J, Jin R, Yan Q, Sokolowska I, Lewis MJ, Hu P. Quantitative analysis of glycation and its impact on antigen binding. MAbs 2018; 10:406-415. [PMID: 29436927 PMCID: PMC5916557 DOI: 10.1080/19420862.2018.1438796] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Glycation has been observed in antibody therapeutics manufactured by the fed-batch fermentation process. It not only increases the heterogeneity of antibodies, but also potentially affects product safety and efficacy. In this study, non-glycated and glycated fractions enriched from a monoclonal antibody (mAb1) as well as glucose-stressed mAb1 were characterized using a variety of biochemical, biophysical and biological assays to determine the effects of glycation on the structure and function of mAb1. Glycation was detected at multiple lysine residues and reduced the antigen binding activity of mAb1. Heavy chain Lys100, which is located in the complementary-determining region of mAb1, had the highest levels of glycation in both stressed and unstressed samples, and glycation of this residue was likely responsible for the loss of antigen binding based on hydrogen/deuterium exchange mass spectrometry analysis. Peptide mapping and intact liquid chromatography-mass spectrometry (LC-MS) can both be used to monitor the glycation levels. Peptide mapping provides site specific glycation results, while intact LC-MS is a quicker and simpler method to quantitate the total glycation levels and is more useful for routine testing. Capillary isoelectric focusing (cIEF) can also be used to monitor glycation because glycation induces an acidic shift in the cIEF profile. As expected, total glycation measured by intact LC-MS correlated very well with the percentage of total acidic peaks or main peak measured by cIEF. In summary, we demonstrated that glycation can affect the function of a representative IgG1 mAb. The analytical characterization, as described here, should be generally applicable for other therapeutic mAbs.
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Affiliation(s)
- Jingjie Mo
- a Large Molecules Analytical Development, Pharmaceutical Development & Manufacturing Sciences , Janssen Research & Development, LLC , Malvern , Pennsylvania , United States
| | - Renzhe Jin
- a Large Molecules Analytical Development, Pharmaceutical Development & Manufacturing Sciences , Janssen Research & Development, LLC , Malvern , Pennsylvania , United States
| | - Qingrong Yan
- a Large Molecules Analytical Development, Pharmaceutical Development & Manufacturing Sciences , Janssen Research & Development, LLC , Malvern , Pennsylvania , United States
| | - Izabela Sokolowska
- a Large Molecules Analytical Development, Pharmaceutical Development & Manufacturing Sciences , Janssen Research & Development, LLC , Malvern , Pennsylvania , United States
| | - Michael J Lewis
- a Large Molecules Analytical Development, Pharmaceutical Development & Manufacturing Sciences , Janssen Research & Development, LLC , Malvern , Pennsylvania , United States
| | - Ping Hu
- a Large Molecules Analytical Development, Pharmaceutical Development & Manufacturing Sciences , Janssen Research & Development, LLC , Malvern , Pennsylvania , United States
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6
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Ahn S, Kim B, Han RX, Yu HD. Characterization of Recombinant Human Erythropoietin Isoforms by Capillary Isoelectric Focusing with Hydroxypropyl Cellulose-Coated Capillaries. Chromatographia 2017. [DOI: 10.1007/s10337-017-3291-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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7
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Ranjbar L, Foley JP, Breadmore MC. Multidimensional liquid-phase separations combining both chromatography and electrophoresis – A review. Anal Chim Acta 2017; 950:7-31. [DOI: 10.1016/j.aca.2016.10.025] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Revised: 10/17/2016] [Accepted: 10/20/2016] [Indexed: 01/31/2023]
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8
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Hühner J, Neusüß C. CIEF-CZE-MS applying a mechanical valve. Anal Bioanal Chem 2016; 408:4055-61. [PMID: 27052774 DOI: 10.1007/s00216-016-9498-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2015] [Revised: 03/14/2016] [Accepted: 03/16/2016] [Indexed: 02/03/2023]
Abstract
Separation and determination of proteins by capillary isoelectric focusing (CIEF) and mass spectrometry (MS) are essential and complementary techniques in the field of bioanalysis. The hyphenation of these two techniques is challenging due to the nonvolatile substances required for the CIEF separation. An additional separation step prior to MS enables the removal of the nonvolatile substances. However, it is complicated due to the small transfer volume and the required high voltages in the CIEF process. In order to remove nonvolatile substances and transfer the analytes toward the mass spectrometer, we applied a four-port valve to couple CIEF online to capillary electrophoresis-mass spectrometry. To demonstrate the power of this concept, hemoglobin and glycated hemoglobin with an isoelectric point difference of 0.037 were separated via isoelectric focusing and characterized by MS. In general, this setup guaranties interference-free mass spectra and will provide an information-rich and sensitive top down protein characterization. Graphical abstract Interference free coupling of capillary isoelectric focusing to mass spectrometry by applying a mechanical valve. The focused proteins were tranferred from the isoelectric focusing to capillary electrophoresis by a mechanical valve. Afterwards, the transferred protein was sepearated from ionization interfering substances in the capillary electrophoresis prior to the mass spectrometry detection.
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Affiliation(s)
- Jens Hühner
- Faculty of Chemistry, Aalen University, Beethovenstr. 1, 73430, Aalen, Germany.,Institute of Pharmaceutical Science, University of Tübingen, Auf der Morgenstelle 8, 72076, Tübingen, Germany
| | - Christian Neusüß
- Faculty of Chemistry, Aalen University, Beethovenstr. 1, 73430, Aalen, Germany.
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9
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Hühner J, Lämmerhofer M, Neusüß C. Capillary isoelectric focusing-mass spectrometry: Coupling strategies and applications. Electrophoresis 2015; 36:2670-2686. [DOI: 10.1002/elps.201500185] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Revised: 07/31/2015] [Accepted: 07/31/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Jens Hühner
- Faculty of Chemistry; Aalen University; Aalen Germany
| | - Michael Lämmerhofer
- Institute of Pharmaceutical Sciences; University of Tübingen; Tübingen Germany
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10
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Kohl FJ, Sánchez-Hernández L, Neusüß C. Capillary electrophoresis in two-dimensional separation systems: Techniques and applications. Electrophoresis 2014; 36:144-58. [DOI: 10.1002/elps.201400368] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Revised: 09/16/2014] [Accepted: 09/17/2014] [Indexed: 12/24/2022]
Affiliation(s)
- Felix J. Kohl
- Department of Chemistry; Aalen University; Aalen Germany
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11
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Kler PA, Sydes D, Huhn C. Column–coupling strategies for multidimensional electrophoretic separation techniques. Anal Bioanal Chem 2014; 407:119-38. [DOI: 10.1007/s00216-014-8099-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 08/06/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022]
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12
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Pirmoradian M, Zhang B, Chingin K, Astorga-Wells J, Zubarev RA. Membrane-Assisted Isoelectric Focusing Device As a Micropreparative Fractionator for Two-Dimensional Shotgun Proteomics. Anal Chem 2014; 86:5728-32. [DOI: 10.1021/ac404180e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mohammad Pirmoradian
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelesväg 2, SE-17177 Stockholm, Sweden
- Biomotif AB, Stockholm, Sweden
| | - Bo Zhang
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelesväg 2, SE-17177 Stockholm, Sweden
| | - Konstantin Chingin
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelesväg 2, SE-17177 Stockholm, Sweden
| | - Juan Astorga-Wells
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelesväg 2, SE-17177 Stockholm, Sweden
- Biomotif AB, Stockholm, Sweden
| | - Roman A. Zubarev
- Department
of Medical Biochemistry and Biophysics, Karolinska Institutet, Scheelesväg 2, SE-17177 Stockholm, Sweden
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13
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Wang Y, Balgley BM, Lee CS. Tissue proteomics using capillary isoelectric focusing-based multidimensional separations. Expert Rev Proteomics 2014; 2:659-67. [PMID: 16209646 DOI: 10.1586/14789450.2.5.659] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The capabilities of capillary isoelectric focusing-based multidimensional separations for performing proteome analysis from minute samples create new opportunities in the pursuit of biomarker discovery using enriched and selected cell populations procured from tissue specimens. In this article, recent advances in online integration of capillary isoelectric focusing with nano-reversed phase liquid chromatography for achieving high-resolution peptide and protein separations prior to mass spectrometry analysis are reviewed, along with its potential application to tissue proteomics. These proteome technological advances combined with recently developed tissue microdissection techniques, provide powerful tools for those seeking to gain a greater understanding at the global level of the cellular machinery associated with human diseases such as cancer.
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Affiliation(s)
- Yueju Wang
- Calibrant Biosystems, Gaithersburg, MD 20878, USA.
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14
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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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15
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Gao M, Qi D, Zhang P, Deng C, Zhang X. Development of multidimensional liquid chromatography and application in proteomic analysis. Expert Rev Proteomics 2014; 7:665-78. [DOI: 10.1586/epr.10.49] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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16
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Zhang Z, Wu S, Stenoien DL, Paša-Tolić L. High-throughput proteomics. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2014; 7:427-454. [PMID: 25014346 DOI: 10.1146/annurev-anchem-071213-020216] [Citation(s) in RCA: 171] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Mass spectrometry (MS)-based high-throughput proteomics is the core technique for large-scale protein characterization. Due to the extreme complexity of proteomes, sophisticated separation techniques and advanced MS instrumentation have been developed to extend coverage and enhance dynamic range and sensitivity. In this review, we discuss the separation and prefractionation techniques applied for large-scale analysis in both bottom-up (i.e., peptide-level) and top-down (i.e., protein-level) proteomics. Different approaches for quantifying peptides or intact proteins, including label-free and stable-isotope-labeling strategies, are also discussed. In addition, we present a brief overview of different types of mass analyzers and fragmentation techniques as well as selected emerging techniques.
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17
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Li S, Dong JY, Guo CG, Wu YX, Zhang W, Fan LY, Cao CX, Zhang WB. A stable and high-resolution isoelectric focusing capillary array device for micropreparative separation of proteins. Talanta 2013; 116:259-65. [DOI: 10.1016/j.talanta.2013.05.041] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2013] [Revised: 05/16/2013] [Accepted: 05/19/2013] [Indexed: 12/13/2022]
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18
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Mostovenko E, Hassan C, Rattke J, Deelder AM, van Veelen PA, Palmblad M. Comparison of peptide and protein fractionation methods in proteomics. EUPA OPEN PROTEOMICS 2013. [DOI: 10.1016/j.euprot.2013.09.001] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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19
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Stoyanov A. IEF-based multidimensional applications in proteomics: Toward higher resolution. Electrophoresis 2012; 33:3281-90. [DOI: 10.1002/elps.201200221] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2012] [Revised: 08/20/2012] [Accepted: 08/21/2012] [Indexed: 01/08/2023]
Affiliation(s)
- Alexander Stoyanov
- Department of Pathology and Anatomical Sciences; University of Missouri; Columbia; MO; USA
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20
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McPhee CK, Balgley BM, Nelson C, Hill JH, Batlevi Y, Fang X, Lee CS, Baehrecke EH. Identification of factors that function in Drosophila salivary gland cell death during development using proteomics. Cell Death Differ 2012; 20:218-25. [PMID: 22935612 DOI: 10.1038/cdd.2012.110] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Proteasome inhibitors induce cell death and are used in cancer therapy, but little is known about the relationship between proteasome impairment and cell death under normal physiological conditions. Here, we investigate the relationship between proteasome function and larval salivary gland cell death during development in Drosophila. Drosophila larval salivary gland cells undergo synchronized programmed cell death requiring both caspases and autophagy (Atg) genes during development. Here, we show that ubiquitin proteasome system (UPS) function is reduced during normal salivary gland cell death, and that ectopic proteasome impairment in salivary gland cells leads to early DNA fragmentation and salivary gland condensation in vivo. Shotgun proteomic analyses of purified dying salivary glands identified the UPS as the top category of proteins enriched, suggesting a possible compensatory induction of these factors to maintain proteolysis during cell death. We compared the proteome following ectopic proteasome impairment to the proteome during developmental cell death in salivary gland cells. Proteins that were enriched in both populations of cells were screened for their function in salivary gland degradation using RNAi knockdown. We identified several factors, including trol, a novel gene CG11880, and the cop9 signalsome component cop9 signalsome 6, as required for Drosophila larval salivary gland degradation.
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Affiliation(s)
- C K McPhee
- Department of Cancer Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA
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21
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Chingin K, Astorga-Wells J, Pirmoradian Najafabadi M, Lavold T, Zubarev RA. Separation of Polypeptides by Isoelectric Point Focusing in Electrospray-Friendly Solution Using a Multiple-Junction Capillary Fractionator. Anal Chem 2012; 84:6856-62. [DOI: 10.1021/ac3013016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Konstantin Chingin
- Department of Medical
Biochemistry
and Biophysics, Karolinska Institutet,
Scheeles väg 2, SE-17177 Stockholm, Sweden
| | - Juan Astorga-Wells
- Department of Medical
Biochemistry
and Biophysics, Karolinska Institutet,
Scheeles väg 2, SE-17177 Stockholm, Sweden
- Biomotif AB, Stockholm,
Sweden
| | - Mohammad Pirmoradian Najafabadi
- Department of Medical
Biochemistry
and Biophysics, Karolinska Institutet,
Scheeles väg 2, SE-17177 Stockholm, Sweden
- Biomotif AB, Stockholm,
Sweden
| | | | - Roman A. Zubarev
- Department of Medical
Biochemistry
and Biophysics, Karolinska Institutet,
Scheeles väg 2, SE-17177 Stockholm, Sweden
- Science for Life Laboratory, Stockholm, Sweden
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22
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Yang F, Shen Y, Camp DG, Smith RD. High-pH reversed-phase chromatography with fraction concatenation for 2D proteomic analysis. Expert Rev Proteomics 2012; 9:129-34. [PMID: 22462785 DOI: 10.1586/epr.12.15] [Citation(s) in RCA: 211] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Orthogonal high-resolution separations are critical for attaining improved analytical dynamic range and protein coverage in proteomic measurements. High-pH reversed-phase liquid chromatography (RPLC), followed by fraction concatenation, affords better peptide analysis than conventional strong cation-exchange chromatography applied for 2D proteomic analysis. For example, concatenated high-pH RPLC increased identification of peptides (by 1.8-fold) and proteins (by 1.6-fold) in shotgun proteomics analyses of a digested human protein sample. Additional advantages of high-pH RPLC with fraction concatenation include improved protein sequence coverage, simplified sample processing and reduced sample losses, making this an attractive alternative to strong cation-exchange chromatography in conjunction with second-dimension low-pH RPLC for 2D proteomics analyses.
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Affiliation(s)
- Feng Yang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA 99352, USA
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23
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Mass Spectrometry-based Proteomics and Peptidomics for Systems Biology and Biomarker Discovery. ACTA ACUST UNITED AC 2012; 7:313-335. [PMID: 24504115 DOI: 10.1007/s11515-012-1218-y] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The scientific community has shown great interest in the field of mass spectrometry-based proteomics and peptidomics for its applications in biology. Proteomics technologies have evolved to produce large datasets of proteins or peptides involved in various biological and disease progression processes producing testable hypothesis for complex biological questions. This review provides an introduction and insight to relevant topics in proteomics and peptidomics including biological material selection, sample preparation, separation techniques, peptide fragmentation, post-translation modifications, quantification, bioinformatics, and biomarker discovery and validation. In addition, current literature and remaining challenges and emerging technologies for proteomics and peptidomics are presented.
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Ramautar R, Heemskerk AAM, Hensbergen PJ, Deelder AM, Busnel JM, Mayboroda OA. CE-MS for proteomics: Advances in interface development and application. J Proteomics 2012; 75:3814-28. [PMID: 22609513 DOI: 10.1016/j.jprot.2012.04.050] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2012] [Revised: 04/23/2012] [Accepted: 04/30/2012] [Indexed: 12/25/2022]
Abstract
Capillary electrophoresis-mass spectrometry (CE-MS) has emerged as a powerful technique for the analysis of proteins and peptides. Over the past few years, significant progress has been made in the development of novel and more effective interfaces for hyphenating CE to MS. This review provides an overview of these new interfacing techniques for coupling CE to MS, covering the scientific literature from January 2007 to December 2011. The potential of these new CE-MS interfacing techniques is demonstrated within the field of (clinical) proteomics, more specifically "bottom-up" proteomics, by showing examples of the analysis of various biological samples. The relevant papers on CE-MS for proteomics are comprehensively summarized in tables, including, e.g. information on sample type and pretreatment, interfacing and MS detection mode. Finally, general conclusions and future perspectives are provided.
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Affiliation(s)
- Rawi Ramautar
- Biomolecular Mass Spectrometry Unit, Department of Parasitology, Leiden University Medical Center, Albinusdreef 2, 2300 RC, Leiden, The Netherlands.
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25
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Abstract
Microscale 2D separation systems have been implemented in capillaries and microfabricated channels. They offer advantages of faster analysis, higher separation efficiency and less sample consumption than the conventional methods, such as liquid chromatography (LC) in a column and slab gel electrophoresis. In this article, we review their recent advancement, focusing on three types of platforms, including 2D capillary electrophoresis (CE), CE coupling with capillary LC, and microfluidic devices. A variety of CE and LC modes have been employed to construct 2D separation systems via sophistically designed interfaces. Coupling of different separation modes has also been realized in a number of microfluidic devices. These separation systems have been applied for the proteomic analysis of various biological samples, ranging from a single cell to tumor tissues.
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Affiliation(s)
- Xin Xu
- Interdisciplinary Microsystems Group, Department of Mechanical & Aerospace Engineering, University of Florida, Gainesville, FL 32611-6250, USA
| | - Ke Liu
- Interdisciplinary Microsystems Group, Department of Mechanical & Aerospace Engineering, University of Florida, Gainesville, FL 32611-6250, USA
| | - Z. Hugh Fan
- Interdisciplinary Microsystems Group, Department of Mechanical & Aerospace Engineering, University of Florida, Gainesville, FL 32611-6250, USA
- J Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, FL 32611-6131, USA
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Seshi B, Raja K, Chandramouli K. Immobilized pH gradient-driven paper-based IEF: a new method for fractionating complex peptide mixtures before MS analysis. Clin Proteomics 2011; 8:10. [PMID: 21906381 PMCID: PMC3170271 DOI: 10.1186/1559-0275-8-10] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2010] [Accepted: 02/11/2011] [Indexed: 11/30/2022] Open
Abstract
Introduction The vast difference in the abundance of different proteins in biological samples limits the determination of the complete proteome of a cell type, requiring fractionation of proteins and peptides before MS analysis. Methods We present a method consisting of electrophoresis of complex mixtures of peptides using a strip of filter paper cut into 20 sections laid end to end over a 24-cm-long IPG strip, the pH gradient of which would drive the electrophoresis. Peptides absorbed onto individual paper pads after electrophoresis are subsequently recovered into a buffer solution, thus dividing a complex peptide mixture according to pI into 20 liquid fractions. This paper-based IEF method (PIEF) was compared side-by-side with a similar but liquid-based Offgel electrophoresis (OGE) by analyzing iTRAQ-labeled peptide mixtures of membrane proteins from four different cell types. Results PIEF outperformed OGE in resolving acidic peptides, whereas OGE did a better job in recovering relatively basic peptides. OGE and PIEF were quite comparable in their coverage, identifying almost equal number of distinct proteins (PIEF =1174; OGE = 1080). Interestingly, however, only 675 were identified by both of them, each method identifying many unique proteins (PIEF = 499; OGE = 415). Thus, the two methods uncovered almost 40% more proteins compared to what is obtained by only one method. Conclusion: This initial investigation demonstrates the technical feasibility of PIEF for complementing OGE. PIEF uses standard IPG IEF equipment, requires no specialized apparatus (e.g., OGE fractionator) and may be integrated into peptide mapping strategies for clinical samples.
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Affiliation(s)
- Beerelli Seshi
- Department of Pathology and Laboratory Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, 1124 West Carson Street, Torrance, California 90502, USA.
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Ko SH, Kim SJ, Cheow LF, Li LD, Kang KH, Han J. Massively parallel concentration device for multiplexed immunoassays. LAB ON A CHIP 2011; 11:1351-8. [PMID: 21321747 DOI: 10.1039/c0lc00349b] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A massively parallel nanofluidic concentration device array for multiplexed and high-throughput biomolecule detection is demonstrated. By optimizing the microchannel/nanojunction design and channel conductivity, an array of up to 128 nanofluidic concentration devices were fabricated. Operation of the entire array requires only one inlet and one outlet reservoir, with the application of a single operational voltage bias across them. Concentration efficiencies of the devices were found to be uniform within the array, within 5% error. Alternatively, concentration speed in each channel can be individually tuned by controlling the length of the inlet microchannel and thus controlling the flow rate based on change of the tangential electric field. This allows immuno-binding reactions at different concentration ranges to be performed in parallel. Using multiplexed, successive-concentration enhanced detection in the device, we have shown that the dynamic range and reliability of the immunoassay can be significantly increased.
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Affiliation(s)
- Sung Hee Ko
- Department of Mechanical Engineering, Pohang University of Science and Technology, San 31, Hyojadong, Gyeongbuk 790-784, Korea
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Wei J, Gu X, Wang Y, Wu Y, Yan C. Two-dimensional separation system by on-line hyphenation of capillary isoelectric focusing with pressurized capillary electrochromatography for peptide and protein mapping. Electrophoresis 2010; 32:230-7. [DOI: 10.1002/elps.201000419] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2010] [Revised: 10/08/2010] [Accepted: 10/11/2010] [Indexed: 11/09/2022]
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Zhou F, Cardoza JD, Ficarro SB, Adelmant GO, Lazaro JB, Marto JA. Online nanoflow RP-RP-MS reveals dynamics of multicomponent Ku complex in response to DNA damage. J Proteome Res 2010; 9:6242-55. [PMID: 20873769 DOI: 10.1021/pr1004696] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Tandem affinity purification (TAP) coupled with mass spectrometry has become the technique of choice for characterization of multicomponent protein complexes. While current TAP protocols routinely provide high yield and specificity for proteins expressed under physiologically relevant conditions, analytical figures of merit required for efficient and in-depth LC-MS analysis remain unresolved. Here we implement a multidimensional chromatography platform, based on two stages of reversed-phase (RP) separation operated at high and low pH, respectively. We compare performance metrics for RP-RP and SCX-RP for the analysis of complex peptide mixtures derived from cell lysate, as well as protein complexes purified via TAP. Our data reveal that RP-RP fractionation outperforms SCX-RP primarily due to increased peak capacity in the first dimension separation. We integrate this system with miniaturized LC assemblies to achieve true online fractionation at low (≤5 nL/min) effluent flow rates. Stable isotope labeling is used to monitor the dynamics of the multicomponent Ku protein complex in response to DNA damage induced by γ radiation.
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Affiliation(s)
- Feng Zhou
- Department of Cancer Biology and Blais Proteomics Center, Dana-Farber Cancer Institute, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusettes, United States
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31
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Mbeunkui F, Scholl EH, Opperman CH, Goshe MB, Bird DM. Proteomic and Bioinformatic Analysis of the Root-Knot Nematode Meloidogyne hapla: The Basis for Plant Parasitism. J Proteome Res 2010; 9:5370-81. [DOI: 10.1021/pr1006069] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Flaubert Mbeunkui
- Department of Molecular and Structural Biochemistry and Plant Nematode Genomes Group, Department of Plant Pathology, NC State University, Raleigh, North Carolina 27695
| | - Elizabeth H. Scholl
- Department of Molecular and Structural Biochemistry and Plant Nematode Genomes Group, Department of Plant Pathology, NC State University, Raleigh, North Carolina 27695
| | - Charles H. Opperman
- Department of Molecular and Structural Biochemistry and Plant Nematode Genomes Group, Department of Plant Pathology, NC State University, Raleigh, North Carolina 27695
| | - Michael B. Goshe
- Department of Molecular and Structural Biochemistry and Plant Nematode Genomes Group, Department of Plant Pathology, NC State University, Raleigh, North Carolina 27695
| | - David McK. Bird
- Department of Molecular and Structural Biochemistry and Plant Nematode Genomes Group, Department of Plant Pathology, NC State University, Raleigh, North Carolina 27695
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Liu J, Chen CF, Yang S, Chang CC, Devoe DL. Mixed-mode electrokinetic and chromatographic peptide separations in a microvalve-integrated polymer chip. LAB ON A CHIP 2010; 10:2122-2129. [PMID: 20556309 DOI: 10.1039/c003505j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
A cycloolefin polymer chip supporting the concatenation of isoelectric focusing (IEF) and reversed-phase liquid chromatography (RPLC) is demonstrated for high throughput two dimensional peptide separations. A unique benefit of the mixed-mode platform is the ability of IEF to act as a highly concentrating electrokinetic separation mode for effective isolation of sample components prior to RPLC. The thermoplastic chip contains integrated high pressure microvalves, enabling uniform sample transfer from the IEF channel to multiple parallel RPLC channels, gradient elution from each RPLC column, and hydrodynamic isolation between the separation dimensions. The reusable system is shown to provide efficient 2-D separations together with facile interfacing with MALDI-MS, suggesting a new path towards effective peptide analysis from complex samples.
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Affiliation(s)
- Jikun Liu
- Department of Mechanical Engineering, University of Maryland, College Park, MD, USA
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Callipo L, Capriotti AL, Cavaliere C, Gubbiotti R, Samperi R, Laganà A. Evaluation of different two-dimensional chromatographic techniques for proteomic analysis of mouse cardiac tissue. Biomed Chromatogr 2010; 25:594-9. [PMID: 20652868 DOI: 10.1002/bmc.1487] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2010] [Revised: 05/24/2010] [Accepted: 06/02/2010] [Indexed: 11/09/2022]
Abstract
In proteomics experiments the first critical step after sampling is certainly sample preparation. Multidimensional chromatography techniques have emerged as a powerful tool for the large-scale analysis of such complex samples as biological samples. In order to evaluate these separation techniques, microgram quantities of protein extracted from mouse heart tissue were fractionated by four different chromatographic methods. Regarding peptide-level fractionation, the first dimension of separation was performed with high-pH reversed-phase chromatography (pH-RP) and strong cation exchange chromatography (SCX). Regarding protein-level fractionation, C(8) protein reversed-phase (C(8) -RP Prot) and high-recovery protein reversed-phase (hr-RP Prot) were used instead. The second dimension consisted of a reversed-phase nano-HPLC on-Chip coupled to an electrospray ionization quadrupole time-of-flight mass spectrometer for tandem mass spectrometric analysis. The performance and relative fractionation efficiencies of each technique were assessed by comparing the total number of proteins identified by each method. The peptide-level pH-RP and the hr-RP Prot protein-level separations were the best methods, identifying 1338 and 1303 proteins, respectively. The peptide-level SCX, with 509 proteins identified, was the worst method.
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Affiliation(s)
- Luciano Callipo
- Department of Chemistry, Sapienza University of Rome, Piazzale Aldo Moro 5, Rome, Italy
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34
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Fang X, Balgley BM, Lee CS. Recent advances in capillary electrophoresis-based proteomic techniques for biomarker discovery. Electrophoresis 2010; 30:3998-4007. [PMID: 19960464 DOI: 10.1002/elps.200900219] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
A compelling need exists for the development of technologies that facilitate and accelerate the discovery of novel protein biomarkers with therapeutic and diagnostic potential. The inherent disadvantage of biomarker dilution in complex biological fluids such as serum/plasma, urine, and saliva necessitates highly sensitive analytical approaches, often exceeding the dynamic range of currently available proteomic platforms. Thus, investigative studies directed at tissues obtained from the primary site of pathology probably afford the best opportunity for the discovery of disease biomarkers. This review therefore focuses on the most recent advances in capillary electrophoresis-based single and multidimensional separations coupled with ESI-MS for performing comprehensive and comparative analysis of protein expression profiles within clinical specimens. Advanced sample preparation techniques, including tissue microdissection, detergent-based membrane protein extraction, and heat-induced protein retrieval, further enable targeted protein profiling of both fresh-frozen, formalin-fixed, and paraffin-embedded tissues. Comparative proteomics involving measurements in changes of biological pathways or functional processes are expected to provide relevant disease-associated markers and networks, molecular relationships among different stages of disease, and molecular mechanisms that drive the progression of disease. From a practical perspective, the evaluation of comparative proteomic dataset within a biological context is essential for high-throughput data validation, prioritization of follow-on biomarker selection, and validation experiments.
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Affiliation(s)
- Xueping Fang
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD 20742, USA
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35
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Mokaddem M, Gareil P, Varenne A. Online CIEF-ESI-MS in glycerol-water media with a view to hydrophobic protein applications. Electrophoresis 2010; 30:4040-8. [PMID: 19960468 DOI: 10.1002/elps.200900091] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
A new online coupling of CIEF with ESI-MS has been developed in glycerol-water media. This improved protocol provides: (i) the electric continuity during the whole analysis by a discontinuous filling of the capillary with 60:40 (cm/cm) catholyte/proteins-ampholyte mixture; (ii) the use of an anticonvective medium, i.e. 30:70 glycerol/water, v/v, compatible with MS detection and as an aid to hydrophobic protein solubilization and (iii) the use of unmodified bare fused-silica capillaries, as the glycerol/water medium strongly reduces EOF. Focusing was performed in positive polarity and cathodic mobilization was achieved by both voltage and pressure application. The setup was optimized with respect to analysis time, sensitivity and precision on pI determination. The optimized anolyte and catholyte were composed of 50 mM formic acid/1 mM glutamic acid (pH 2.35) and 100 mM NH(3)/1 mM lysine (pH 10.6), respectively. The effects of ampholyte concentration, focusing time and ESI parameters were presented for model proteins and discussed. This new integrated protocol should be an easy and effective additional tool in the field of proteome analysis, providing a means for the characterization of a large number of hydrophilic and hydrophobic proteins.
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Affiliation(s)
- Meriem Mokaddem
- Laboratoire de Physicochimie des Electrolytes, Colloïdes et Sciences Analytiques, UMR CNRS-UPMC, Ecole Nationale Supérieure de Chimie de Paris, 75231 Paris, France
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36
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Abstract
We review microfluidic devices designed for multidimensional sample analysis, with a primer on relevant theory, an emphasis on protein analysis, and an eye towards future improvements and challenges to the field. Image shows results of an on-chip IEF-CE separation of a protein mixture; unpublished surface plot data from A. E. Herr.
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Affiliation(s)
- Samuel Tia
- Department of Bioengineering, University of California, Berkeley, 308B Stanley Hall, MC # 1762 Berkeley, CA 94720-1762, USA
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37
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Kim KH, Moon MH. High Speed Two-Dimensional Protein Separation without Gel by Isoelectric Focusing−Asymmetrical Flow Field Flow Fractionation: Application to Urinary Proteome. J Proteome Res 2009; 8:4272-8. [DOI: 10.1021/pr900363s] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ki Hun Kim
- Department of Chemistry, Yonsei University, Seoul, 120-749, Korea
| | - Myeong Hee Moon
- Department of Chemistry, Yonsei University, Seoul, 120-749, Korea
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38
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Ahmed FE. The role of capillary electrophoresis–mass spectrometry to proteome analysis and biomarker discovery. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:1963-81. [DOI: 10.1016/j.jchromb.2009.05.023] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2008] [Revised: 04/24/2009] [Accepted: 05/10/2009] [Indexed: 01/25/2023]
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39
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Slebos RJC, Brock JWC, Winters NF, Stuart SR, Martinez MA, Li M, Chambers MC, Zimmerman LJ, Ham AJ, Tabb DL, Liebler DC. Evaluation of strong cation exchange versus isoelectric focusing of peptides for multidimensional liquid chromatography-tandem mass spectrometry. J Proteome Res 2009; 7:5286-94. [PMID: 18939861 DOI: 10.1021/pr8004666] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Shotgun proteome analysis platforms based on multidimensional liquid chromatography-tandem mass spectrometry (LC-MS/MS) provide a powerful means to discover biomarker candidates in tissue specimens. Analysis platforms must balance sensitivity for peptide detection, reproducibility of detected peptide inventories and analytical throughput for protein amounts commonly present in tissue biospecimens (< 100 microg), such that platform stability is sufficient to detect modest changes in complex proteomes. We compared shotgun proteomics platforms by analyzing tryptic digests of whole cell and tissue proteomes using strong cation exchange (SCX) and isoelectric focusing (IEF) separations of peptides prior to LC-MS/MS analysis on a LTQ-Orbitrap hybrid instrument. IEF separations provided superior reproducibility and resolution for peptide fractionation from samples corresponding to both large (100 microg) and small (10 microg) protein inputs. SCX generated more peptide and protein identifications than did IEF with small (10 microg) samples, whereas the two platforms yielded similar numbers of identifications with large (100 microg) samples. In nine replicate analyses of tryptic peptides from 50 microg colon adenocarcinoma protein, overlap in protein detection by the two platforms was 77% of all proteins detected by both methods combined. IEF more quickly approached maximal detection, with 90% of IEF-detectable medium abundance proteins (those detected with a total of 3-4 peptides) detected within three replicate analyses. In contrast, the SCX platform required six replicates to detect 90% of SCX-detectable medium abundance proteins. High reproducibility and efficient resolution of IEF peptide separations make the IEF platform superior to the SCX platform for biomarker discovery via shotgun proteomic analyses of tissue specimens.
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Affiliation(s)
- Robbert J C Slebos
- Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Medical Research Building III, 465 21st Avenue South, Nashville, Tennessee 37232, USA
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40
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Ahmed FE. Sample preparation and fractionation for proteome analysis and cancer biomarker discovery by mass spectrometry. J Sep Sci 2009; 32:771-98. [PMID: 19219839 DOI: 10.1002/jssc.200800622] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Sample preparation and fractionation technologies are one of the most crucial processes in proteomic analysis and biomarker discovery in solubilized samples. Chromatographic or electrophoretic proteomic technologies are also available for separation of cellular protein components. There are, however, considerable limitations in currently available proteomic technologies as none of them allows for the analysis of the entire proteome in a simple step because of the large number of peptides, and because of the wide concentration dynamic range of the proteome in clinical blood samples. The results of any undertaken experiment depend on the condition of the starting material. Therefore, proper experimental design and pertinent sample preparation is essential to obtain meaningful results, particularly in comparative clinical proteomics in which one is looking for minor differences between experimental (diseased) and control (nondiseased) samples. This review discusses problems associated with general and specialized strategies of sample preparation and fractionation, dealing with samples that are solution or suspension, in a frozen tissue state, or formalin-preserved tissue archival samples, and illustrates how sample processing might influence detection with mass spectrometric techniques. Strategies that dramatically improve the potential for cancer biomarker discovery in minimally invasive, blood-collected human samples are also presented.
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Affiliation(s)
- Farid E Ahmed
- Department of Radiation Oncology, Leo W. Jenkins Cancer Center, The Brody School of Medicine at East Carolina University, Greenville, NC, USA.
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41
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Balgley BM, Guo T, Zhao K, Fang X, Tavassoli FA, Lee CS. Evaluation of archival time on shotgun proteomics of formalin-fixed and paraffin-embedded tissues. J Proteome Res 2009; 8:917-25. [PMID: 19128014 DOI: 10.1021/pr800503u] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
There is increasing acceptance of the critical importance of correlating the morphologic features of tissue with the data obtained from various molecular analytic techniques. Access to archived formalin-fixed and paraffin-embedded (FFPE) tissue specimens via shotgun-based proteomic analyses may, therefore, open new avenues for both prospective and retrospective translational research. However, one of the remaining issues in performing comparative proteomic measurements among FFPE tissues relates to potential variability in protein composition and retrieval based on length of storage periods. Optimized protein extraction and digestion procedures for handling FFPE tissues are coupled with the capillary isotachophoresis-based proteome technology to evaluate the effects of length of storage period on archival tissue proteome analysis across 10 archived uterine mesenchymal tumor tissue blocks, including 9 uterine leiomyomas dating from 1990 to 2002 and a single case of alveolar soft part sarcoma (ASPS) from 1980. Several statistical measures, including the Pearson correlation coefficient, coefficient of variance, k-means clustering, and ANOVA, are employed to evaluate the possibility of an archival effect on individual proteins or groups of proteins within nine leiomyomas. Low abundance proteins may be more susceptible to the long-term storage as these proteins are more difficult to be retrieved and extracted as the tissue block ages in paraffin. Despite using tissue blocks stored for as many as 28 years, high confidence and comparative proteome analysis between the leiomyomas and the sarcoma is achieved. Though sharing over 1800 common proteins in a core set, a total of 80 proteins unique to the sarcoma are identified distinguishing the ASPS from the leiomyomas. Vacuolar proton translocating ATPase 116 kDa subunit isoform a3, one of the unique proteins expressed in the ASPS, is further validated by immunohistochemistry (IHC). Although IHC is highly sensitive and provides the subcellular resolution, mass spectrometry-based proteome profiling enables global identification and quantification of thousands of proteins without a priori knowledge of individual proteins being analyzed or the need of validated antibodies.
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42
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Geng X, Ke C, Chen G, Liu P, Wang F, Zhang H, Sun X. On-line separation of native proteins by two-dimensional liquid chromatography using a single column. J Chromatogr A 2009; 1216:3553-62. [DOI: 10.1016/j.chroma.2009.01.085] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2008] [Revised: 01/21/2009] [Accepted: 01/26/2009] [Indexed: 11/16/2022]
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43
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Zhang ZX, Zhang XW, Zhang SS. Heart-cut capillary electrophoresis for drug analysis in mouse blood with electrochemical detection. Anal Biochem 2009; 387:171-7. [DOI: 10.1016/j.ab.2009.01.026] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2008] [Revised: 01/20/2009] [Accepted: 01/21/2009] [Indexed: 11/28/2022]
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44
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François I, Cabooter D, Sandra K, Lynen F, Desmet G, Sandra P. Tryptic digest analysis by comprehensive reversed phase×two reversed phase liquid chromatography (RP-LC×2RP-LC) at different pH's. J Sep Sci 2009; 32:1137-44. [DOI: 10.1002/jssc.200800578] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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45
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Abstract
In the postgenomic era, proteomics has become a dominant field for identifying and quantifying the complex protein machinery of the cell. The expression levels, posttranslational modifications, and specific interactions of proteins control the biology of such processes as development, differentiation, and signal transduction. Studies of the proteins involved in these processes often lead to a better understanding of biology and of human disease. Powerful separation techniques and sensitive detection methods enable researchers to untangle these complicated networks of processes. CE coupled with either MS or LIF are two of the techniques that make this possible. This review will cover proven CE-based methods for proteomics on the cell and tissue level and their application in biological and clinical studies, relevant new developments in enabling technology such as microfluidic CE-MS demonstrated on model systems, and comment on the future of CE in proteomics.
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MESH Headings
- Amino Acid Sequence
- Electrophoresis, Capillary/instrumentation
- Electrophoresis, Capillary/methods
- Humans
- Molecular Sequence Data
- Proteins/analysis
- Proteins/genetics
- Proteome/analysis
- Proteomics/methods
- Sequence Alignment
- Spectrometry, Mass, Electrospray Ionization/instrumentation
- Spectrometry, Mass, Electrospray Ionization/methods
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/instrumentation
- Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods
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Affiliation(s)
- Bryan R Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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46
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Kim J, Chun MS, Choi K, Chung DS. Large volume stacking using an EOF pump in NACE-MS. Electrophoresis 2009; 30:1046-51. [DOI: 10.1002/elps.200800396] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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47
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Kim KH, Moon MH. Development of a Multilane Channel System for Nongel-Based Two-Dimensional Protein Separations Using Isoelectric Focusing and Asymmetrical Flow Field-Flow Fractionation. Anal Chem 2009; 81:1715-21. [DOI: 10.1021/ac802357s] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ki Hun Kim
- Department of Chemistry, Yonsei University, Seoul, 120-749, Korea
| | - Myeong Hee Moon
- Department of Chemistry, Yonsei University, Seoul, 120-749, Korea
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48
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Lee CS, Balgley BM. Capillary isoelectric focusing/reversed phase liquid chromatography/mass spectrometry. Methods Mol Biol 2009; 492:233-240. [PMID: 19241036 DOI: 10.1007/978-1-59745-493-3_13] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
The vast number of proteins present in the proteome of a typical organism requires that separations be performed on the mixture prior to introduction into a mass spectrometer for protein identification and quantification. An integrated protein separation platform, combining capillary isoelectric focusing (CIEF) with reversed phase liquid chromatography (RPLC), is described to provide high resolving power for the analysis of complex protein mixtures. Thus, the proteins are systematically resolved according to their differences in isoelectric point and hydrophobicity using combined CIEF/RPLC separations. A key feature of the CIEF-based multidimensional separation platform is the elimination of protein loss and dilution in an integrated platform while achieving comprehensive and ultrasensitive analysis of protein profiles within small cell populations or limited tissue samples.
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Affiliation(s)
- Cheng S Lee
- Department of Chemistry and Biochemistry, University of Maryland, College Park, MD, USA
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Chapter 3 Proteome Characterization of Mouse Brain Mitochondria Using Electrospray Ionization Tandem Mass Spectrometry. Methods Enzymol 2009; 457:49-62. [DOI: 10.1016/s0076-6879(09)05003-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
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