101
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Söllner JF, Leparc G, Hildebrandt T, Klein H, Thomas L, Stupka E, Simon E. An RNA-Seq atlas of gene expression in mouse and rat normal tissues. Sci Data 2017; 4:170185. [PMID: 29231921 PMCID: PMC5726313 DOI: 10.1038/sdata.2017.185] [Citation(s) in RCA: 78] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 10/27/2017] [Indexed: 12/21/2022] Open
Abstract
Gene functionality is closely connected to its expression specificity across tissues and cell types. RNA-Seq is a powerful quantitative tool to explore genome wide expression. The aim of this study is to provide a comprehensive RNA-Seq dataset across the same 13 tissues for mouse and rat, two of the most relevant species for biomedical research. The dataset provides the transcriptome across tissues from three male C57BL6 mice and three male Han Wistar rats. We also describe our bioinformatics pipeline to process and technically validate the data. Principal component analysis shows that tissue samples from both species cluster similarly. We show by comparative genomics that many genes with high sequence identity with respect to their human orthologues also have a highly correlated tissue distribution profile and are in agreement with manually curated literature data for human. In summary, the present study provides a unique resource for comparative genomics and will facilitate the analysis of tissue specificity and cross-species conservation in higher organisms.
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Affiliation(s)
- Julia F Söllner
- Target Discovery, Research Boehringer Ingelheim Pharma GmbH & CoKG, Biberach 88397, Germany.,Integrative Transcriptomics, Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - German Leparc
- Target Discovery, Research Boehringer Ingelheim Pharma GmbH & CoKG, Biberach 88397, Germany
| | - Tobias Hildebrandt
- Target Discovery, Research Boehringer Ingelheim Pharma GmbH & CoKG, Biberach 88397, Germany
| | - Holger Klein
- Target Discovery, Research Boehringer Ingelheim Pharma GmbH & CoKG, Biberach 88397, Germany
| | - Leo Thomas
- Cardiometabolic Research, Research Boehringer Ingelheim Pharma GmbH & CoKG, Biberach 88397, Germany
| | - Elia Stupka
- Target Discovery, Research Boehringer Ingelheim Pharma GmbH & CoKG, Biberach 88397, Germany
| | - Eric Simon
- Target Discovery, Research Boehringer Ingelheim Pharma GmbH & CoKG, Biberach 88397, Germany
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102
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Wang YA, Wu D, Auclair JR, Salisbury JP, Sarin R, Tang Y, Mozdzierz NJ, Shah K, Zhang AF, Wu SL, Agar JN, Love JC, Love KR, Hancock WS. Integrated Bottom-Up and Top-Down Liquid Chromatography-Mass Spectrometry for Characterization of Recombinant Human Growth Hormone Degradation Products. Anal Chem 2017; 89:12771-12777. [PMID: 29096433 DOI: 10.1021/acs.analchem.7b03026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
With the advent of biosimilars to the U.S. market, it is important to have better analytical tools to ensure product quality from batch to batch. In addition, the recent popularity of using a continuous process for production of biopharmaceuticals, the traditional bottom-up method, alone for product characterization and quality analysis is no longer sufficient. Bottom-up method requires large amounts of material for analysis and is labor-intensive and time-consuming. Additionally, in this analysis, digestion of the protein with enzymes such as trypsin could induce artifacts and modifications which would increase the complexity of the analysis. On the other hand, a top-down method requires a minimum amount of sample and allows for analysis of the intact protein mass and sequence generated from fragmentation within the instrument. However, fragmentation usually occurs at the N-terminal and C-terminal ends of the protein with less internal fragmentation. Herein, we combine the use of the complementary techniques, a top-down and bottom-up method, for the characterization of human growth hormone degradation products. Notably, our approach required small amounts of sample, which is a requirement due to the sample constraints of small scale manufacturing. Using this approach, we were able to characterize various protein variants, including post-translational modifications such as oxidation and deamidation, residual leader sequence, and proteolytic cleavage. Thus, we were able to highlight the complementarity of top-down and bottom-up approaches, which achieved the characterization of a wide range of product variants in samples of human growth hormone secreted from Pichia pastoris.
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Affiliation(s)
- Yu Annie Wang
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Di Wu
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Jared R Auclair
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Joseph P Salisbury
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Richa Sarin
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Yang Tang
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Nicholas J Mozdzierz
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , 500 Main Street, Cambridge, Massachusetts 02142, United States
| | - Kartik Shah
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , 500 Main Street, Cambridge, Massachusetts 02142, United States
| | - Anna Fan Zhang
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - Shiaw-Lin Wu
- BioAnalytix Inc. , 790 Memorial Drive, Cambridge, Massachusetts 02139, United States
| | - Jeffery N Agar
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
| | - J Christopher Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , 500 Main Street, Cambridge, Massachusetts 02142, United States
| | - Kerry R Love
- Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology , 500 Main Street, Cambridge, Massachusetts 02142, United States
| | - William S Hancock
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , 360 Huntington Avenue, Boston, Massachusetts 02115, United States
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103
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Wei L, Gregorich ZR, Lin Z, Cai W, Jin Y, McKiernan SH, McIlwain S, Aiken JM, Moss RL, Diffee GM, Ge Y. Novel Sarcopenia-related Alterations in Sarcomeric Protein Post-translational Modifications (PTMs) in Skeletal Muscles Identified by Top-down Proteomics. Mol Cell Proteomics 2017; 17:134-145. [PMID: 29046390 DOI: 10.1074/mcp.ra117.000124] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 10/17/2017] [Indexed: 11/06/2022] Open
Abstract
Sarcopenia, the age-related loss of skeletal muscle mass and strength, is a significant cause of morbidity in the elderly and is a major burden on health care systems. Unfortunately, the underlying molecular mechanisms in sarcopenia remain poorly understood. Herein, we utilized top-down proteomics to elucidate sarcopenia-related changes in the fast- and slow-twitch skeletal muscles of aging rats with a focus on the sarcomeric proteome, which includes both myofilament and Z-disc proteins-the proteins that constitute the contractile apparatuses. Top-down quantitative proteomics identified significant changes in the post-translational modifications (PTMs) of critical myofilament proteins in the fast-twitch skeletal muscles of aging rats, in accordance with the vulnerability of fast-twitch muscles to sarcopenia. Surprisingly, age-related alterations in the phosphorylation of Cypher isoforms, proteins that localize to the Z-discs in striated muscles, were also noted in the fast-twitch skeletal muscle of aging rats. This represents the first report of changes in the phosphorylation of Z-disc proteins in skeletal muscle during aging. In addition, increased glutathionylation of slow skeletal troponin I, a novel modification that may help protect against oxidative damage, was observed in slow-twitch skeletal muscles. Furthermore, we have identified and characterized novel muscle type-specific proteoforms of myofilament proteins and Z-disc proteins, including a novel isoform of the Z-disc protein Enigma. The finding that the phosphorylation of Z-disc proteins is altered in response to aging in the fast-twitch skeletal muscles of aging rats opens new avenues for the investigation of the role of Z-discs in age-related muscle dysfunction.
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Affiliation(s)
- Liming Wei
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,§Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Zachery R Gregorich
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,¶Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705
| | - Ziqing Lin
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,‖Human Proteomics Program,University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705
| | - Wenxuan Cai
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,¶Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705
| | - Yutong Jin
- **Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin, 53706
| | - Susan H McKiernan
- ‡‡Department of Kinesiology, University of Wisconsin-Madison, 2000 Observatory Dr., Madison, Wisconsin, 53705
| | - Sean McIlwain
- §§Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, 600 Highland Ave., Madison, Wisconsin, 53792.,¶¶UW Carbone Cancer Center, University of Wisconsin-Madison, 600 Highland Ave., Madison, Wisconsin, 53792
| | - Judd M Aiken
- ‖‖Departments of Agriculture, Food, and Nutritional Sciences, University of Alberta-Edmonton, Edmonton, AB, Canada
| | - Richard L Moss
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,‖Human Proteomics Program,University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705
| | - Gary M Diffee
- ‡‡Department of Kinesiology, University of Wisconsin-Madison, 2000 Observatory Dr., Madison, Wisconsin, 53705
| | - Ying Ge
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705; .,¶Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,‖Human Proteomics Program,University of Wisconsin-Madison, 1111 Highland Ave., Madison, Wisconsin, 53705.,**Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, Wisconsin, 53706
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104
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Chen B, Guo X, Tucholski T, Lin Z, McIlwain S, Ge Y. The Impact of Phosphorylation on Electron Capture Dissociation of Proteins: A Top-Down Perspective. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:1805-1814. [PMID: 28685494 PMCID: PMC5711594 DOI: 10.1007/s13361-017-1710-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/04/2017] [Accepted: 05/07/2017] [Indexed: 05/12/2023]
Abstract
Electron capture dissociation (ECD) is well suited for the characterization of phosphoproteins, with which labile phosphate groups are generally preserved during the fragmentation process. However, the impact of phosphorylation on ECD fragmentation of intact proteins remains unclear. Here, we have performed a systematic investigation of the phosphorylation effect on ECD of intact proteins by comparing the ECD cleavages of mono-phosphorylated α-casein, multi-phosphorylated β-casein, and immunoaffinity-purified phosphorylated cardiac troponin I with those of their unphosphorylated counterparts, respectively. In contrast to phosphopeptides, phosphorylation has significantly reduced deleterious effects on the fragmentation of intact proteins during ECD. On a global scale, the fragmentation patterns are highly comparable between unphosphorylated and phosphorylated precursors under the same ECD conditions, despite a slight decrease in the number of fragment ions observed for the phosphorylated forms. On a local scale, single phosphorylation of intact proteins imposes minimal effects on fragmentation near the phosphorylation sites, but multiple phosphorylations in close proximity result in a significant reduction of ECD bond cleavages. Graphical Abstract ᅟ.
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Affiliation(s)
- Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Xiao Guo
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Sean McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison, Madison, WI, USA
- UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA.
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
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105
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Cai W, Tucholski T, Chen B, Alpert AJ, McIlwain S, Kohmoto T, Jin S, Ge Y. Top-Down Proteomics of Large Proteins up to 223 kDa Enabled by Serial Size Exclusion Chromatography Strategy. Anal Chem 2017; 89:5467-5475. [PMID: 28406609 DOI: 10.1021/acs.analchem.7b00380] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Mass spectrometry (MS)-based top-down proteomics is a powerful method for the comprehensive analysis of proteoforms that arise from genetic variations and post-translational modifications (PTMs). However, top-down MS analysis of high molecular weight (MW) proteins remains challenging mainly due to the exponential decay of signal-to-noise ratio with increasing MW. Size exclusion chromatography (SEC) is a favored method for size-based separation of biomacromolecules but typically suffers from low resolution. Herein, we developed a serial size exclusion chromatography (sSEC) strategy to enable high-resolution size-based fractionation of intact proteins (10-223 kDa) from complex protein mixtures. The sSEC fractions could be further separated by reverse phase chromatography (RPC) coupled online with high-resolution MS. We have shown that two-dimensional (2D) sSEC-RPC allowed for the identification of 4044 more unique proteoforms and a 15-fold increase in the detection of proteins above 60 kDa, compared to one-dimensional (1D) RPC. Notably, effective sSEC-RPC separation of proteins significantly enhanced the detection of high MW proteins up to 223 kDa and also revealed low abundance proteoforms that are post-translationally modified. This sSEC method is MS-friendly, robust, and reproducible and, thus, can be applied to both high-efficiency protein purification and large-scale proteomics analysis of cell or tissue lysate for enhanced proteome coverage, particularly for low abundance and high MW proteoforms.
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Affiliation(s)
- Wenxuan Cai
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.,Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Andrew J Alpert
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.,PolyLC Inc. , Columbia, Maryland 21045, United States
| | - Sean McIlwain
- Department of Biostatistics and Medical Informatics, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.,UW Carbone Cancer Center, School of Medicine and Public Health, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Takushi Kohmoto
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.,Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison , Madison, Wisconsin 53705, United States.,Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin 53706, United States
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106
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Jin Y, Wei L, Cai W, Lin Z, Wu Z, Peng Y, Kohmoto T, Moss RL, Ge Y. Complete Characterization of Cardiac Myosin Heavy Chain (223 kDa) Enabled by Size-Exclusion Chromatography and Middle-Down Mass Spectrometry. Anal Chem 2017; 89:4922-4930. [PMID: 28366003 PMCID: PMC5526197 DOI: 10.1021/acs.analchem.7b00113] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Myosin heavy chain (MHC), the major component of the myosin motor molecule, plays an essential role in force production during muscle contraction. However, a comprehensive analysis of MHC proteoforms arising from sequence variations and post-translational modifications (PTMs) remains challenging due to the difficulties in purifying MHC (∼223 kDa) and achieving complete sequence coverage. Herein, we have established a strategy to effectively purify and comprehensively characterize MHC from heart tissue by combining size-exclusion chromatography (SEC) and middle-down mass spectrometry (MS). First, we have developed a MS-compatible SEC method for purifying MHC from heart tissue with high efficiency. Next, we have optimized the Glu-C, Asp-N, and trypsin limited digestion conditions for middle-down MS. Subsequently, we have applied this strategy with optimized conditions to comprehensively characterize human MHC and identified β-MHC as the predominant isoform in human left ventricular tissue. Full sequence coverage based on highly accurate mass measurements has been achieved using middle-down MS combining 1 Glu-C, 1 Asp-N, and 1 trypsin digestion. Three different PTMs: acetylation, methylation, and trimethylation were identified in human β-MHC and the corresponding sites were localized to the N-terminal Gly, Lys34, and Lys129, respectively, by electron capture dissociation (ECD). Taken together, we have demonstrated this strategy is highly efficient for purification and characterization of MHC, which can be further applied to studies of the role of MHC proteoforms in muscle-related diseases. We also envision that this integrated SEC/middle-down MS strategy can be extended for the characterization of other large proteins over 200 kDa.
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Affiliation(s)
- Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Liming Wei
- Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Wenxuan Cai
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ying Peng
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Takushi Kohmoto
- Institutes of Biomedical Sciences, Fudan University, Shanghai, P. R. China
| | - Richard L. Moss
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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107
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Baucum AJ. Proteomic Analysis of Postsynaptic Protein Complexes Underlying Neuronal Plasticity. ACS Chem Neurosci 2017; 8:689-701. [PMID: 28211672 DOI: 10.1021/acschemneuro.7b00008] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Normal neuronal communication and synaptic plasticity at glutamatergic synapses requires dynamic regulation of postsynaptic molecules. Protein expression and protein post-translational modifications regulate protein interactions that underlie this organization. In this Review, we highlight data obtained over the last 20 years that have used qualitative and quantitative proteomics-based approaches to identify postsynaptic protein complexes. Herein, we describe how these proteomics studies have helped lay the foundation for understanding synaptic physiology and perturbations in synaptic signaling observed in different pathologies. We also describe emerging technologies that can be useful in these analyses. We focus on protein complexes associated with the highly abundant and functionally critical proteins: calcium/calmodulin-dependent protein kinase II, the N-methyl-d-aspartate, and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid glutamate receptors, and postsynaptic density protein of 95 kDa.
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Affiliation(s)
- Anthony J. Baucum
- Department of Biology, Stark Neurosciences
Research Institute, Indiana University-Purdue University Indianapolis, 723 W. Michigan St., Indianapolis, Indiana 46202, United States
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108
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Cleland TP, DeHart CJ, Fellers RT, VanNispen AJ, Greer JB, LeDuc RD, Parker WR, Thomas PM, Kelleher NL, Brodbelt JS. High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer. J Proteome Res 2017; 16:2072-2079. [PMID: 28412815 DOI: 10.1021/acs.jproteome.7b00043] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The analysis of intact proteins (top-down strategy) by mass spectrometry has great potential to elucidate proteoform variation, including patterns of post-translational modifications (PTMs), which may not be discernible by analysis of peptides alone (bottom-up approach). To maximize sequence coverage and localization of PTMs, various fragmentation modes have been developed to produce fragment ions from deep within intact proteins. Ultraviolet photodissociation (UVPD) has recently been shown to produce high sequence coverage and PTM retention on a variety of proteins, with increasing evidence of efficacy on a chromatographic time scale. However, utilization of UVPD for high-throughput top-down analysis to date has been limited by bioinformatics. Here we detected 153 proteins and 489 proteoforms using UVPD and 271 proteins and 982 proteoforms using higher energy collisional dissociation (HCD) in a comparative analysis of HeLa whole-cell lysate by qualitative top-down proteomics. Of the total detected proteoforms, 286 overlapped between the UVPD and HCD data sets, with 68% of proteoforms having C scores greater than 40 for UVPD and 63% for HCD. The average sequence coverage (28 ± 20% for UVPD versus 17 ± 8% for HCD, p < 0.0001) was found to be higher for UVPD than HCD and with a trend toward improvement in q value for the UVPD data set. This study demonstrates the complementarity of UVPD and HCD for more extensive protein profiling and proteoform characterization.
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Affiliation(s)
- Timothy P Cleland
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Caroline J DeHart
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Ryan T Fellers
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Alexandra J VanNispen
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Joseph B Greer
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - Richard D LeDuc
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States
| | - W Ryan Parker
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
| | - Paul M Thomas
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States.,Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston, Illinois 60208, United States
| | - Neil L Kelleher
- National Resource for Translational and Developmental Proteomics, Northwestern University , Evanston, Illinois 60208, United States.,Departments of Chemistry, Molecular Biosciences, and the Feinberg School of Medicine, Northwestern University , Evanston, Illinois 60208, United States
| | - Jennifer S Brodbelt
- Department of Chemistry, University of Texas at Austin , Austin, Texas 78712, United States
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109
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Gregorich ZR, Cai W, Lin Z, Chen AJ, Peng Y, Kohmoto T, Ge Y. Distinct sequences and post-translational modifications in cardiac atrial and ventricular myosin light chains revealed by top-down mass spectrometry. J Mol Cell Cardiol 2017; 107:13-21. [PMID: 28427997 DOI: 10.1016/j.yjmcc.2017.04.002] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/23/2017] [Accepted: 04/15/2017] [Indexed: 01/01/2023]
Abstract
Myosin is the principal component of the thick filaments that, through interactions with the actin thin filaments, mediates force production during muscle contraction. Myosin is a hexamer, consisting of two heavy chains, each associated with an essential (ELC) and a regulatory (RLC) light chain, which bind the lever-arm of the heavy chain and play important modulatory roles in striated muscle contraction. Nevertheless, a comprehensive assessment of the sequences of the ELC and RLC isoforms, as well as their post-translational modifications, in the heart remains lacking. Herein, utilizing top-down high-resolution mass spectrometry (MS), we have comprehensively characterized the sequences and N-terminal modifications of the atrial and ventricular isoforms of the myosin light chains from human and swine hearts, as well as the sites of phosphorylation in the swine proteins. In addition to the correction of disparities in the database sequences of the swine proteins, we show for the first time that, whereas the ventricular isoforms of the ELC and RLC are methylated at their N-termini, which is consistent with previous studies, the atrial isoforms of the ELC and RLC from both human and swine are Nα-methylated and Nα-acetylated, respectively. Furthermore, top-down MS with electron capture dissociation enabled localization of the sites of phosphorylation in swine RLC isoforms from the ventricles and atria to Ser14 and Ser22, respectively. Collectively, these results provide new insights into the sequences and modifications of myosin light chain isoforms in the human and swine hearts, which will pave the way for a better understanding of their functional roles in cardiac physiology and pathophysiology.
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Affiliation(s)
- Zachery R Gregorich
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Wenxuan Cai
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Albert J Chen
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ying Peng
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Takushi Kohmoto
- Department of Surgery, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Ying Ge
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705, USA; Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705, USA; Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA.
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110
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Chen B, Hwang L, Ochowicz W, Lin Z, Guardado-Alvarez TM, Cai W, Xiu L, Dani K, Colah C, Jin S, Ge Y. Coupling functionalized cobalt ferrite nanoparticle enrichment with online LC/MS/MS for top-down phosphoproteomics. Chem Sci 2017; 8:4306-4311. [PMID: 28660060 PMCID: PMC5472028 DOI: 10.1039/c6sc05435h] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 03/30/2017] [Indexed: 01/02/2023] Open
Abstract
An integrated top-down phosphoproteomics strategy enabled by functionalized cobalt ferrite nanoparticle enrichment and online LC/MS/MS for identification, quantification, and characterization of low abundance phosphoproteins is presented.
Phosphorylation plays pivotal roles in cellular processes and dysregulated phosphorylation is considered as an underlying mechanism in many human diseases. Top-down mass spectrometry (MS) analyzes intact proteins and provides a comprehensive analysis of protein phosphorylation. However, top-down MS-based phosphoproteomics is challenging due to the difficulty in enriching low abundance intact phosphoproteins as well as separating and detecting the enriched phosphoproteins from complex mixtures. Herein, we have designed and synthesized the next generation functionalized superparamagnetic cobalt ferrite (CoFe2O4) nanoparticles (NPs), and have further developed a top-down phosphoproteomics strategy coupling phosphoprotein enrichment enabled by the functionalized CoFe2O4 NPs with online liquid chromatography (LC)/MS/MS for comprehensive characterization of phosphoproteins. We have demonstrated the highly specific enrichment of a minimal amount of spike-in β-casein from a complex tissue lysate as well as effective separation and quantification of its phosphorylated genetic variants. More importantly, this integrated top-down phosphoproteomics strategy allows for enrichment, identification, quantification, and comprehensive characterization of low abundance endogenous phosphoproteins from complex tissue extracts on a chromatographic time scale.
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Affiliation(s)
- Bifan Chen
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA .
| | - Leekyoung Hwang
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA .
| | - William Ochowicz
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA .
| | - Ziqing Lin
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA
| | | | - Wenxuan Cai
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA
| | - Lichen Xiu
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA .
| | - Kunal Dani
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA .
| | - Cyrus Colah
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA
| | - Song Jin
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA .
| | - Ying Ge
- Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA . .,Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,Human Proteomics Program , School of Medicine and Public Health , University of Wisconsin-Madison , Madison , WI , USA
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111
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Impact and influence of “omics” technology on hyper tension studies. Int J Cardiol 2017; 228:1022-1034. [DOI: 10.1016/j.ijcard.2016.11.179] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 11/06/2016] [Indexed: 12/14/2022]
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112
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Miller CF, Kulyk DS, Kim JW, Badu-Tawiah AK. Re-configurable, multi-mode contained-electrospray ionization for protein folding and unfolding on the millisecond time scale. Analyst 2017; 142:2152-2160. [DOI: 10.1039/c7an00362e] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Contained-electrospray ionization enables online selection of protein charge states by a direct infusion of reactive vapors and liquids into charged micro-droplets.
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Affiliation(s)
- Colbert F. Miller
- Department of Chemistry and Biochemistry
- The Ohio State University
- Columbus
- USA
| | - Dmytro S. Kulyk
- Department of Chemistry and Biochemistry
- The Ohio State University
- Columbus
- USA
| | - Jongin W. Kim
- Department of Chemistry and Biochemistry
- The Ohio State University
- Columbus
- USA
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113
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Top-Down Proteomics and Farm Animal and Aquatic Sciences. Proteomes 2016; 4:proteomes4040038. [PMID: 28248248 PMCID: PMC5260971 DOI: 10.3390/proteomes4040038] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2016] [Revised: 11/25/2016] [Accepted: 12/05/2016] [Indexed: 01/16/2023] Open
Abstract
Proteomics is a field of growing importance in animal and aquatic sciences. Similar to other proteomic approaches, top-down proteomics is slowly making its way within the vast array of proteomic approaches that researchers have access to. This opinion and mini-review article is dedicated to top-down proteomics and how its use can be of importance to animal and aquatic sciences. Herein, we include an overview of the principles of top-down proteomics and how it differs regarding other more commonly used proteomic methods, especially bottom-up proteomics. In addition, we provide relevant sections on how the approach was or can be used as a research tool and conclude with our opinions of future use in animal and aquatic sciences.
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114
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Zhang X, Wang Y, Liu P. Omic studies reveal the pathogenic lipid droplet proteins in non-alcoholic fatty liver disease. Protein Cell 2016; 8:4-13. [PMID: 27757845 PMCID: PMC5233612 DOI: 10.1007/s13238-016-0327-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Accepted: 09/19/2016] [Indexed: 12/21/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is an epidemic metabolic condition driven by an underlying lipid homeostasis disorder. The lipid droplet (LD), the main organelle involved in neutral lipid storage and hydrolysis, is a potential target for NAFLD therapeutic treatment. In this review, we summarize recent progress elucidating the connections between LD-associated proteins and NAFLD found by genome-wide association studies (GWAS), genomic and proteomic studies. Finally, we discuss a possible mechanism by which the protein 17β-hydroxysteroid dehydrogenase 13 (17β-HSD13) may promote the development of NAFLD.
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Affiliation(s)
- Xuelin Zhang
- School of Kinesiology and Health, Capital University of Physical Education and Sports, Beijing, 100191, China.
| | - Yang Wang
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China
| | - Pingsheng Liu
- National Laboratory of Biomacromolecules, CAS Center for Excellence in Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101, China.
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115
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116
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Tentori AM, Yamauchi KA, Herr AE. Detection of Isoforms Differing by a Single Charge Unit in Individual Cells. Angew Chem Int Ed Engl 2016; 55:12431-5. [PMID: 27595864 PMCID: PMC5201312 DOI: 10.1002/anie.201606039] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Indexed: 11/10/2022]
Abstract
To measure protein isoforms in individual mammalian cells, we report single-cell resolution isoelectric focusing (scIEF) and high-selectivity immunoprobing. Microfluidic design and photoactivatable materials establish the tunable pH gradients required by IEF and precisely control the transport and handling of each 17-pL cell lysate during analysis. The scIEF assay resolves protein isoforms with resolution down to a single-charge unit, including both endogenous cytoplasmic and nuclear proteins from individual mammalian cells.
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Affiliation(s)
- Augusto M Tentori
- The UC Berkeley/UCSF Graduate Program in Bioengineering, Berkeley, CA, USA
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Kevin A Yamauchi
- The UC Berkeley/UCSF Graduate Program in Bioengineering, Berkeley, CA, USA
| | - Amy E Herr
- The UC Berkeley/UCSF Graduate Program in Bioengineering, Berkeley, CA, USA.
- Department of Bioengineering, UC Berkeley, 308B Stanley Hall, Berkeley, CA, 94720, USA.
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117
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Tentori AM, Yamauchi KA, Herr AE. Detection of Isoforms Differing by a Single Charge Unit in Individual Cells. Angew Chem Int Ed Engl 2016. [DOI: 10.1002/ange.201606039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Augusto M. Tentori
- The UC Berkeley/UCSF Graduate Program in Bioengineering Berkeley CA USA
- Department of Chemical Engineering Massachusetts Institute of Technology Cambridge MA USA
| | - Kevin A. Yamauchi
- The UC Berkeley/UCSF Graduate Program in Bioengineering Berkeley CA USA
| | - Amy E. Herr
- The UC Berkeley/UCSF Graduate Program in Bioengineering Berkeley CA USA
- Department of Bioengineering UC Berkeley 308B Stanley Hall Berkeley CA 94720 USA
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118
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Astefanei A, Dapic I, Camenzuli M. Different Stationary Phase Selectivities and Morphologies for Intact Protein Separations. Chromatographia 2016; 80:665-687. [PMID: 28529348 PMCID: PMC5413533 DOI: 10.1007/s10337-016-3168-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Revised: 08/17/2016] [Accepted: 09/06/2016] [Indexed: 12/18/2022]
Abstract
The central dogma of biology proposed that one gene encodes for one protein. We now know that this does not reflect reality. The human body has approximately 20,000 protein-encoding genes; each of these genes can encode more than one protein. Proteins expressed from a single gene can vary in terms of their post-translational modifications, which often regulate their function within the body. Understanding the proteins within our bodies is a key step in understanding the cause, and perhaps the solution, to disease. This is one of the application areas of proteomics, which is defined as the study of all proteins expressed within an organism at a given point in time. The human proteome is incredibly complex. The complexity of biological samples requires a combination of technologies to achieve high resolution and high sensitivity analysis. Despite the significant advances in mass spectrometry, separation techniques are still essential in this field. Liquid chromatography is an indispensable tool by which low-abundant proteins in complex samples can be enriched and separated. However, advances in chromatography are not as readily adapted in proteomics compared to advances in mass spectrometry. Biologists in this field still favour reversed-phase chromatography with fully porous particles. The purpose of this review is to highlight alternative selectivities and stationary phase morphologies that show potential for application in top-down proteomics; the study of intact proteins.
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Affiliation(s)
- A. Astefanei
- Centre for Analytical Science in Amsterdam (CASA), Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - I. Dapic
- Centre for Analytical Science in Amsterdam (CASA), Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - M. Camenzuli
- Centre for Analytical Science in Amsterdam (CASA), Van’t Hoff Institute for Molecular Sciences, University of Amsterdam, Science Park 904, 1098 XH Amsterdam, The Netherlands
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119
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Morris JS. Genomic and proteomic profiling for cancer diagnosis in dogs. Vet J 2016; 215:101-9. [DOI: 10.1016/j.tvjl.2016.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Revised: 12/01/2015] [Accepted: 01/01/2016] [Indexed: 11/25/2022]
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120
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Raghow R. An 'Omics' Perspective on Cardiomyopathies and Heart Failure. Trends Mol Med 2016; 22:813-827. [PMID: 27499035 DOI: 10.1016/j.molmed.2016.07.007] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Revised: 07/15/2016] [Accepted: 07/15/2016] [Indexed: 12/27/2022]
Abstract
Pathological enlargement of the heart, represented by hypertrophic cardiomyopathy (HCM) and dilated cardiomyopathy (DCM), occurs in response to many genetic and non-genetic factors. The clinical course of cardiac hypertrophy is remarkably variable, ranging from lifelong absence of symptoms to rapidly declining heart function and sudden cardiac death (SCD). Unbiased omics studies have begun to provide a glimpse into the molecular framework underpinning altered mechanotransduction, mitochondrial energetics, oxidative stress, and extracellular matrix in the heart undergoing physiological and pathological hypertrophy. Omics analyses indicate that post-transcriptional regulation of gene expression plays an overriding role in the normal and diseased heart. Studies to date highlight a need for more effective bioinformatics to better integrate patient omics data with their comprehensive clinical histories.
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Affiliation(s)
- Rajendra Raghow
- Department of Pharmacology, College of Medicine, The University of Tennessee Health Science Center and the VA Medical Center, Memphis, TN 38104, USA.
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121
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Gregorich ZR, Peng Y, Cai W, Jin Y, Wei L, Chen AJ, McKiernan SH, Aiken JM, Moss RL, Diffee GM, Ge Y. Top-Down Targeted Proteomics Reveals Decrease in Myosin Regulatory Light-Chain Phosphorylation That Contributes to Sarcopenic Muscle Dysfunction. J Proteome Res 2016; 15:2706-16. [PMID: 27362462 PMCID: PMC4975644 DOI: 10.1021/acs.jproteome.6b00244] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Sarcopenia, the loss of skeletal muscle mass and function with advancing age, is a significant cause of disability and loss of independence in the elderly and thus, represents a formidable challenge for the aging population. Nevertheless, the molecular mechanism(s) underlying sarcopenia-associated muscle dysfunction remain poorly understood. In this study, we employed an integrated approach combining top-down targeted proteomics with mechanical measurements to dissect the molecular mechanism(s) in age-related muscle dysfunction. Top-down targeted proteomic analysis uncovered a progressive age-related decline in the phosphorylation of myosin regulatory light chain (RLC), a critical protein involved in the modulation of muscle contractility, in the skeletal muscle of aging rats. Top-down tandem mass spectrometry analysis identified a previously unreported bis-phosphorylated proteoform of fast skeletal RLC and localized the sites of decreasing phosphorylation to Ser14/15. Of these sites, Ser14 phosphorylation represents a previously unidentified site of phosphorylation in RLC from fast-twitch skeletal muscle. Subsequent mechanical analysis of single fast-twitch fibers isolated from the muscles of rats of different ages revealed that the observed decline in RLC phosphorylation can account for age-related decreases in the contractile properties of sarcopenic fast-twitch muscles. These results strongly support a role for decreasing RLC phosphorylation in sarcopenia-associated muscle dysfunction and suggest that therapeutic modulation of RLC phosphorylation may represent a new avenue for the treatment of sarcopenia.
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Affiliation(s)
- Zachery R. Gregorich
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
| | - Ying Peng
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
| | - Wenxuan Cai
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
| | - Yutong Jin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706
| | - Liming Wei
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China
| | - Albert J. Chen
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
| | - Susan H. McKiernan
- Department of Kinesiology, University of Wisconsin-Madison, 2000 Observatory Dr., Madison, WI, 53705
| | - Judd M. Aiken
- Departments of Agriculture, Food, and Nutritional Sciences, University of Alberta-Edmonton, Edmonton, AB, Canada
| | - Richard L. Moss
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
- Human Proteomics Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
- UW Cardiovascular Research Center, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
| | - Gary M. Diffee
- Department of Kinesiology, University of Wisconsin-Madison, 2000 Observatory Dr., Madison, WI, 53705
- UW Cardiovascular Research Center, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706
- Human Proteomics Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
- UW Cardiovascular Research Center, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705
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122
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Cai W, Tucholski TM, Gregorich ZR, Ge Y. Top-down Proteomics: Technology Advancements and Applications to Heart Diseases. Expert Rev Proteomics 2016; 13:717-30. [PMID: 27448560 DOI: 10.1080/14789450.2016.1209414] [Citation(s) in RCA: 75] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
INTRODUCTION Heart diseases are a leading cause of morbidity and mortality for both men and women worldwide, and impose significant economic burdens on the healthcare systems. Despite substantial effort over the last several decades, the molecular mechanisms underlying diseases of the heart remain poorly understood. AREAS COVERED Altered protein post-translational modifications (PTMs) and protein isoform switching are increasingly recognized as important disease mechanisms. Top-down high-resolution mass spectrometry (MS)-based proteomics has emerged as the most powerful method for the comprehensive analysis of PTMs and protein isoforms. Here, we will review recent technology developments in the field of top-down proteomics, as well as highlight recent studies utilizing top-down proteomics to decipher the cardiac proteome for the understanding of the molecular mechanisms underlying diseases of the heart. Expert commentary: Top-down proteomics is a premier method for the global and comprehensive study of protein isoforms and their PTMs, enabling the identification of novel protein isoforms and PTMs, characterization of sequence variations, and quantification of disease-associated alterations. Despite significant challenges, continuous development of top-down proteomics technology will greatly aid the dissection of the molecular mechanisms underlying diseases of the hearts for the identification of novel biomarkers and therapeutic targets.
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Affiliation(s)
- Wenxuan Cai
- a Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,b Molecular and Cellular Pharmacology Training Program , University of Wisconsin-Madison , Madison , WI , USA
| | - Trisha M Tucholski
- c Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA
| | - Zachery R Gregorich
- a Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,b Molecular and Cellular Pharmacology Training Program , University of Wisconsin-Madison , Madison , WI , USA
| | - Ying Ge
- a Department of Cell and Regenerative Biology , University of Wisconsin-Madison , Madison , WI , USA.,c Department of Chemistry , University of Wisconsin-Madison , Madison , WI , USA.,d Human Proteomics Program , University of Wisconsin-Madison , Madison , WI , USA
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123
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Barroso A, Giménez E, Benavente F, Barbosa J, Sanz-Nebot V. Classification of congenital disorders of glycosylation based on analysis of transferrin glycopeptides by capillary liquid chromatography-mass spectrometry. Talanta 2016; 160:614-623. [PMID: 27591658 DOI: 10.1016/j.talanta.2016.07.055] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2016] [Revised: 07/22/2016] [Accepted: 07/24/2016] [Indexed: 01/30/2023]
Abstract
In this work, we describe a multivariate data analysis approach for data exploration and classification of the complex and large data sets generated to study the alteration of human transferrin (Tf) N-glycopeptides in patients with congenital disorders of glycosylation (CDG). Tf from healthy individuals and two types of CDG patients (CDG-I and CDG-II) is purified by immunoextraction from serum samples before trypsin digestion and separation by capillary liquid chromatography mass spectrometry (CapLC-MS). Following a targeted data analysis approach, partial least squares discriminant analysis (PLS-DA) is applied to the relative abundance of Tf glycopeptide glycoforms obtained after integration of the extracted ion chromatograms of the different samples. The performance of PLS-DA for classification of the different samples and for providing a novel insight into Tf glycopeptide glycoforms alteration in CDGs is demonstrated. Only six out of fourteen of the detected glycoforms are enough for an accurate classification. This small glycoform set may be considered a sensitive and specific novel biomarker panel for CDGs.
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Affiliation(s)
- Albert Barroso
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Estela Giménez
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Fernando Benavente
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain.
| | - José Barbosa
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
| | - Victoria Sanz-Nebot
- Department of Chemical Engineering and Analytical Chemistry, University of Barcelona, Diagonal 645, 08028 Barcelona, Spain
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124
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Challenges in biomarker discovery with MALDI-TOF MS. Clin Chim Acta 2016; 458:84-98. [PMID: 27134187 DOI: 10.1016/j.cca.2016.04.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 04/21/2016] [Accepted: 04/27/2016] [Indexed: 12/30/2022]
Abstract
MALDI-TOF MS technique is commonly used in system biology and clinical studies to search for new potential markers associated with pathological conditions. Despite numerous concerns regarding a sample preparation or processing of complex data, this strategy is still recognized as a popular tool and its awareness has risen in the proteomic community over the last decade. In this review, we present comprehensive application of MALDI mass spectrometry with special focus on profiling research. We also discuss major advantages and disadvantages of universal sample preparation methods such as micro-SPE columns, immunodepletion or magnetic beads, and we show the potential of nanostructured materials in capturing low molecular weight subproteomes. Furthermore, as the general protocol considerably affects spectra quality and interpretation, an alternative solution for improved ion detection, including hydrophobic constituents, data processing and statistical analysis is being considered in up-to-date profiling pattern. In conclusion, many reports involving MALDI-TOF MS indicated highly abundant proteins as valuable indicators, and at the same time showed the inaccuracy of available methods in the detection of low abundant proteome that is the most interesting from the clinical perspective. Therefore, the analytical aspects of sample preparation methods should be standardized to provide a reproducible, low sample handling and credible procedure.
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125
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Canut H, Albenne C, Jamet E. Post-translational modifications of plant cell wall proteins and peptides: A survey from a proteomics point of view. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2016; 1864:983-90. [PMID: 26945515 DOI: 10.1016/j.bbapap.2016.02.022] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Revised: 02/12/2016] [Accepted: 02/24/2016] [Indexed: 12/21/2022]
Abstract
Plant cell wall proteins (CWPs) and peptides are important players in cell walls contributing to their assembly and their remodeling during development and in response to environmental constraints. Since the rise of proteomics technologies at the beginning of the 2000's, the knowledge of CWPs has greatly increased leading to the discovery of new CWP families and to the description of the cell wall proteomes of different organs of many plants. Conversely, cell wall peptidomics data are still lacking. In addition to the identification of CWPs and peptides by mass spectrometry (MS) and bioinformatics, proteomics has allowed to describe their post-translational modifications (PTMs). At present, the best known PTMs consist in proteolytic cleavage, N-glycosylation, hydroxylation of P residues into hydroxyproline residues (O), O-glycosylation and glypiation. In this review, the methods allowing the capture of the modified proteins based on the specific properties of their PTMs as well as the MS technologies used for their characterization are briefly described. A focus is done on proteolytic cleavage leading to protein maturation or release of signaling peptides and on O-glycosylation. Some new technologies, like top-down proteomics and terminomics, are described. They aim at a finer description of proteoforms resulting from PTMs or degradation mechanisms. This article is part of a Special Issue entitled: Plant Proteomics--a bridge between fundamental processes and crop production, edited by Dr. Hans-Peter Mock.
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Affiliation(s)
- Hervé Canut
- Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France
| | - Cécile Albenne
- Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France
| | - Elisabeth Jamet
- Université de Toulouse, CNRS, UPS, 24 chemin de Borde Rouge, Auzeville, BP42617, 31326 Castanet Tolosan, France.
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126
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Sun RX, Luo L, Wu L, Wang RM, Zeng WF, Chi H, Liu C, He SM. pTop 1.0: A High-Accuracy and High-Efficiency Search Engine for Intact Protein Identification. Anal Chem 2016; 88:3082-90. [DOI: 10.1021/acs.analchem.5b03963] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Rui-Xiang Sun
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
| | - Lan Luo
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Long Wu
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Rui-Min Wang
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Wen-Feng Zeng
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hao Chi
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
| | - Chao Liu
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
| | - Si-Min He
- Key
Lab of Intelligent Information Processing of Chinese Academy of Sciences
(CAS), Institute of Computing Technology, CAS, Beijing 100190, China
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127
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Sanchez-Lucas R, Mehta A, Valledor L, Cabello-Hurtado F, Romero-Rodrıguez MC, Simova-Stoilova L, Demir S, Rodriguez-de-Francisco LE, Maldonado-Alconada AM, Jorrin-Prieto AL, Jorrín-Novo JV. A year (2014-2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists. Proteomics 2016; 16:866-76. [PMID: 26621614 DOI: 10.1002/pmic.201500351] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2015] [Revised: 10/26/2015] [Accepted: 11/04/2015] [Indexed: 12/23/2022]
Abstract
The present review is an update of the previous one published in Proteomics 2015 Reviews special issue [Jorrin-Novo, J. V. et al., Proteomics 2015, 15, 1089-1112] covering the July 2014-2015 period. It has been written on the bases of the publications that appeared in Proteomics journal during that period and the most relevant ones that have been published in other high-impact journals. Methodological advances and the contribution of the field to the knowledge of plant biology processes and its translation to agroforestry and environmental sectors will be discussed. This review has been organized in four blocks, with a starting general introduction (literature survey) followed by sections focusing on the methodology (in vitro, in vivo, wet, and dry), proteomics integration with other approaches (systems biology and proteogenomics), biological information, and knowledge (cell communication, receptors, and signaling), ending with a brief mention of some other biological and translational topics to which proteomics has made some contribution.
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Affiliation(s)
- Rosa Sanchez-Lucas
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Angela Mehta
- Embrapa Recursos Genéticos e Biotecnologia (CENARGEN), Brasília, DF, Brazil
| | - Luis Valledor
- Department of Biology of Organisms and Systems (BOS), University of Oviedo, Oviedo, Spain
| | | | - M Cristina Romero-Rodrıguez
- Centro Multidisciplinario de Investigaciones Tecnológicas, and Departamento de Fitoquímica, Facultad de Ciencias Químicas, Universidad Nacional de Asunción, San Lorenzo, Paraguay
| | - Lyudmila Simova-Stoilova
- Plant Molecular Biology Department, Institute of Plant Physiology and Genetics, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Sekvan Demir
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Luis E Rodriguez-de-Francisco
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain.,INTEC-Sto. Domingo, Santo Domingo, República Dominicana
| | - Ana M Maldonado-Alconada
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Ana L Jorrin-Prieto
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
| | - Jesus V Jorrín-Novo
- Agroforestry and Plant Biochemistry and Proteomics Research Group, Department of Biochemistry and Molecular Biology, University of Córdoba-CeiA3, Córdoba, Spain
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128
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Steffen P, Kwiatkowski M, Robertson WD, Zarrine-Afsar A, Deterra D, Richter V, Schlüter H. Protein species as diagnostic markers. J Proteomics 2016; 134:5-18. [DOI: 10.1016/j.jprot.2015.12.015] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Revised: 11/28/2015] [Accepted: 12/09/2015] [Indexed: 02/07/2023]
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129
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Yu D, Peng Y, Ayaz-Guner S, Gregorich ZR, Ge Y. Comprehensive Characterization of AMP-Activated Protein Kinase Catalytic Domain by Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:220-32. [PMID: 26489410 PMCID: PMC4840101 DOI: 10.1007/s13361-015-1286-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2015] [Revised: 09/25/2015] [Accepted: 09/26/2015] [Indexed: 05/12/2023]
Abstract
AMP-activated protein kinase (AMPK) is a serine/threonine protein kinase that is essential in regulating energy metabolism in all eukaryotic cells. It is a heterotrimeric protein complex composed of a catalytic subunit (α) and two regulatory subunits (β and γ). C-terminal truncation of AMPKα at residue 312 yielded a protein that is active upon phosphorylation of Thr172 in the absence of β and γ subunits, which is refered to as the AMPK catalytic domain and commonly used to substitute for the AMPK heterotrimeric complex in in vitro kinase assays. However, a comprehensive characterization of the AMPK catalytic domain is lacking. Herein, we expressed a His-tagged human AMPK catalytic domin (denoted as AMPKΔ) in E. coli, comprehensively characterized AMPKΔ in its basal state and after in vitro phosphorylation using top-down mass spectrometry (MS), and assessed how phosphorylation of AMPKΔ affects its activity. Unexpectedly, we found that bacterially-expressed AMPKΔ was basally phosphorylated and localized the phosphorylation site to the His-tag. We found that AMPKΔ had noticeable basal activity and was capable of phosphorylating itself and its substrates without activating phosphorylation at Thr172. Moreover, our data suggested that Thr172 is the only site phosphorylated by its upstream kinase, liver kinase B1, and that this phosphorylation dramatically increases the kinase activity of AMPKΔ. Importantly, we demonstrated that top-down MS in conjunction with in vitro phosphorylation assay is a powerful approach for monitoring phosphorylation reaction and determining sequential order of phosphorylation events in kinase-substrate systems.
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Affiliation(s)
- Deyang Yu
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Environmental Toxicology Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Ying Peng
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Serife Ayaz-Guner
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Zachery R. Gregorich
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Environmental Toxicology Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Address reprint requests to: Dr. Ying Ge, 1300 University Ave., SMI 130, Madison, Wisconsin, USA. Tel: 608-263-9212, Fax: 608-265-5512,
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130
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Chen B, Peng Y, Valeja SG, Xiu L, Alpert AJ, Ge Y. Online Hydrophobic Interaction Chromatography-Mass Spectrometry for Top-Down Proteomics. Anal Chem 2016; 88:1885-91. [PMID: 26729044 DOI: 10.1021/acs.analchem.5b04285] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Recent progress in top-down proteomics has led to a demand for mass spectrometry (MS)-compatible chromatography techniques to separate intact proteins using volatile mobile phases. Conventional hydrophobic interaction chromatography (HIC) provides high-resolution separation of proteins under nondenaturing conditions but requires high concentrations of nonvolatile salts. Herein, we introduce a series of more-hydrophobic HIC materials that can retain proteins using MS-compatible concentrations of ammonium acetate. The new HIC materials appear to function as a hybrid form of conventional HIC and reverse phase chromatography. The function of the salt seems to be preserving protein structure rather than promoting retention. Online HIC-MS is feasible for both qualitative and quantitative analysis. This is demonstrated with standard proteins and a complex cell lysate. The mass spectra of proteins from the online HIC-MS exhibit low charge-state distributions, consistent with those commonly observed in native MS. Furthermore, HIC-MS can chromatographically separate proteoforms differing by minor modifications. Hence, this new HIC-MS combination is promising for top-down proteomics.
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Affiliation(s)
- Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin, United States
| | - Ying Peng
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin, United States
| | - Santosh G Valeja
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin, United States
| | - Lichen Xiu
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin, United States
| | - Andrew J Alpert
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin, United States.,PolyLC, Inc., 9151 Rumsey Rd., Suite 180, Columbia, Maryland, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison , Madison, Wisconsin, United States.,Department of Cell and Regenerative Biology, University of Wisconsin-Madison , Madison, Wisconsin, United States.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison , Madison, Wisconsin, United States
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131
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Zhou L, Li Q, Wang J, Huang C, Nice EC. Oncoproteomics: Trials and tribulations. Proteomics Clin Appl 2015; 10:516-31. [PMID: 26518147 DOI: 10.1002/prca.201500081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/19/2015] [Accepted: 10/27/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
- Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou Hainan P. R. China
| | - Qifu Li
- Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou Hainan P. R. China
| | - Jiandong Wang
- Department of Biomedical; Chengdu Medical College; Chengdu Sichuan Province P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
| | - Edouard C. Nice
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Australia
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132
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Cai W, Guner H, Gregorich ZR, Chen AJ, Ayaz-Guner S, Peng Y, Valeja SG, Liu X, Ge Y. MASH Suite Pro: A Comprehensive Software Tool for Top-Down Proteomics. Mol Cell Proteomics 2015; 15:703-14. [PMID: 26598644 DOI: 10.1074/mcp.o115.054387] [Citation(s) in RCA: 96] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2015] [Indexed: 12/25/2022] Open
Abstract
Top-down mass spectrometry (MS)-based proteomics is arguably a disruptive technology for the comprehensive analysis of all proteoforms arising from genetic variation, alternative splicing, and posttranslational modifications (PTMs). However, the complexity of top-down high-resolution mass spectra presents a significant challenge for data analysis. In contrast to the well-developed software packages available for data analysis in bottom-up proteomics, the data analysis tools in top-down proteomics remain underdeveloped. Moreover, despite recent efforts to develop algorithms and tools for the deconvolution of top-down high-resolution mass spectra and the identification of proteins from complex mixtures, a multifunctional software platform, which allows for the identification, quantitation, and characterization of proteoforms with visual validation, is still lacking. Herein, we have developed MASH Suite Pro, a comprehensive software tool for top-down proteomics with multifaceted functionality. MASH Suite Pro is capable of processing high-resolution MS and tandem MS (MS/MS) data using two deconvolution algorithms to optimize protein identification results. In addition, MASH Suite Pro allows for the characterization of PTMs and sequence variations, as well as the relative quantitation of multiple proteoforms in different experimental conditions. The program also provides visualization components for validation and correction of the computational outputs. Furthermore, MASH Suite Pro facilitates data reporting and presentation via direct output of the graphics. Thus, MASH Suite Pro significantly simplifies and speeds up the interpretation of high-resolution top-down proteomics data by integrating tools for protein identification, quantitation, characterization, and visual validation into a customizable and user-friendly interface. We envision that MASH Suite Pro will play an integral role in advancing the burgeoning field of top-down proteomics.
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Affiliation(s)
- Wenxuan Cai
- From the ‡Department of Cell and Regenerative Biology, §Molecular Pharmacology Training Program
| | - Huseyin Guner
- From the ‡Department of Cell and Regenerative Biology, ¶Human Proteomics Program
| | - Zachery R Gregorich
- From the ‡Department of Cell and Regenerative Biology, §Molecular Pharmacology Training Program
| | - Albert J Chen
- From the ‡Department of Cell and Regenerative Biology
| | | | - Ying Peng
- From the ‡Department of Cell and Regenerative Biology
| | | | - Xiaowen Liu
- **Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 West 10th Street, Indianapolis, IN 46202
| | - Ying Ge
- From the ‡Department of Cell and Regenerative Biology, ¶Human Proteomics Program, ‡‡Department of Chemistry, University of Wisconsin-Madison, 1300 University Ave., Madison, WI 53706,Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Ave., Indianapolis, IN 46202,
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133
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Rai AN, Epperson WB, Nanduri B. Application of Functional Genomics for Bovine Respiratory Disease Diagnostics. Bioinform Biol Insights 2015; 9:13-23. [PMID: 26526746 PMCID: PMC4620937 DOI: 10.4137/bbi.s30525] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 08/24/2015] [Accepted: 08/26/2015] [Indexed: 12/27/2022] Open
Abstract
Bovine respiratory disease (BRD) is the most common economically important disease affecting cattle. For developing accurate diagnostics that can predict disease susceptibility/resistance and stratification, it is necessary to identify the molecular mechanisms that underlie BRD. To study the complex interactions among the bovine host and the multitude of viral and bacterial pathogens, as well as the environmental factors associated with BRD etiology, genome-scale high-throughput functional genomics methods such as microarrays, RNA-seq, and proteomics are helpful. In this review, we summarize the progress made in our understanding of BRD using functional genomics approaches. We also discuss some of the available bioinformatics resources for analyzing high-throughput data, in the context of biological pathways and molecular interactions. Although resources for studying host response to infection are avail-able, the corresponding information is lacking for majority of BRD pathogens, impeding progress in identifying diagnostic signatures for BRD using functional genomics approaches.
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Affiliation(s)
- Aswathy N Rai
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, MS, USA
| | - William B Epperson
- Department of Pathobiology and Population Medicine, College of Veterinary Medicine, Mississippi State University, MS, USA
| | - Bindu Nanduri
- Department of Basic Sciences, College of Veterinary Medicine, Mississippi State University, MS, USA. ; Institute for Genomics, Biocomputing, and Biotechnology, Mississippi State University, MS, USA
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134
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Chang CW, Dalgliesh AJ, López JE, Griffiths LG. Cardiac extracellular matrix proteomics: Challenges, techniques, and clinical implications. Proteomics Clin Appl 2015. [PMID: 26200932 DOI: 10.1002/prca.201500030] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Extracellular matrix (ECM) has emerged as a dynamic tissue component, providing not only structural support, but also functionally participating in a wide range of signaling events during development, injury, and disease remodeling. Investigation of dynamic changes in cardiac ECM proteome is challenging due to the relative insolubility of ECM proteins, which results from their macromolecular nature, extensive post-translational modification (PTM), and tendency to form protein complexes. Finally, the relative abundance of cellular and mitochondrial proteins in cardiac tissue further complicates cardiac ECM proteomic approaches. Recent developments of various techniques to enrich and analyze ECM proteins are playing a major role in overcoming these challenges. Application of cardiac ECM proteomics in disease tissues can further provide spatial and temporal information relevant to disease diagnosis, prognosis, treatment, and engineering of therapeutic candidates for cardiac repair and regeneration.
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Affiliation(s)
- Chia Wei Chang
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Ailsa J Dalgliesh
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - Javier E López
- Department of Internal Medicine, School of Medicine, University of California, Davis, CA, USA
| | - Leigh G Griffiths
- Department of Veterinary Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, CA, USA
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135
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Schmidlin T, Boender AJ, Frese CK, Heck AJR, Adan RAH, Altelaar AFM. Diet-Induced Neuropeptide Expression: Feasibility of Quantifying Extended and Highly Charged Endogenous Peptide Sequences by Selected Reaction Monitoring. Anal Chem 2015; 87:9966-73. [DOI: 10.1021/acs.analchem.5b03334] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Thierry Schmidlin
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Arjen J. Boender
- Department
of Translational Neuroscience, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - Christian K. Frese
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J. R. Heck
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Roger A. H. Adan
- Department
of Translational Neuroscience, University Medical Center Utrecht, Universiteitsweg 100, 3584 CG, Utrecht, The Netherlands
| | - A. F. Maarten Altelaar
- Biomolecular
Mass Spectrometry and Proteomics, Bijvoet Center for Biomolecular
Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University and Netherlands Proteomics Centre, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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136
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Ménoret A, Crocker SJ, Rodriguez A, Rathinam VA, Clark RB, Vella AT. Transition from identity to bioactivity-guided proteomics for biomarker discovery with focus on the PF2D platform. Proteomics Clin Appl 2015. [PMID: 26201056 DOI: 10.1002/prca.201500029] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Proteomic strategies provide a valuable tool kit to identify proteins involved in diseases. With recent progress in MS technology, high throughput proteomics has accelerated protein identification for potential biomarkers. Numerous biomarker candidates have been identified in several diseases, and many are common among pathologies. An overall strategy that could complement and strengthen the search for biomarkers is combining protein identity with biological outcomes. This review describes an emerging framework of bridging bioactivity to protein identity, exploring the possibility that some biomarkers will have a mechanistic role in the disease process. A review of pulmonary, cardiovascular, and CNS biomarkers will be discussed to demonstrate the utility of combining bioactivity with identification as a means to not only find meaningful biomarkers, but also to uncover functional mediators of disease.
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Affiliation(s)
- Antoine Ménoret
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Stephen J Crocker
- Department of Neuroscience, University of Connecticut Health Center, Farmington, CT, USA
| | - Annabelle Rodriguez
- Department of Cell Biology, University of Connecticut Health Center, Farmington, CT, USA
| | - Vijay A Rathinam
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Robert B Clark
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
| | - Anthony T Vella
- Department of Immunology, University of Connecticut Health Center, Farmington, CT, USA
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137
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Gregorich ZR, Peng Y, Lane NM, Wolff JJ, Wang S, Guo W, Guner H, Doop J, Hacker TA, Ge Y. Comprehensive assessment of chamber-specific and transmural heterogeneity in myofilament protein phosphorylation by top-down mass spectrometry. J Mol Cell Cardiol 2015; 87:102-12. [PMID: 26268593 DOI: 10.1016/j.yjmcc.2015.08.007] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 08/04/2015] [Accepted: 08/08/2015] [Indexed: 11/28/2022]
Abstract
The heart is characterized by a remarkable degree of heterogeneity, the basis of which is a subject of active investigation. Myofilament protein post-translational modifications (PTMs) represent a critical mechanism regulating cardiac contractility, and emerging evidence shows that pathological cardiac conditions induce contractile heterogeneity that correlates with transmural variations in the modification status of myofilament proteins. Nevertheless, whether there exists basal heterogeneity in myofilament protein PTMs in the heart remains unclear. Here we have systematically assessed chamber-specific and transmural variations in myofilament protein PTMs, specifically, the phosphorylation of cardiac troponin I (cTnI), cardiac troponin T (cTnT), tropomyosin (Tpm), and myosin light chain 2 (MLC2). We show that the phosphorylation of cTnI and αTm vary in the different chambers of the heart, whereas the phosphorylation of MLC2 and cTnT does not. In contrast, no significant transmural differences were observed in the phosphorylation of any of the myofilament proteins analyzed. These results highlight the importance of appropriate tissue sampling-particularly for studies aimed at elucidating disease mechanisms and biomarker discovery-in order to minimize potential variations arising from basal heterogeneity in myofilament PTMs in the heart.
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Affiliation(s)
- Zachery R Gregorich
- Molecular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ying Peng
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Nicole M Lane
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Cellular and Molecular Pathology Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | | | - Sijian Wang
- Department of Biostatistics & Medical Informatics, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Statistics, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Wei Guo
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Huseyin Guner
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Justin Doop
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Timothy A Hacker
- Department of Medicine, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Ying Ge
- Molecular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA; Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53706, USA; Cellular and Molecular Pathology Training Program, University of Wisconsin-Madison, Madison, WI 53706, USA; Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53706, USA.
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138
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Chen YC, Ayaz-Guner S, Peng Y, Lane NM, Locher M, Kohmoto T, Larsson L, Moss RL, Ge Y. Effective top-down LC/MS+ method for assessing actin isoforms as a potential cardiac disease marker. Anal Chem 2015; 87:8399-8406. [PMID: 26189812 DOI: 10.1021/acs.analchem.5b01745] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Actin is the major component of the cytoskeleton, playing an essential role in the structure and motility of both muscle and nonmuscle cells. It is highly conserved and encoded by a multigene family. α-Cardiac actin (αCAA) and α-skeletal actin (αSKA), encoded by two different genes, are the primary actin isoforms expressed in striated muscles. The relative expression levels of αSKA and αCAA have been shown to vary between species and under pathological conditions. In particular, an increased αSKA expression is believed to be a programmed response of a diseased heart. Therefore, it is essential to quantify the relative expression of αSKA and αCAA, which remains challenging due to the high degree of sequence similarity between these isoforms (98.9%). Herein, we developed a top-down liquid chromatography/mass spectrometry-based ("LC/MS+") method for the rapid purification and comprehensive analysis of α-actin extracted from muscle tissues. We thoroughly investigated all of the actin isoforms in healthy human cardiac and skeletal muscles. We found that αSKA is the only isoform expressed in skeletal muscle, whereas αCAA and αSKA are coexpressed in cardiac muscle. We then applied our method to quantify the α-actin isoforms in human healthy hearts and failing hearts with dilated cardiomyopathy (DCM). We found that αSKA is augmented in DCM compared with healthy controls, 43.1 ± 0.9% versus 23.7 ± 1.7%, respectively. As demonstrated, top-down LC/MS+ provides an effective and comprehensive method for the purification, quantification, and characterization of α-actin isoforms, enabling assessment of their clinical potential as cardiac disease markers.
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Affiliation(s)
- Yi-Chen Chen
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Serife Ayaz-Guner
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ying Peng
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Nicole M Lane
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Matthew Locher
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Takushi Kohmoto
- Department of Surgery, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lars Larsson
- Department of Physiology and Pharmacology, Department of Clinical Neuroscience, Karolinska Institutet, Stockholm, Sweden
| | - Richard L Moss
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Department of Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA.,Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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139
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Lermyte F, Sobott F. Electron transfer dissociation provides higher-order structural information of native and partially unfolded protein complexes. Proteomics 2015; 15:2813-22. [DOI: 10.1002/pmic.201400516] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2014] [Revised: 03/13/2015] [Accepted: 06/15/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Frederik Lermyte
- UA-VITO Center for Proteomics; University of Antwerp; Antwerp Belgium
- Biomolecular & Analytical Mass Spectrometry group; Department of Chemistry; University of Antwerp; Antwerp Belgium
| | - Frank Sobott
- UA-VITO Center for Proteomics; University of Antwerp; Antwerp Belgium
- Biomolecular & Analytical Mass Spectrometry group; Department of Chemistry; University of Antwerp; Antwerp Belgium
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140
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Zhao Y, Riley NM, Sun L, Hebert AS, Yan X, Westphall MS, Rush MJP, Zhu G, Champion MM, Medie FM, DiGiuseppe Champion PA, Coon JJ, Dovichi NJ. Coupling capillary zone electrophoresis with electron transfer dissociation and activated ion electron transfer dissociation for top-down proteomics. Anal Chem 2015; 87:5422-9. [PMID: 25893372 PMCID: PMC4439324 DOI: 10.1021/acs.analchem.5b00883] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Top-down proteomics offers the potential for full protein characterization, but many challenges remain for this approach, including efficient protein separations and effective fragmentation of intact proteins. Capillary zone electrophoresis (CZE) has shown great potential for separation of intact proteins, especially for differentially modified proteoforms of the same gene product. To date, however, CZE has been used only with collision-based fragmentation methods. Here we report the first implementation of electron transfer dissociation (ETD) with online CZE separations for top-down proteomics, analyzing a mixture of four standard proteins and a complex protein mixture from the Mycobacterium marinum bacterial secretome. Using a multipurpose dissociation cell on an Orbitrap Elite system, we demonstrate that CZE is fully compatible with ETD as well as higher energy collisional dissociation (HCD), and that the two complementary fragmentation methods can be used in tandem on the electrophoretic time scale for improved protein characterization. Furthermore, we show that activated ion electron transfer dissociation (AI-ETD), a recently introduced method for enhanced ETD fragmentation, provides useful performance with CZE separations to greatly increase protein characterization. When combined with HCD, AI-ETD improved the protein sequence coverage by more than 200% for proteins from both standard and complex mixtures, highlighting the benefits electron-driven dissociation methods can add to CZE separations.
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Affiliation(s)
- Yimeng Zhao
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Nicholas M. Riley
- Department of Biomolecular Chemistry, Genome Center of Wisconsin, and Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Liangliang Sun
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Alexander S. Hebert
- Department of Biomolecular Chemistry, Genome Center of Wisconsin, and Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Xiaojing Yan
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Michael S. Westphall
- Department of Biomolecular Chemistry, Genome Center of Wisconsin, and Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Matthew J. P. Rush
- Department of Biomolecular Chemistry, Genome Center of Wisconsin, and Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Guijie Zhu
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Matthew M. Champion
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
| | - Felix Mba Medie
- Department of Biological Sciences, University of Notre Dame, Notre Dame, IN 46556, USA
| | | | - Joshua J. Coon
- Department of Biomolecular Chemistry, Genome Center of Wisconsin, and Department of Chemistry, University of Wisconsin, Madison, WI 53706, USA
| | - Norman J. Dovichi
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, IN 46556, USA
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141
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Valeja SG, Xiu L, Gregorich ZR, Guner H, Jin S, Ge Y. Three dimensional liquid chromatography coupling ion exchange chromatography/hydrophobic interaction chromatography/reverse phase chromatography for effective protein separation in top-down proteomics. Anal Chem 2015; 87:5363-5371. [PMID: 25867201 PMCID: PMC4575680 DOI: 10.1021/acs.analchem.5b00657] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
To address the complexity of the proteome in mass spectrometry (MS)-based top-down proteomics, multidimensional liquid chromatography (MDLC) strategies that can effectively separate proteins with high resolution and automation are highly desirable. Although various MDLC methods that can effectively separate peptides from protein digests exist, very few MDLC strategies, primarily consisting of 2DLC, are available for intact protein separation, which is insufficient to address the complexity of the proteome. We recently demonstrated that hydrophobic interaction chromatography (HIC) utilizing a MS-compatible salt can provide high resolution separation of intact proteins for top-down proteomics. Herein, we have developed a novel 3DLC strategy by coupling HIC with ion exchange chromatography (IEC) and reverse phase chromatography (RPC) for intact protein separation. We demonstrated that a 3D (IEC-HIC-RPC) approach greatly outperformed the conventional 2D IEC-RPC approach. For the same IEC fraction (out of 35 fractions) from a crude HEK 293 cell lysate, a total of 640 proteins were identified in the 3D approach (corresponding to 201 nonredundant proteins) as compared to 47 in the 2D approach, whereas simply prolonging the gradients in RPC in the 2D approach only led to minimal improvement in protein separation and identifications. Therefore, this novel 3DLC method has great potential for effective separation of intact proteins to achieve deep proteome coverage in top-down proteomics.
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Affiliation(s)
- Santosh G. Valeja
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Lichen Xiu
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Zachery R. Gregorich
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Wisconsin, USA
| | - Huseyin Guner
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Song Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
| | - Ying Ge
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Wisconsin, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, Wisconsin, USA
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142
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Multiple proteases to localize oxidation sites. PLoS One 2015; 10:e0116606. [PMID: 25775238 PMCID: PMC4361631 DOI: 10.1371/journal.pone.0116606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2014] [Accepted: 12/12/2014] [Indexed: 11/19/2022] Open
Abstract
Proteins present in cellular environments with high levels of reactive oxygen and nitrogen species and/or low levels of antioxidants are highly susceptible to oxidative post-translational modification (PTM). Irreversible oxidative PTMs can generate a complex distribution of modified protein molecules, recently termed as proteoforms. Using ubiquitin as a model system, we mapped oxidative modification sites using trypsin, Lys-C, and Glu-C peptides. Several M+16 Da proteoforms were detected as well as proteoforms that include other previously unidentified oxidative modifications. This work highlights the use of multiple protease digestions to give insights to the complexity of oxidative modifications possible in bottom-up analyses.
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143
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Chang YH, Gregorich ZR, Chen AJ, Hwang L, Guner H, Yu D, Zhang J, Ge Y. New mass-spectrometry-compatible degradable surfactant for tissue proteomics. J Proteome Res 2015; 14:1587-99. [PMID: 25589168 DOI: 10.1021/pr5012679] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Tissue proteomics is increasingly recognized for its role in biomarker discovery and disease mechanism investigation. However, protein solubility remains a significant challenge in mass spectrometry (MS)-based tissue proteomics. Conventional surfactants such as sodium dodecyl sulfate (SDS), the preferred surfactant for protein solubilization, are not compatible with MS. Herein, we have screened a library of surfactant-like compounds and discovered an MS-compatible degradable surfactant (MaSDeS) for tissue proteomics that solubilizes all categories of proteins with performance comparable to SDS. The use of MaSDeS in the tissue extraction significantly improves the total number of protein identifications from commonly used tissues, including tissue from the heart, liver, and lung. Notably, MaSDeS significantly enriches membrane proteins, which are often under-represented in proteomics studies. The acid degradable nature of MaSDeS makes it amenable for high-throughput MS-based proteomics. In addition, the thermostability of MaSDeS allows for its use in experiments requiring high temperature to facilitate protein extraction and solubilization. Furthermore, we have shown that MaSDeS outperforms the other MS-compatible surfactants in terms of overall protein solubility and the total number of identified proteins in tissue proteomics. Thus, the use of MaSDeS will greatly advance tissue proteomics and realize its potential in basic biomedical and clinical research. MaSDeS could be utilized in a variety of proteomics studies as well as general biochemical and biological experiments that employ surfactants for protein solubilization.
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Affiliation(s)
- Ying-Hua Chang
- Department of Cell and Regenerative Biology, ‡Molecular and Cellular Pharmacology Program, §Department of Chemistry, ∥Human Proteomics Program, and ⊥Molecular and Environmental Toxicology Program, University of Wisconsin-Madison , 1300 University Avenue, Madison 53706, Wisconsin, United States
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144
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Dissecting human skeletal muscle troponin proteoforms by top-down mass spectrometry. J Muscle Res Cell Motil 2015; 36:169-81. [PMID: 25613324 DOI: 10.1007/s10974-015-9404-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2014] [Accepted: 01/07/2015] [Indexed: 01/26/2023]
Abstract
Skeletal muscles are the most abundant tissues in the human body. They are composed of a heterogeneous collection of muscle fibers that perform various functions. Skeletal muscle troponin (sTn) regulates skeletal muscle contraction and relaxation. sTn consists of 3 subunits, troponin I (TnI), troponin T (TnT), and troponin C (TnC). TnI inhibits the actomyosin Mg(2+)-ATPase, TnC binds Ca(2+), and TnT is the tropomyosin (Tm)-binding subunit. The cardiac and skeletal isoforms of Tn share many similarities but the roles of modifications of Tn in the two muscles may differ. The modifications of cardiac Tn are known to alter muscle contractility and have been well-characterized. However, the modification status of sTn remains unclear. Here, we have employed top-down mass spectrometry (MS) to decipher the modifications of human sTnT and sTnI. We have extensively characterized sTnT and sTnI proteoforms, including alternatively spliced isoforms and post-translationally modified forms, found in human skeletal muscle with high mass accuracy and comprehensive sequence coverage. Moreover, we have localized the phosphorylation site of slow sTnT isoform III to Ser1 by tandem MS with electron capture dissociation. This is the first study to comprehensively characterize human sTn and also the first to identify the basal phosphorylation site for human sTnT by top-down MS.
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145
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MS-based methods for biomarkers of Parkinson's disease: what is the future? Bioanalysis 2015; 7:149-51. [DOI: 10.4155/bio.14.273] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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146
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Chen J, Liu Z, Wang F, Mao J, Zhou Y, Liu J, Zou H, Zhang Y. Enhancing the performance of LC-MS for intact protein analysis by counteracting the signal suppression effects of trifluoroacetic acid during electrospray. Chem Commun (Camb) 2015; 51:14758-60. [DOI: 10.1039/c5cc06072a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We develop an acidic vapor assisted electrospray ionization strategy within an enclosed electrospray ionization source to counteract the ion suppression effects caused by trifluoroacetic acid.
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Affiliation(s)
- Jin Chen
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Zheyi Liu
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Fangjun Wang
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Jiawei Mao
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Ye Zhou
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Jing Liu
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Hanfa Zou
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Yukui Zhang
- Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
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147
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Bouvier ES, Koza SM. Advances in size-exclusion separations of proteins and polymers by UHPLC. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2014.08.002] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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148
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Xiu L, Valeja SG, Alpert A, Jin S, Ge Y. Effective protein separation by coupling hydrophobic interaction and reverse phase chromatography for top-down proteomics. Anal Chem 2014; 86:7899-906. [PMID: 24968279 PMCID: PMC4144745 DOI: 10.1021/ac501836k] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 06/26/2014] [Indexed: 01/16/2023]
Abstract
One of the challenges in proteomics is the proteome's complexity, which necessitates the fractionation of proteins prior to the mass spectrometry (MS) analysis. Despite recent advances in top-down proteomics, separation of intact proteins remains challenging. Hydrophobic interaction chromatography (HIC) appears to be a promising method that provides high-resolution separation of intact proteins, but unfortunately the salts conventionally used for HIC are incompatible with MS. In this study, we have identified ammonium tartrate as a MS-compatible salt for HIC with comparable separation performance as the conventionally used ammonium sulfate. Furthermore, we found that the selectivity obtained with ammonium tartrate in the HIC mobile phases is orthogonal to that of reverse phase chromatography (RPC). By coupling HIC and RPC as a novel two-dimensional chromatographic method, we have achieved effective high-resolution intact protein separation as demonstrated with standard protein mixtures and a complex cell lysate. Subsequently, the separated intact proteins were identified by high-resolution top-down MS. For the first time, these results have shown the high potential of HIC as a high-resolution protein separation method for top-down proteomics.
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Affiliation(s)
- Lichen Xiu
- Department
of Chemistry, University of Wisconsin—Madison, Madison 53706, Wisconsin, United States
| | - Santosh G. Valeja
- Department of Cell and Regenerative Biology, University of Wisconsin—Madison, Madison 53706, Wisconsin, United States
| | - Andrew
J. Alpert
- Department of Cell and Regenerative Biology, University of Wisconsin—Madison, Madison 53706, Wisconsin, United States
- PolyLC Inc., Columbia 21045, Maryland, United States
| | - Song Jin
- Department
of Chemistry, University of Wisconsin—Madison, Madison 53706, Wisconsin, United States
| | - Ying Ge
- Department
of Chemistry, University of Wisconsin—Madison, Madison 53706, Wisconsin, United States
- Department of Cell and Regenerative Biology, University of Wisconsin—Madison, Madison 53706, Wisconsin, United States
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin—Madison, Madison, Wisconsin 53706, United States
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149
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Ying P, Serife AG, Deyang Y, Ying G. Top-down mass spectrometry of cardiac myofilament proteins in health and disease. Proteomics Clin Appl 2014; 8:554-68. [PMID: 24945106 PMCID: PMC4231170 DOI: 10.1002/prca.201400043] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 05/21/2014] [Accepted: 06/12/2014] [Indexed: 12/29/2022]
Abstract
Myofilaments are composed of thin and thick filaments that coordinate with each other to regulate muscle contraction and relaxation. PTMs together with genetic variations and alternative splicing of the myofilament proteins play essential roles in regulating cardiac contractility in health and disease. Therefore, a comprehensive characterization of the myofilament proteins in physiological and pathological conditions is essential for better understanding the molecular basis of cardiac function and dysfunction. Due to the vast complexity and dynamic nature of proteins, it is challenging to obtain a holistic view of myofilament protein modifications. In recent years, top-down MS has emerged as a powerful approach to study isoform composition and PTMs of proteins owing to its advantage of complete sequence coverage and its ability to identify PTMs and sequence variants without a priori knowledge. In this review, we will discuss the application of top-down MS to the study of cardiac myofilaments and highlight the insights it provides into the understanding of molecular mechanisms in contractile dysfunction of heart failure. Particularly, recent results of cardiac troponin and tropomyosin modifications will be elaborated. The limitations and perspectives on the use of top-down MS for myofilament protein characterization will also be briefly discussed.
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Affiliation(s)
- Peng Ying
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Ayaz-Guner Serife
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Yu Deyang
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Environmental Toxicology Program, University of Wisconsin-Madison, Madison, WI, USA
| | - Ge Ying
- Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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150
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Peng Y, Gregorich ZR, Valeja SG, Zhang H, Cai W, Chen YC, Guner H, Chen AJ, Schwahn DJ, Hacker TA, Liu X, Ge Y. Top-down proteomics reveals concerted reductions in myofilament and Z-disc protein phosphorylation after acute myocardial infarction. Mol Cell Proteomics 2014; 13:2752-64. [PMID: 24969035 PMCID: PMC4189000 DOI: 10.1074/mcp.m114.040675] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Heart failure (HF) is a leading cause of morbidity and mortality worldwide and is most often precipitated by myocardial infarction. However, the molecular changes driving cardiac dysfunction immediately after myocardial infarction remain poorly understood. Myofilament proteins, responsible for cardiac contraction and relaxation, play critical roles in signal reception and transduction in HF. Post-translational modifications of myofilament proteins afford a mechanism for the beat-to-beat regulation of cardiac function. Thus it is of paramount importance to gain a comprehensive understanding of post-translational modifications of myofilament proteins involved in regulating early molecular events in the post-infarcted myocardium. We have developed a novel liquid chromatography–mass spectrometry-based top-down proteomics strategy to comprehensively assess the modifications of key cardiac proteins in the myofilament subproteome extracted from a minimal amount of myocardial tissue with high reproducibility and throughput. The entire procedure, including tissue homogenization, myofilament extraction, and on-line LC/MS, takes less than three hours. Notably, enabled by this novel top-down proteomics technology, we discovered a concerted significant reduction in the phosphorylation of three crucial cardiac proteins in acutely infarcted swine myocardium: cardiac troponin I and myosin regulatory light chain of the myofilaments and, unexpectedly, enigma homolog isoform 2 (ENH2) of the Z-disc. Furthermore, top-down MS allowed us to comprehensively sequence these proteins and pinpoint their phosphorylation sites. For the first time, we have characterized the sequence of ENH2 and identified it as a phosphoprotein. ENH2 is localized at the Z-disc, which has been increasingly recognized for its role as a nodal point in cardiac signaling. Thus our proteomics discovery opens up new avenues for the investigation of concerted signaling between myofilament and Z-disc in the early molecular events that contribute to cardiac dysfunction and progression to HF.
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Affiliation(s)
- Ying Peng
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Zachery R Gregorich
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; §Molecular Pharmacology Training Program, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Santosh G Valeja
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Han Zhang
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Wenxuan Cai
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; §Molecular Pharmacology Training Program, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Yi-Chen Chen
- ¶Department of Chemistry, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Huseyin Guner
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; ‖Human Proteomics Program, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Albert J Chen
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Denise J Schwahn
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Timothy A Hacker
- ‡‡Department of Medicine, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706
| | - Xiaowen Liu
- §§Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, 719 Indiana Ave., Indianapolis, Indiana 46202; ¶¶Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 West 10th Street, Indianapolis, Indiana 46202
| | - Ying Ge
- From the ‡Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; ¶Department of Chemistry, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706; ‖Human Proteomics Program, University of Wisconsin-Madison, 1300 University Ave., Madison, Wisconsin 53706;
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