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Karpov OA, Stotland A, Raedschelders K, Chazarin B, Ai L, Murray CI, Van Eyk JE. Proteomics of the heart. Physiol Rev 2024; 104:931-982. [PMID: 38300522 DOI: 10.1152/physrev.00026.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Revised: 12/25/2023] [Accepted: 01/14/2024] [Indexed: 02/02/2024] Open
Abstract
Mass spectrometry-based proteomics is a sophisticated identification tool specializing in portraying protein dynamics at a molecular level. Proteomics provides biologists with a snapshot of context-dependent protein and proteoform expression, structural conformations, dynamic turnover, and protein-protein interactions. Cardiac proteomics can offer a broader and deeper understanding of the molecular mechanisms that underscore cardiovascular disease, and it is foundational to the development of future therapeutic interventions. This review encapsulates the evolution, current technologies, and future perspectives of proteomic-based mass spectrometry as it applies to the study of the heart. Key technological advancements have allowed researchers to study proteomes at a single-cell level and employ robot-assisted automation systems for enhanced sample preparation techniques, and the increase in fidelity of the mass spectrometers has allowed for the unambiguous identification of numerous dynamic posttranslational modifications. Animal models of cardiovascular disease, ranging from early animal experiments to current sophisticated models of heart failure with preserved ejection fraction, have provided the tools to study a challenging organ in the laboratory. Further technological development will pave the way for the implementation of proteomics even closer within the clinical setting, allowing not only scientists but also patients to benefit from an understanding of protein interplay as it relates to cardiac disease physiology.
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Affiliation(s)
- Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Aleksandr Stotland
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Koen Raedschelders
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Blandine Chazarin
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Lizhuo Ai
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, United States
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2
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Tabb DL, Jeong K, Druart K, Gant MS, Brown KA, Nicora C, Zhou M, Couvillion S, Nakayasu E, Williams JE, Peterson HK, McGuire MK, McGuire MA, Metz TO, Chamot-Rooke J. Comparing Top-Down Proteoform Identification: Deconvolution, PrSM Overlap, and PTM Detection. J Proteome Res 2023. [PMID: 37235544 DOI: 10.1021/acs.jproteome.2c00673] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Generating top-down tandem mass spectra (MS/MS) from complex mixtures of proteoforms benefits from improvements in fractionation, separation, fragmentation, and mass analysis. The algorithms to match MS/MS to sequences have undergone a parallel evolution, with both spectral alignment and match-counting approaches producing high-quality proteoform-spectrum matches (PrSMs). This study assesses state-of-the-art algorithms for top-down identification (ProSight PD, TopPIC, MSPathFinderT, and pTop) in their yield of PrSMs while controlling false discovery rate. We evaluated deconvolution engines (ThermoFisher Xtract, Bruker AutoMSn, Matrix Science Mascot Distiller, TopFD, and FLASHDeconv) in both ThermoFisher Orbitrap-class and Bruker maXis Q-TOF data (PXD033208) to produce consistent precursor charges and mass determinations. Finally, we sought post-translational modifications (PTMs) in proteoforms from bovine milk (PXD031744) and human ovarian tissue. Contemporary identification workflows produce excellent PrSM yields, although approximately half of all identified proteoforms from these four pipelines were specific to only one workflow. Deconvolution algorithms disagree on precursor masses and charges, contributing to identification variability. Detection of PTMs is inconsistent among algorithms. In bovine milk, 18% of PrSMs produced by pTop and TopMG were singly phosphorylated, but this percentage fell to 1% for one algorithm. Applying multiple search engines produces more comprehensive assessments of experiments. Top-down algorithms would benefit from greater interoperability.
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Affiliation(s)
- David L Tabb
- Université Paris Cité, Institut Pasteur, CNRS UAR 2024, Mass Spectrometry for Biology Unit, Paris 75015, France
| | - Kyowon Jeong
- Applied Bioinformatics, Computer Science Department, University of Tübingen, Tübingen 72076, Germany
| | - Karen Druart
- Université Paris Cité, Institut Pasteur, CNRS UAR 2024, Mass Spectrometry for Biology Unit, Paris 75015, France
| | - Megan S Gant
- Université Paris Cité, Institut Pasteur, CNRS UAR 2024, Mass Spectrometry for Biology Unit, Paris 75015, France
| | - Kyle A Brown
- School of Medicine and Public Health, University of Wisconsin, Madison, Wisconsin 53705, United States
| | - Carrie Nicora
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Mowei Zhou
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Sneha Couvillion
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Ernesto Nakayasu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Janet E Williams
- Department of Animal, Veterinary, and Food Sciences, University of Idaho, Moscow, Idaho 83844, United States
| | - Haley K Peterson
- Department of Animal, Veterinary, and Food Sciences, University of Idaho, Moscow, Idaho 83844, United States
| | - Michelle K McGuire
- Margaret Ritchie School of Family and Consumer Sciences, University of Idaho, Moscow, Idaho 83844, United States
| | - Mark A McGuire
- Department of Animal, Veterinary, and Food Sciences, University of Idaho, Moscow, Idaho 83844, United States
| | - Thomas O Metz
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Julia Chamot-Rooke
- Université Paris Cité, Institut Pasteur, CNRS UAR 2024, Mass Spectrometry for Biology Unit, Paris 75015, France
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3
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Tucholski T, Ge Y. Fourier-transform ion cyclotron resonance mass spectrometry for characterizing proteoforms. MASS SPECTROMETRY REVIEWS 2022; 41:158-177. [PMID: 32894796 PMCID: PMC7936991 DOI: 10.1002/mas.21653] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 08/26/2020] [Accepted: 08/26/2020] [Indexed: 05/05/2023]
Abstract
Proteoforms contribute functional diversity to the proteome and aberrant proteoforms levels have been implicated in biological dysfunction and disease. Fourier-transform ion cyclotron resonance mass spectrometry (FT-ICR MS), with its ultrahigh mass-resolving power, mass accuracy, and versatile tandem MS capabilities, has empowered top-down, middle-down, and native MS-based approaches for characterizing proteoforms and their complexes in biological systems. Herein, we review the features which make FT-ICR MS uniquely suited for measuring proteoform mass with ultrahigh resolution and mass accuracy; obtaining in-depth proteoform sequence coverage with expansive tandem MS capabilities; and unambiguously identifying and localizing post-translational and noncovalent modifications. We highlight examples from our body of work in which we have quantified and comprehensively characterized proteoforms from cardiac and skeletal muscle to better understand conditions such as chronic heart failure, acute myocardial infarction, and sarcopenia. Structural characterization of monoclonal antibodies and their proteoforms by FT-ICR MS and emerging applications, such as native top-down FT-ICR MS and high-throughput top-down FT-ICR MS-based proteomics at 21 T, are also covered. Historically, the information gleaned from FT-ICR MS analyses have helped provide biological insights. We predict FT-ICR MS will continue to enable the study of proteoforms of increasing size from increasingly complex endogenous mixtures and facilitate the benchmarking of sensitive and specific assays for clinical diagnostics. © 2020 John Wiley & Sons Ltd. Mass Spec Rev.
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Affiliation(s)
- Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53706
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI, 53705
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4
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Akhremko A, Vasilevskaya ER, Fedulova L. Adaptation of two-dimensional electrophoresis for muscle tissue analysis. POTRAVINARSTVO 2020. [DOI: 10.5219/1380] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is important to understand the molecular mechanisms that take place in muscle tissues and to predict meat quality characteristics. One of the most popular methods is two-dimensional electrophoresis, which allows us to visualize, share and identify different molecules, including meat proteins. However, the standard conditions of this method are not universal for all types of raw material, so the authors suggest a new variation of two-dimensional electrophoresis for muscle tissue analysis. Samples were tested by the classical version of isoelectric focusing (cathode buffer in the top and anode buffer in the bottom chamber of the electrophoresis cell) and its variation (anode buffer in the top and cathode buffer in the bottom chamber of the electrophoresis cell). Next, extruded gels were incubated in two different buffer systems: the first was equilibration buffer I (6 M urea, 20% w/v glycerol, 2% w/v SDS and 1% w/v Ditiothreitol in 375 mM Tris-HCl buffer, pH 8.8) followed by equilibration buffer II (6 M urea, 20% w/v glycerol, 2% w/v SDS and 4% w/v iodoacetamide in 375 mM Tris-HCl buffer pH 8.8 and the second, buffer А, consisting of 5 M urea, 2% w/v SDS, 5% v/v mercaptoethanol, 62.5 mM Tris-HCl buffer, pH 6.8 and 0.01% w/v bromophenol blue. Electrophoretic studies of muscle tissue revealed the best protein separation after changing the direction of the current (authors' variation), while no differences were detected after changing incubation buffers.
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5
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Melby JA, Jin Y, Lin Z, Tucholski T, Wu Z, Gregorich ZR, Diffee GM, Ge Y. Top-Down Proteomics Reveals Myofilament Proteoform Heterogeneity among Various Rat Skeletal Muscle Tissues. J Proteome Res 2020; 19:446-454. [PMID: 31647247 PMCID: PMC7487979 DOI: 10.1021/acs.jproteome.9b00623] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Heterogeneity in skeletal muscle contraction time, peak power output, and resistance to fatigue, among others, is necessary to accommodate the wide range of functional demands imposed on the body. Underlying this functional heterogeneity are a myriad of differences in the myofilament protein isoform expression and post-translational modifications; yet, characterizing this heterogeneity remains challenging. Herein, we have utilized top-down liquid chromatography (LC)-mass spectrometry (MS)-based proteomics to characterize myofilament proteoform heterogeneity in seven rat skeletal muscle tissues including vastus lateralis, vastus medialis, vastus intermedius, rectus femoris, soleus, gastrocnemius, and plantaris. Top-down proteomics revealed that myofilament proteoforms varied greatly across the seven different rat skeletal muscle tissues. Subsequently, we quantified and characterized myofilament proteoforms using online LC-MS. We have comprehensively characterized the fast and slow skeletal troponin I isoforms, which demonstrates the ability of top-down MS to decipher isoforms with high sequence homology. Taken together, we have shown that top-down proteomics can be used as a robust and high-throughput method to characterize the molecular heterogeneity of myofilament proteoforms from various skeletal muscle tissues.
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Affiliation(s)
- Jake A. Melby
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705
| | - Trisha Tucholski
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Zhijie Wu
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
| | - Zachery R. Gregorich
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705
| | - Gary M. Diffee
- Department of Kinesiology, University of Wisconsin-Madison, Madison, WI 53706
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI 53706
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI 53705
- Human Proteomics Program, University of Wisconsin-Madison, Madison, WI 53705
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Basharat AR, Iman K, Khalid MF, Anwar Z, Hussain R, Kabir HG, Tahreem M, Shahid A, Humayun M, Hayat HA, Mustafa M, Shoaib MA, Ullah Z, Zarina S, Ahmed S, Uddin E, Hamera S, Ahmad F, Chaudhary SU. SPECTRUM - A MATLAB Toolbox for Proteoform Identification from Top-Down Proteomics Data. Sci Rep 2019; 9:11267. [PMID: 31375721 PMCID: PMC6677810 DOI: 10.1038/s41598-019-47724-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Accepted: 06/10/2019] [Indexed: 01/07/2023] Open
Abstract
Top-Down Proteomics (TDP) is an emerging proteomics protocol that involves identification, characterization, and quantitation of intact proteins using high-resolution mass spectrometry. TDP has an edge over other proteomics protocols in that it allows for: (i) accurate measurement of intact protein mass, (ii) high sequence coverage, and (iii) enhanced identification of post-translational modifications (PTMs). However, the complexity of TDP spectra poses a significant impediment to protein search and PTM characterization. Furthermore, limited software support is currently available in the form of search algorithms and pipelines. To address this need, we propose 'SPECTRUM', an open-architecture and open-source toolbox for TDP data analysis. Its salient features include: (i) MS2-based intact protein mass tuning, (ii) de novo peptide sequence tag analysis, (iii) propensity-driven PTM characterization, (iv) blind PTM search, (v) spectral comparison, (vi) identification of truncated proteins, (vii) multifactorial coefficient-weighted scoring, and (viii) intuitive graphical user interfaces to access the aforementioned functionalities and visualization of results. We have validated SPECTRUM using published datasets and benchmarked it against salient TDP tools. SPECTRUM provides significantly enhanced protein identification rates (91% to 177%) over its contemporaries. SPECTRUM has been implemented in MATLAB, and is freely available along with its source code and documentation at https://github.com/BIRL/SPECTRUM/.
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Affiliation(s)
- Abdul Rehman Basharat
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Kanzal Iman
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Farhan Khalid
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Zohra Anwar
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Rashid Hussain
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Humnah Gohar Kabir
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Maria Tahreem
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Anam Shahid
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Maheen Humayun
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Hira Azmat Hayat
- Department of Computer Science, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Mustafa
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Muhammad Ali Shoaib
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Zakir Ullah
- King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
- Lahore University of Management Sciences, Lahore, Pakistan
| | - Shamshad Zarina
- National Center for Proteomics, University of Karachi, Karachi, Pakistan
| | - Sameer Ahmed
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan
| | - Emad Uddin
- Department of Mechanical Engineering, National University of Sciences and Technology, Islamabad, Pakistan
| | - Sadia Hamera
- Institute of Life Sciences, University of Rostock, Rostock, Germany
- Lahore University of Management Sciences, Lahore, Pakistan
| | - Fayyaz Ahmad
- Department of Statistics, University of Gujrat, Gujrat, Pakistan
| | - Safee Ullah Chaudhary
- Biomedical Informatics Research Laboratory, Department of Biology, Lahore University of Management Sciences, Lahore, Pakistan.
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7
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Tucholski T, Knott SJ, Chen B, Pistono P, Lin Z, Ge Y. A Top-Down Proteomics Platform Coupling Serial Size Exclusion Chromatography and Fourier Transform Ion Cyclotron Resonance Mass Spectrometry. Anal Chem 2019; 91:3835-3844. [PMID: 30758949 DOI: 10.1021/acs.analchem.8b04082] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Mass spectrometry (MS) based top-down proteomics provides rich information about proteoforms arising from combinatorial amino acid sequence variations and post-translational modifications (PTMs). Fourier transform ion cyclotron resonance (FT-ICR) MS affords ultrahigh resolving power and provides high-accuracy mass measurements, presenting a powerful tool for top-down MS characterization of proteoforms. However, the detection and characterization of large proteins from complex mixtures remain challenging due to the exponential decrease in S: N with increasing molecular weight (MW) and coeluting low-MW proteins; thus, size-based fractionation of complex protein mixtures prior to MS analysis is necessary. Here, we directly combine MS-compatible serial size exclusion chromatography (sSEC) fractionation with 12 T FT-ICR MS for targeted top-down characterization of proteins from complex mixtures extracted from human and swine heart tissue. Benefiting from the ultrahigh resolving power of FT-ICR, we isotopically resolved 31 distinct proteoforms (30-50 kDa) simultaneously in a single mass spectrum within a 100 m/ z window. Notably, within a 5 m/ z window, we obtained baseline isotopic resolution for 6 distinct large proteoforms (30-50 kDa). The ultrahigh resolving power of FT-ICR MS combined with sSEC fractionation enabled targeted top-down analysis of large proteoforms (>30 kDa) from the human heart proteome without extensive chromatographic separation or protein purification. Further separation of proteoforms inside the mass spectrometer (in-MS) allowed for isolation of individual proteoforms and targeted electron capture dissociation (ECD), yielding high sequence coverage. sSEC/FT-ICR ECD facilitated the identification and sequence characterization of important metabolic enzymes. This platform, which facilitates deep interrogation of proteoform primary structure, is highly tunable, allows for adjustment of MS and MS/MS parameters in real time, and can be utilized for a variety of complex protein mixtures.
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Affiliation(s)
- Trisha Tucholski
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Samantha J Knott
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Bifan Chen
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States
| | - Paige Pistono
- Department of Biochemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology , University of Wisconsin-Madison , 1111 Highland Avenue , WIMR II 8551, Madison , Wisconsin 53705 , United States
| | - Ying Ge
- Department of Chemistry , University of Wisconsin-Madison , Madison , Wisconsin 53706 , United States.,Human Proteomics Program , University of Wisconsin-Madison , Madison , Wisconsin 53705 , United States.,Department of Cell and Regenerative Biology , University of Wisconsin-Madison , 1111 Highland Avenue , WIMR II 8551, Madison , Wisconsin 53705 , United States
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8
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Lin Z, Guo F, Gregorich ZR, Sun R, Zhang H, Hu Y, Shanmuganayagam D, Ge Y. Comprehensive Characterization of Swine Cardiac Troponin T Proteoforms by Top-Down Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2018; 29:1284-1294. [PMID: 29633223 PMCID: PMC6109964 DOI: 10.1007/s13361-018-1925-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 02/14/2018] [Accepted: 02/14/2018] [Indexed: 05/12/2023]
Abstract
Cardiac troponin T (cTnT) regulates the Ca2+-mediated interaction between myosin thick filaments and actin thin filaments during cardiac contraction and relaxation. cTnT is released into the blood following injury, and increased serum levels of the protein are used clinically as a biomarker for myocardial infarction. Moreover, mutations in cTnT are causative in a number of familial cardiomyopathies. With the increasing use of large animal (swine) model to recapitulate human diseases, it is essential to characterize species-dependent protein sequence variants, alternative RNA splicing, and post-translational modifications (PTMs), but challenges remain due to the incomplete database and lack of validation of the predicted splicing isoforms. Herein, we integrated top-down mass spectrometry (MS) with online liquid chromatography (LC) and immunoaffinity purification to comprehensively characterize miniature swine cTnT proteoforms, including those arising from alternative RNA splicing and PTMs. A total of seven alternative splicing isoforms of cTnT were identified by LC/MS from swine left ventricular tissue, with each isoform containing un-phosphorylated and mono-phosphorylated proteoforms. The phosphorylation site was localized to Ser1 for the mono-phosphorylated proteoforms of cTnT1, 3, 4, and 6 by online MS/MS combining collisionally activated dissociation (CAD) and electron transfer dissociation (ETD). Offline MS/MS on Fourier-transform ion cyclotron resonance (FT-ICR) mass spectrometer with CAD and electron capture dissociation (ECD) was then utilized to achieve deep sequencing of mono-phosphorylated cTnT1 (35.2 kDa) with a high sequence coverage of 87%. Taken together, this study demonstrated the unique advantage of top-down MS in the comprehensive characterization of protein alternative splicing isoforms together with PTMs. Graphical Abstract ᅟ.
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Affiliation(s)
- Ziqing Lin
- 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
| | - Fang Guo
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Department of Cardiology, Shandong Provincial Hospital, Jinan, 250021, Shandong, People's Republic of China
| | - Zachery R Gregorich
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | - Ruixiang Sun
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA
- Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190, People's Republic of China
| | - Han Zhang
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706, USA
| | - Yang Hu
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, WI, 53705, USA
| | | | - Ying Ge
- 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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9
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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: 35] [Impact Index Per Article: 5.0] [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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10
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Glasner H, Riml C, Micura R, Breuker K. Label-free, direct localization and relative quantitation of the RNA nucleobase methylations m6A, m5C, m3U, and m5U by top-down mass spectrometry. Nucleic Acids Res 2017; 45:8014-8025. [PMID: 28549193 PMCID: PMC5570050 DOI: 10.1093/nar/gkx470] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 05/23/2017] [Indexed: 01/28/2023] Open
Abstract
Nucleobase methylations are ubiquitous posttranscriptional modifications of ribonucleic acids (RNA) that can substantially increase the structural diversity of RNA in a highly dynamic fashion with implications for gene expression and human disease. However, high throughput, deep sequencing does not generally provide information on posttranscriptional modifications (PTMs). A promising alternative approach for the characterization of PTMs, i.e. their identification, localization, and relative quantitation, is top-down mass spectrometry (MS). In this study, we have investigated how specific nucleobase methylations affect RNA ionization in electrospray ionization (ESI), and backbone cleavage in collisionally activated dissociation (CAD) and electron detachment dissociation (EDD). For this purpose, we have developed two new approaches for the characterization of RNA methylations in mixtures of either isomers of RNA or nonisomeric RNA forms. Fragment ions from dissociation experiments were analyzed to identify the modification type, to localize the modification sites, and to reveal the site-specific, relative extent of modification for each site.
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Affiliation(s)
- Heidelinde Glasner
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Christian Riml
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Ronald Micura
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
| | - Kathrin Breuker
- Institute of Organic Chemistry and Center for Molecular Biosciences Innsbruck (CMBI), University of Innsbruck, Innrain 80-82, 6020 Innsbruck, Austria
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11
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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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12
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Capitanio D, Moriggi M, Gelfi C. Mapping the human skeletal muscle proteome: progress and potential. Expert Rev Proteomics 2017; 14:825-839. [PMID: 28780899 DOI: 10.1080/14789450.2017.1364996] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
INTRODUCTION Human skeletal muscle represents 40% of our body mass and deciphering its proteome composition to further understand mechanisms regulating muscle function under physiological and pathological conditions has proved a challenge. The inter-individual variability, the presence of structurally and functionally different muscle types and the high protein dynamic range require carefully selected methodologies for the assessment of the muscle proteome. Furthermore, physiological studies are understandingly hampered by ethical issues related to biopsies on healthy subjects, making it difficult to recruit matched controls essential for comparative studies. Areas covered: This review critically analyses studies performed on muscle to date and identifies what still remains unknown or poorly investigated in physiological and pathological states, such as training, aging, metabolic disorders and muscular dystrophies. Expert commentary: Efforts should be made on biological fluid analyses targeting low abundant/low molecular weight fragments generated from muscle cell disruption to improve diagnosis and clinical monitoring. From a methodological point of view, particular attention should be paid to improve the characterization of intact proteins and unknown post translational modifications to better understand the molecular mechanisms of muscle disorders.
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Affiliation(s)
- Daniele Capitanio
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
| | - Manuela Moriggi
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
| | - Cecilia Gelfi
- a Department of Biomedical Sciences for Health , University of Milan , Segrate , Milan , Italy
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13
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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: 25] [Impact Index Per Article: 3.6] [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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14
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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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15
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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: 76] [Impact Index Per Article: 9.5] [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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16
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Zhang X. Instant Integrated Ultradeep Quantitative-structural Membrane Proteomics Discovered Post-translational Modification Signatures for Human Cys-loop Receptor Subunit Bias. Mol Cell Proteomics 2016; 15:3665-3684. [PMID: 27073180 DOI: 10.1074/mcp.m114.047514] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2014] [Revised: 11/17/2015] [Indexed: 12/31/2022] Open
Abstract
Neurotransmitter ligand-gated ion channels (LGICs) are widespread and pivotal in brain functions. Unveiling their structure-function mechanisms is crucial to drive drug discovery, and demands robust proteomic quantitation of expression, post-translational modifications (PTMs) and dynamic structures. Yet unbiased digestion of these modified transmembrane proteins-at high efficiency and peptide reproducibility-poses the obstacle. Targeting both enzyme-substrate contacts and PTMs for peptide formation and detection, we devised flow-and-detergent-facilitated protease and de-PTM digestions for deep sequencing (FDD) method that combined omni-compatible detergent, tandem immobilized protease/PNGase columns, and Cys-selective reduction/alkylation, to achieve streamlined ultradeep peptide preparation within minutes not days, at high peptide reproducibility and low abundance-bias. FDD transformed enzyme-protein contacts into equal catalytic travel paths through enzyme-excessive columns regardless of protein abundance, removed products instantly preventing inhibition, tackled intricate structures via sequential multiple micro-digestions along the flow, and precisely controlled peptide formation by flow rate. Peptide-stage reactions reduced steric bias; low contamination deepened MS/MS scan; distinguishing disulfide from M oxidation and avoiding gain/loss artifacts unmasked protein-endogenous oxidation states. Using a recent interactome of 285-kDa human GABA type A receptor, this pilot study validated FDD platform's applicability to deep sequencing (up to 99% coverage), H/D-exchange and TMT-based structural mapping. FDD discovered novel subunit-specific PTM signatures, including unusual nontop-surface N-glycosylations, that may drive subunit biases in human Cys-loop LGIC assembly and pharmacology, by redefining subunit/ligand interfaces and connecting function domains.
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Affiliation(s)
- Xi Zhang
- From the ‡Department of Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, .,§Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
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17
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Jin Y, Peng Y, Lin Z, Chen YC, Wei L, Hacker TA, Larsson L, Ge Y. Comprehensive analysis of tropomyosin isoforms in skeletal muscles by top-down proteomics. J Muscle Res Cell Motil 2016; 37:41-52. [PMID: 27090236 PMCID: PMC4955698 DOI: 10.1007/s10974-016-9443-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Accepted: 04/07/2016] [Indexed: 01/09/2023]
Abstract
Mammalian skeletal muscles are heterogeneous in nature and are capable of performing various functions. Tropomyosin (Tpm) is a major component of the thin filament in skeletal muscles and plays an important role in controlling muscle contraction and relaxation. Tpm is known to consist of multiple isoforms resulting from different encoding genes and alternative splicing, along with post-translational modifications. However, a systematic characterization of Tpm isoforms in skeletal muscles is still lacking. Therefore, we employed top-down mass spectrometry (MS) to identify and characterize Tpm isoforms present in different skeletal muscles from multiple species, including swine, rat, and human. Our study revealed that Tpm1.1 and Tpm2.2 are the two major Tpm isoforms in swine and rat skeletal muscles, whereas Tpm1.1, Tpm2.2, and Tpm3.12 are present in human skeletal muscles. Tandem MS was utilized to identify the sequences of the major Tpm isoforms. Furthermore, quantitative analysis revealed muscle-type specific differences in the abundance of un-modified and modified Tpm isoforms in rat and human skeletal muscles. This study represents the first systematic investigation of Tpm isoforms in skeletal muscles, which not only demonstrates the capabilities of top-down MS for the comprehensive characterization of skeletal myofilament proteins but also provides the basis for further studies on these Tpm isoforms in muscle-related diseases.
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Affiliation(s)
- Yutong Jin
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Ying Peng
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA
- Human Proteomics Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA
- Human Proteomics Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Yi-Chen Chen
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA
| | - Liming Wei
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA
- Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P.R. China
| | - Timothy A Hacker
- Department of Medicine, School of Medicine and Public Health, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA
| | - Lars Larsson
- Department of Physiology and Pharmacology, Department of Clinical Neuroscience, Clinical Neurophysiology Section, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Ave., Madison, WI, 53706, USA.
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA.
- Human Proteomics Program, University of Wisconsin-Madison, 1111 Highland Ave., Madison, WI, 53705, USA.
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18
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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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19
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Liu F, Koval M, Ranganathan S, Fanayan S, Hancock WS, Lundberg EK, Beavis RC, Lane L, Duek P, McQuade L, Kelleher NL, Baker MS. Systems Proteomics View of the Endogenous Human Claudin Protein Family. J Proteome Res 2016; 15:339-59. [PMID: 26680015 DOI: 10.1021/acs.jproteome.5b00769] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Claudins are the major transmembrane protein components of tight junctions in human endothelia and epithelia. Tissue-specific expression of claudin members suggests that this protein family is not only essential for sustaining the role of tight junctions in cell permeability control but also vital in organizing cell contact signaling by protein-protein interactions. How this protein family is collectively processed and regulated is key to understanding the role of junctional proteins in preserving cell identity and tissue integrity. The focus of this review is to first provide a brief overview of the functional context, on the basis of the extensive body of claudin biology research that has been thoroughly reviewed, for endogenous human claudin members and then ascertain existing and future proteomics techniques that may be applicable to systematically characterizing the chemical forms and interacting protein partners of this protein family in human. The ability to elucidate claudin-based signaling networks may provide new insight into cell development and differentiation programs that are crucial to tissue stability and manipulation.
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Affiliation(s)
| | - Michael Koval
- Department of Medicine, Division of Pulmonary, Allergy, Critical Care and Sleep Medicine, and Department of Cell Biology, Emory University School of Medicine , 205 Whitehead Biomedical Research Building, 615 Michael Street, Atlanta, Georgia 30322, United States
| | | | | | - William S Hancock
- Barnett Institute and Department of Chemistry and Chemical Biology, Northeastern University , Boston, Massachusetts 02115, United States
| | - Emma K Lundberg
- SciLifeLab, School of Biotechnology, Royal Institute of Technology (KTH) , SE-171 21 Solna, Stockholm, Sweden
| | - Ronald C Beavis
- Department of Biochemistry and Medical Genetics, University of Manitoba , 744 Bannatyne Avenue, Winnipeg, Manitoba R3E 0W3, Canada
| | - Lydie Lane
- SIB-Swiss Institute of Bioinformatics , CMU - Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | - Paula Duek
- SIB-Swiss Institute of Bioinformatics , CMU - Rue Michel-Servet 1, 1211 Geneva, Switzerland
| | | | - Neil L Kelleher
- Department of Chemistry, Department of Molecular Biosciences, and Proteomics Center of Excellence, Northwestern University , 2145 North Sheridan Road, Evanston, Illinois 60208, United States
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20
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Targeted Proteomics Enables Simultaneous Quantification of Folate Receptor Isoforms and Potential Isoform-based Diagnosis in Breast Cancer. Sci Rep 2015; 5:16733. [PMID: 26573433 PMCID: PMC4648081 DOI: 10.1038/srep16733] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2015] [Accepted: 10/19/2015] [Indexed: 01/03/2023] Open
Abstract
The distinct roles of protein isoforms in cancer are becoming increasingly evident. FRα and FRβ, two major isoforms of the folate receptor family, generally have different cellular distribution and tissue specificity. However, the presence of FRβ in breast tumors, where FRα is normally expressed, complicates this situation. Prior to applying any FR isoform-based diagnosis and therapeutics, it is essential to monitor the expression profile of FR isoforms in a more accurate manner. An LC-MS/MS-based targeted proteomics assay was developed and validated in this study because of the lack of suitable methodology for the simultaneous and specific measurement of highly homologous isoforms occurring at low concentrations. FRα and FRβ monitoring was achieved by measuring their surrogate isoform-specific peptides. Five human breast cell lines, isolated macrophages and 60 matched pairs of breast tissue samples were subjected to the analysis. The results indicated that FRβ was overexpressed in tumor-associated macrophages (TAMs) but not epithelial cells, in addition to an enhanced level of FRα in breast cancer cells and tissue samples. Moreover, the levels of the FR isoforms were evaluated according to the histology, histopathological features and molecular subtypes of breast cancer. Several positive associations with PR/ER and HER2 status and metastasis were revealed.
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21
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Robotham SA, Brodbelt JS. Comparison of Ultraviolet Photodissociation and Collision Induced Dissociation of Adrenocorticotropic Hormone Peptides. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2015; 26:1570-9. [PMID: 26122515 DOI: 10.1007/s13361-015-1186-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2015] [Revised: 04/19/2015] [Accepted: 05/10/2015] [Indexed: 05/16/2023]
Abstract
In an effort to better characterize the fragmentation pathways promoted by ultraviolet photoexcitation in comparison to collision induced dissociation (CID), six adrenocorticotropic hormone (ACTH) peptides in a range of charge states were subjected to 266 nm ultraviolet photodissociation (UVPD), 193 nm UVPD, and CID. Similar fragment ions and distributions were observed for 266 nm UVPD and 193 nm UVPD for all peptides investigated. While both UVPD and CID led to preferential cleavage of the Y-S bond for all ACTH peptides [except ACTH (1-39)], UVPD was far less dependent on charge state and location of basic sites for the production of C-terminal and N-terminal ions. For ACTH (1-16), ACTH (1-17), ACTH (1-24), and ACTH (1-39), changes in the distributions of fragment ion types (a, b, c, x, y, z, and collectively N-terminal ions versus C-terminal ions) showed only minor changes upon UVPD for all charge states. In contrast, CID displayed significant changes in the fragment ion type distributions as a function of charge state, an outcome consistent with the dependence on the number and location of mobile protons that is not prominent for UVPD. Sequence coverages obtained by UVPD showed less dependence on charge state than those determined by CID, with the latter showing a consistent decrease in coverage as charge state increased.
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Affiliation(s)
- Scott A Robotham
- Department of Chemistry, University of Texas, Austin, TX, 78712, USA
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22
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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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23
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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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24
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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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25
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Kooij V, Venkatraman V, Kirk JA, Ubaida-Mohien C, Graham DR, Faber MJ, Van Eyk JE. Identification of cardiac myofilament protein isoforms using multiple mass spectrometry based approaches. Proteomics Clin Appl 2015; 8:578-589. [PMID: 24974818 DOI: 10.1002/prca.201400039] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/30/2014] [Accepted: 06/24/2014] [Indexed: 02/01/2023]
Abstract
PURPOSE The identification of protein isoforms in complex biological samples is challenging. We, therefore, used an MS approach to unambiguously identify cardiac myofilament protein isoforms based on the observation of a tryptic peptide consisting of a sequence unique to a particular isoform. EXPERIMENTAL DESIGN Three different workflows were used to isolate and fractionate rat cardiac myofilament subproteomes. All fractions were analyzed on an LTQ-Orbitrap MS, proteins were identified using various search engines (MASCOT, X!Tandem, X!Tandem Kscore, and OMSSA) with results combined via PepArML Meta-Search engine, and a postsearch analysis was performed by MASPECTRAS. All MS data have been deposited in the ProteomeXchange with identifier PXD000874 (http://proteomecentral.proteomexchange.org/dataset/PXD000874). RESULTS The combination of multiple workflows and search engines resulted in a larger number of nonredundant proteins identified than with individual methods. A total of 102 myofilament annotated proteins were observed overlapping in two or three of the workflows. Literature search for myofilament presence with manual validation of the MS spectra was carried out for unambiguous identification: ten cardiac myofilament and 17 cardiac myofilament-associated proteins were identified with 39 isoforms and subisoforms. CONCLUSION AND CLINICAL RELEVANCE We have identified multiple isoforms of myofilament proteins that are present in cardiac tissue using unique tryptic peptides. Changes in distribution of these protein isoforms under pathological conditions could ultimately allow for clinical diagnostics or as therapeutic targets.
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Affiliation(s)
- Viola Kooij
- Department of medicine, Division of Cardiology, The Johns Hopkins University, Baltimore, USA
| | - Vidya Venkatraman
- Department of medicine, Division of Cardiology, The Johns Hopkins University, Baltimore, USA.,Advanced Clinical Biosystems Research Institute, Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, USA
| | - Jonathan A Kirk
- Department of medicine, Division of Cardiology, The Johns Hopkins University, Baltimore, USA
| | - Ceereena Ubaida-Mohien
- Department of Molecular and Comparative Pathobiology, The Johns Hopkins University, Baltimore, MD, USA
| | - David R Graham
- Department of medicine, Division of Cardiology, The Johns Hopkins University, Baltimore, USA.,Department of Molecular and Comparative Pathobiology, The Johns Hopkins University, Baltimore, MD, USA
| | - Matthijs J Faber
- Erasmus MC-Sophia, Department of Pediatrics, Division of Pediatric Cardiology, Rotterdam, The Netherlands
| | - Jennifer E Van Eyk
- Department of medicine, Division of Cardiology, The Johns Hopkins University, Baltimore, USA.,Advanced Clinical Biosystems Research Institute, Heart Institute and Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, USA
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26
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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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27
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Wang Z, Chen X, Deng L, Li W, Wong YLE, Chan TWD. Letter: Evaluation and comparison of collision-induced dissociation and electron-capture dissociation for top-down analysis of intact ribonuclease B. EUROPEAN JOURNAL OF MASS SPECTROMETRY (CHICHESTER, ENGLAND) 2015; 21:707-711. [PMID: 26353993 DOI: 10.1255/ejms.1386] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
It has been previously reported that the glycosylation site and protein-sequence information could be obtained for ribonuclease B by top-down electron-capture dissociation (ECD) and collision-induced dissociation (CID) mass spectrometry (MS). However, the sequence coverage of ribonuclease B was limited in a single activation, and the structural information on the glycan moiety was not probed successfully in previous experiments. Here, we demonstrate that ECD and CID techniques can be used together as an effective top- down method for the structural characterization of intact glycoprotein. Even without an elaborate pre- or post- ECD activation, a high sequence coverage (<90%) of ribonuclease B could be achieved with substantial amounts of structural information for the glycan moiety. By comparing our work with previous results, it is postulated that the disulfide bond reduction strategy might play a significant role in determining the efficiency of top-down MS.
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Affiliation(s)
- Ze Wang
- Department of Chemistry, the Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, PR China.
| | - Xiangfeng Chen
- Department of Chemistry, the Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, PR China. Shandong Academy of Science, Shandong, 250014, PR China.
| | - Liulin Deng
- Department of Chemistry, the Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, PR China. Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Washington 99352, USA
| | - Wan Li
- Department of Chemistry, the Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, PR China.
| | - Y-L Elaine Wong
- Department of Chemistry, the Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, PR China.
| | - T-W Dominic Chan
- Department of Chemistry, the Chinese University of Hong Kong, Shatin, NT, Hong Kong SAR, PR China.
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28
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Gregorich ZR, Ge Y. Top-down proteomics in health and disease: challenges and opportunities. Proteomics 2014; 14:1195-210. [PMID: 24723472 DOI: 10.1002/pmic.201300432] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 03/10/2014] [Accepted: 03/24/2014] [Indexed: 01/06/2023]
Abstract
Proteomics is essential for deciphering how molecules interact as a system and for understanding the functions of cellular systems in human disease; however, the unique characteristics of the human proteome, which include a high dynamic range of protein expression and extreme complexity due to a plethora of PTMs and sequence variations, make such analyses challenging. An emerging "top-down" MS-based proteomics approach, which provides a "bird's eye" view of all proteoforms, has unique advantages for the assessment of PTMs and sequence variations. Recently, a number of studies have showcased the potential of top-down proteomics for the unraveling of disease mechanisms and discovery of new biomarkers. Nevertheless, the top-down approach still faces significant challenges in terms of protein solubility, separation, and the detection of large intact proteins, as well as underdeveloped data analysis tools. Consequently, new technological developments are urgently needed to advance the field of top-down proteomics. Herein, we intend to provide an overview of the recent applications of top-down proteomics in biomedical research. Moreover, we will outline the challenges and opportunities facing top-down proteomics strategies aimed at understanding and diagnosing human diseases.
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Affiliation(s)
- Zachery R Gregorich
- Molecular and Cellular Pharmacology Training Program, 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
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29
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An B, Zhang M, Qu J. Toward sensitive and accurate analysis of antibody biotherapeutics by liquid chromatography coupled with mass spectrometry. Drug Metab Dispos 2014; 42:1858-66. [PMID: 25185260 DOI: 10.1124/dmd.114.058917] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Remarkable methodological advances in the past decade have expanded the application of liquid chromatography coupled with mass spectrometry (LC/MS) analysis of biotherapeutics. Currently, LC/MS represents a promising alternative or supplement to the traditional ligand binding assay (LBA) in the pharmacokinetic, pharmacodynamic, and toxicokinetic studies of protein drugs, owing to the rapid and cost-effective method development, high specificity and reproducibility, low sample consumption, the capacity of analyzing multiple targets in one analysis, and the fact that a validated method can be readily adapted across various matrices and species. While promising, technical challenges associated with sensitivity, sample preparation, method development, and quantitative accuracy need to be addressed to enable full utilization of LC/MS. This article introduces the rationale and technical challenges of LC/MS techniques in biotherapeutics analysis and summarizes recently developed strategies to alleviate these challenges. Applications of LC/MS techniques on quantification and characterization of antibody biotherapeutics are also discussed. We speculate that despite the highly attractive features of LC/MS, it will not fully replace traditional assays such as LBA in the foreseeable future; instead, the forthcoming trend is likely the conjunction of biochemical techniques with versatile LC/MS approaches to achieve accurate, sensitive, and unbiased characterization of biotherapeutics in highly complex pharmaceutical/biologic matrices. Such combinations will constitute powerful tools to tackle the challenges posed by the rapidly growing needs for biotherapeutics development.
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Affiliation(s)
- Bo An
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York (B.A., M.Z., J.Q.); New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York (B.A., M.Z., J.Q.)
| | - Ming Zhang
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York (B.A., M.Z., J.Q.); New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York (B.A., M.Z., J.Q.)
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York (B.A., M.Z., J.Q.); New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York (B.A., M.Z., J.Q.)
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30
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Hildonen S, Halvorsen TG, Reubsaet L. Why less is more when generating tryptic peptides in bottom-up proteomics. Proteomics 2014; 14:2031-41. [DOI: 10.1002/pmic.201300479] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2013] [Revised: 06/11/2014] [Accepted: 07/10/2014] [Indexed: 12/23/2022]
Affiliation(s)
- Siri Hildonen
- Department of Pharmaceutical Chemistry; School of Pharmacy; University of Oslo; Oslo Norway
| | | | - Léon Reubsaet
- Department of Pharmaceutical Chemistry; School of Pharmacy; University of Oslo; Oslo Norway
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31
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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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32
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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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33
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Gregorich ZR, Chang YH, Ge Y. Proteomics in heart failure: top-down or bottom-up? Pflugers Arch 2014; 466:1199-209. [PMID: 24619480 DOI: 10.1007/s00424-014-1471-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Revised: 01/31/2014] [Accepted: 02/04/2014] [Indexed: 01/11/2023]
Abstract
The pathophysiology of heart failure (HF) is diverse, owing to multiple etiologies and aberrations in a number of cellular processes. Therefore, it is essential to understand how defects in the molecular pathways that mediate cellular responses to internal and external stressors function as a system to drive the HF phenotype. Mass spectrometry (MS)-based proteomics strategies have great potential for advancing our understanding of disease mechanisms at the systems level because proteins are the effector molecules for all cell functions and, thus, are directly responsible for determining cell phenotype. Two MS-based proteomics strategies exist: peptide-based bottom-up and protein-based top-down proteomics--each with its own unique strengths and weaknesses for interrogating the proteome. In this review, we will discuss the advantages and disadvantages of bottom-up and top-down MS for protein identification, quantification, and analysis of post-translational modifications, as well as highlight how both of these strategies have contributed to our understanding of the molecular and cellular mechanisms underlying HF. Additionally, the challenges associated with both proteomics approaches will be discussed and insights will be offered regarding the future of MS-based proteomics in HF research.
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Affiliation(s)
- Zachery R Gregorich
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA
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Guner H, Close PL, Cai W, Zhang H, Peng Y, Gregorich ZR, Ge Y. MASH Suite: a user-friendly and versatile software interface for high-resolution mass spectrometry data interpretation and visualization. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:464-70. [PMID: 24385400 PMCID: PMC3940544 DOI: 10.1007/s13361-013-0789-4] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2013] [Revised: 11/15/2013] [Accepted: 11/19/2013] [Indexed: 05/06/2023]
Abstract
The rapid advancements in mass spectrometry (MS) instrumentation, particularly in Fourier transform (FT) MS, have made the acquisition of high-resolution and high-accuracy mass measurements routine. However, the software tools for the interpretation of high-resolution MS data are underdeveloped. Although several algorithms for the automatic processing of high-resolution MS data are available, there is still an urgent need for a user-friendly interface with functions that allow users to visualize and validate the computational output. Therefore, we have developed MASH Suite, a user-friendly and versatile software interface for processing high-resolution MS data. MASH Suite contains a wide range of features that allow users to easily navigate through data analysis, visualize complex high-resolution MS data, and manually validate automatically processed results. Furthermore, it provides easy, fast, and reliable interpretation of top-down, middle-down, and bottom-up MS data. MASH Suite is convenient, easily operated, and freely available. It can greatly facilitate the comprehensive interpretation and validation of high-resolution MS data with high accuracy and reliability.
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Affiliation(s)
- Huseyin Guner
- Human Proteomics Program, School of Medicine and Public Health, 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
| | - Patrick L. Close
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Wenxuan Cai
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
| | - Han Zhang
- Human Proteomics Program, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
| | - Ying Peng
- Human Proteomics Program, School of Medicine and Public Health, 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
| | - 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
- Human Proteomics Program, School of Medicine and Public Health, 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
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, USA
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA
- Corresponding author: Dr. Ying Ge, 1300 University Ave., SMI 130, Madison, Wisconsin, USA. Tel: 608-263-9212, Fax: 608-265-5512,
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35
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Cannon JR, Cammarata M, Robotham SA, Cotham VC, Shaw JB, Fellers RT, Early BP, Thomas PM, Kelleher NL, Brodbelt JS. Ultraviolet photodissociation for characterization of whole proteins on a chromatographic time scale. Anal Chem 2014; 86:2185-92. [PMID: 24447299 PMCID: PMC3958131 DOI: 10.1021/ac403859a] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2013] [Accepted: 01/21/2014] [Indexed: 02/01/2023]
Abstract
Intact protein characterization using mass spectrometry thus far has been achieved at the cost of throughput. Presented here is the application of 193 nm ultraviolet photodissociation (UVPD) for top down identification and characterization of proteins in complex mixtures in an online fashion. Liquid chromatographic separation at the intact protein level coupled with fast UVPD and high-resolution detection resulted in confident identification of 46 unique sequences compared to 44 using HCD from prepared Escherichia coli ribosomes. Importantly, nearly all proteins identified in both the UVPD and optimized HCD analyses demonstrated a substantial increase in confidence in identification (as defined by an average decrease in E value of ∼40 orders of magnitude) due to the higher number of matched fragment ions. Also shown is the potential for high-throughput characterization of intact proteins via liquid chromatography (LC)-UVPD-MS of molecular weight-based fractions of a Saccharomyces cerevisiae lysate. In total, protein products from 215 genes were identified and found in 292 distinct proteoforms, 168 of which contained some type of post-translational modification.
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Affiliation(s)
- Joe R. Cannon
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Michael
B. Cammarata
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Scott A. Robotham
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Victoria C. Cotham
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Jared B. Shaw
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
| | - Ryan T. Fellers
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Bryan P. Early
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Paul M. Thomas
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Neil L. Kelleher
- Departments
of Chemistry and Molecular Biosciences and the Proteomics Center of
Excellence, Northwestern University, Evanston, Illinois 60208, United States
| | - Jennifer S. Brodbelt
- Department
of Chemistry, University of Texas at Austin, 1 University Station A5300, Austin, Texas 78712, United States
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36
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Zhang J, Roth MJ, Chang AN, Plymire DA, Corbett JR, Greenberg BM, Patrie SM. Top-Down Mass Spectrometry on Tissue Extracts and Biofluids with Isoelectric Focusing and Superficially Porous Silica Liquid Chromatography. Anal Chem 2013; 85:10377-84. [DOI: 10.1021/ac402394w] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Junmei Zhang
- UT Southwestern Medical Center, 5323
Harry Hines Blvd., Dallas, Texas 75390-9072
| | - Michael J. Roth
- UT Southwestern Medical Center, 5323
Harry Hines Blvd., Dallas, Texas 75390-9072
| | - Audrey N. Chang
- UT Southwestern Medical Center, 5323
Harry Hines Blvd., Dallas, Texas 75390-9072
| | - Daniel A. Plymire
- UT Southwestern Medical Center, 5323
Harry Hines Blvd., Dallas, Texas 75390-9072
| | - John R. Corbett
- UT Southwestern Medical Center, 5323
Harry Hines Blvd., Dallas, Texas 75390-9072
| | | | - Steven M. Patrie
- UT Southwestern Medical Center, 5323
Harry Hines Blvd., Dallas, Texas 75390-9072
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Abstract
American Society for Mass Spectrometry Sanibel meeting on top-down mass spectrometry St Pete Beach, FL, USA, 24-27 January 2013 Top-down mass spectrometry involves analysis of intact proteins, typically using electrospray ionization, as multiple charging enhances dissociation and thus identification by comparison of precursor and product ion masses with protein sequence databases. Traditionally a low-throughput, precision technology performed on high-resolution Fourier-transform ion cyclotron resonance mass analyzers, top-down proteomics aims to increase throughput for whole proteome analysis while preserving the inherent value of an intact protein mass measurement. This years' American Society for Mass Spectrometry Sanibel meeting brought together established scientists who have demonstrated the viability of the top-down approach and its applicability to virtually all segments of the proteome, mixing them with researchers from diverse areas and with the common interest of advancing top-down into the high-throughput proteomics mainstream. Advances in instrumentation including the orbitrap analyzer, ionization mechanisms, dissociation strategies and informatics, as well as a wide variety of applications, were discussed in depth, leading to the inescapable conclusion that the future for top-down is bright.
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Affiliation(s)
- Julian Whitelegge
- The Pasarow Mass Spectrometry Laboratory, UCLA, Jane and Terry Semel Institute for Neuroscience and Human Behavior, Los Angeles, CA 90095, USA.
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In-depth proteomic analysis of human tropomyosin by top-down mass spectrometry. J Muscle Res Cell Motil 2013; 34:199-210. [PMID: 23881156 DOI: 10.1007/s10974-013-9352-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 06/27/2013] [Indexed: 01/29/2023]
Abstract
Tropomyosins (Tms) are a family of highly conserved actin-binding proteins that play critical roles in a variety of processes, most notably, in the regulation of muscle contraction and relaxation. It is well known that different Tm isoforms have distinct functions and that altered expression of Tm isoforms could lead to changes in cardiac structure and function. To precisely define Tm isoform expression in the human heart, towards a better understanding of their functional roles, we have employed top-down mass spectrometry for in-depth proteomic characterization of Tm isoforms. Using a minimal amount of human heart tissue from rejected donor organs, we confirmed the presence of multiple Tm isoforms including α-Tm, β-Tm and κ-Tm in the human heart, with α-Tm being the predominant isoform, followed by minor isoforms of β-Tm and κ-Tm. Interestingly, our data revealed regional variations of Tm isoforms and post-translational modifications in the human heart. Specifically, the expression level of κ-Tm was highest in the left atrium but nearly undetectable in the left ventricle. The phosphorylation level of α-Tm (pα-Tm) was significantly higher in the atria than it was in the ventricles. The sequences of all Tm isoforms were characterized and the sites of post-translational modifications were localized. Clearly, top-down mass spectrometry is an attractive method for comprehensive characterization of Tm isoforms and post-translational modifications since it can universally detect and quantify all types of protein modifications without a priori knowledge and without the need for specific antibodies.
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Tropomyosin isoform expression and phosphorylation in the human heart in health and disease. J Muscle Res Cell Motil 2013; 34:189-97. [PMID: 23712688 DOI: 10.1007/s10974-013-9347-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 05/09/2013] [Indexed: 01/08/2023]
Abstract
We determined the isoforms of tropomyosin expressed and the level of tropomyosin phosphorylation in donor, end-stage failing and hypertrophic obstructive cardiomyopathy samples of human heart muscle. Western blots and isoform-specific antibodies showed that α-tropomyosin was the only significant isoform expressed and that tropomyosin was 25-30% phosphorylated at serine 283. Mass spectrometry confirmed directly that α-tropomyosin made up over 95% of tropomyosin but also indicated the presence of up to 4% κ-tropomyosin and much smaller amounts of β-, γ- and smooth β-tropomyosin and about 26% phosphorylation. Neither the isoform distribution nor the level of phosphorylation changed significantly in the pathological heart muscle samples.
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