1
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Rider MH, Vertommen D, Johanns M. How mass spectrometry can be exploited to study AMPK. Essays Biochem 2024:EBC20240009. [PMID: 39056150 DOI: 10.1042/ebc20240009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2024] [Revised: 07/12/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024]
Abstract
AMP-activated protein kinase (AMPK) is a key regulator of metabolism and a recognised target for the treatment of metabolic diseases such as Type 2 diabetes (T2D). Here, we review how mass spectrometry (MS) can be used to study short-term control by AMPK via protein phosphorylation and long-term control due to changes in protein expression. We discuss how MS can quantify AMPK subunit levels in tissues from different species. We propose hydrogen-deuterium exchange (HDX)-MS to investigate molecular mechanisms of AMPK activation and thermoproteomic profiling (TPP) to assess off-target effects of pharmacological AMPK activators/inhibitors. Lastly, because large MS data sets are generated, we consider different approaches that can be used for their interpretation.
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Affiliation(s)
- Mark H Rider
- Protein Phosphorylation (PHOS) laboratory, Université catholique de Louvain and de Duve Institute, Avenue Hippocrate 75, B-1200 Brussels, Belgium
| | - Didier Vertommen
- Protein Phosphorylation (PHOS) laboratory, Université catholique de Louvain and de Duve Institute, Avenue Hippocrate 75, B-1200 Brussels, Belgium
| | - Manuel Johanns
- Protein Phosphorylation (PHOS) laboratory, Université catholique de Louvain and de Duve Institute, Avenue Hippocrate 75, B-1200 Brussels, Belgium
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2
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Mons E, Kim RQ, Mulder MPC. Technologies for Direct Detection of Covalent Protein—Drug Adducts. Pharmaceuticals (Basel) 2023; 16:ph16040547. [PMID: 37111304 PMCID: PMC10146396 DOI: 10.3390/ph16040547] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/29/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023] Open
Abstract
In the past two decades, drug candidates with a covalent binding mode have gained the interest of medicinal chemists, as several covalent anticancer drugs have successfully reached the clinic. As a covalent binding mode changes the relevant parameters to rank inhibitor potency and investigate structure-activity relationship (SAR), it is important to gather experimental evidence on the existence of a covalent protein–drug adduct. In this work, we review established methods and technologies for the direct detection of a covalent protein–drug adduct, illustrated with examples from (recent) drug development endeavors. These technologies include subjecting covalent drug candidates to mass spectrometric (MS) analysis, protein crystallography, or monitoring intrinsic spectroscopic properties of the ligand upon covalent adduct formation. Alternatively, chemical modification of the covalent ligand is required to detect covalent adducts by NMR analysis or activity-based protein profiling (ABPP). Some techniques are more informative than others and can also elucidate the modified amino acid residue or bond layout. We will discuss the compatibility of these techniques with reversible covalent binding modes and the possibilities to evaluate reversibility or obtain kinetic parameters. Finally, we expand upon current challenges and future applications. Overall, these analytical techniques present an integral part of covalent drug development in this exciting new era of drug discovery.
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Affiliation(s)
- Elma Mons
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
- Institute of Biology Leiden, Leiden University, 2333 BE Leiden, The Netherlands
| | - Robbert Q. Kim
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Monique P. C. Mulder
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
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3
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Ali R, Parelkar SS, Thompson PR, Mitroka-Batsford S, Yerramilli S, Scarlata SF, Mistretta KS, Coburn JM, Mattson AE. Phomoxanthone A Targets ATP Synthase. Chemistry 2022; 28:e202202397. [PMID: 36082977 PMCID: PMC9942271 DOI: 10.1002/chem.202202397] [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: 08/01/2022] [Indexed: 11/06/2022]
Abstract
Phomoxanthone A is a naturally occurring molecule and a powerful anti-cancer agent, although its mechanism of action is unknown. To facilitate the determination of its biological target(s), we used affinity-based labelling using a phomoxanthone A probe. Labelled proteins were pulled down, subjected to chemoproteomics analysis using LC-MS/MS and ATP synthase was identified as a likely target. Mitochondrial ATP synthase was validated in cultured cells lysates and in live intact cells. Our studies show sixty percent inhibition of ATP synthase by 260 μM phomoxanthone A.
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Affiliation(s)
- Rameez Ali
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01609, USA
| | - Sangram S Parelkar
- Department of Chemical Biology, University of Massachusetts Medical School, 364 Plantation St., Wocester, MA 01605, USA
| | - Paul R Thompson
- Department of Chemical Biology, University of Massachusetts Medical School, 364 Plantation St., Wocester, MA 01605, USA
| | - Susan Mitroka-Batsford
- Department of Chemistry and Biochemistry, Worcester State University, 486 Chandler St., Worcester, MA 10602, USA
| | - Siddartha Yerramilli
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01609, USA
| | - Suzanne F Scarlata
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01609, USA
| | - Katelyn S Mistretta
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01609, USA
| | - Jeannine M Coburn
- Department of Biomedical Engineering, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01609, USA
| | - Anita E Mattson
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, 60 Prescott St., Worcester, MA 01609, USA
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4
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Fadil F, Samol C, Berger RS, Kellermeier F, Gronwald W, Oefner PJ, Dettmer K. Isotope Ratio Outlier Analysis (IROA) for HPLC-TOFMS-Based Metabolomics of Human Urine. Metabolites 2022; 12:741. [PMID: 36005614 PMCID: PMC9414531 DOI: 10.3390/metabo12080741] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 08/04/2022] [Accepted: 08/10/2022] [Indexed: 11/16/2022] Open
Abstract
Metabolic fingerprinting by mass spectrometry aims at the comprehensive, semiquantitative analysis of metabolites. Isotope dilution, if successfully implemented, may provide a more reliable, relative quantification. Therefore, the 13C labeled yeast extract of the IROA TruQuant kit was added as an internal standard (IS) to human urine samples measured in full-scan mode on a high-performance liquid chromatography-time-of-flight mass spectrometer (HPLC-TOFMS) system. The isotope ratio approach enabled the analysis of 112 metabolites. The correlation with reference data did not improve significantly using 12C/13C ratios compared to absolute 12C peak areas. Moreover, using an intricate 13C-labeled standard increased the complexity of the mass spectra, which made correct signal annotation more challenging. On the positive side, the ratio approach helps to reduce batch effects, but it does not perform better than computational methods such as the "removebatcheffect" function in the R package Limma.
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Affiliation(s)
| | | | | | | | | | | | - Katja Dettmer
- Institute of Functional Genomics, University of Regensburg, 93053 Regensburg, Germany
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5
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Characterization and determination of bovine immunoglobulin G subtypes in milk and dairy products by UPLC-MS. Food Chem 2022; 390:133170. [PMID: 35597093 DOI: 10.1016/j.foodchem.2022.133170] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 05/02/2022] [Accepted: 05/04/2022] [Indexed: 02/07/2023]
Abstract
In this study, ultra-high performance liquid chromatography mass spectrometry (UPLC-MS) method was established for the characterization and quantitative determination of immunoglobulin G (IgG) subtypes (IgG1, IgG2, IgG3) in bovine dairy products. High-resolution mass spectrometry (HRMS) was applied to qualitatively confirm the theoretical peptides with specificity, enzymatic hydrolysis curve and stability among in heavy chain constant (CH1, CH2 and CH3) regions. The characteristic peptides VHNEGLPAPIVR, EPSVFIFPPKPK, GLPAPIVR, VVSALR were screened to quantitative analysis bovine IgG1, IgG2, IgG3 and the total amount of bovine IgG1 and IgG3, respectively. Isotope-labeled peptides were obtained by isotope dimethylation reaction, which aimed to correct the matrix effects. The results showed that the recovery was between 98.7% and 103.5%, and the precision of inter-day and intra-day was less than 6.8%. Moreover, this method had good linearity (R2 ≥ 0.999). Therefore, this research provided an effective method for quantitatively detecting bovine IgG subtypes in milk and dairy products.
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6
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Quantitative Mass Spectrometry by SILAC in Haloferax volcanii. Methods Mol Biol 2022; 2522:255-266. [PMID: 36125755 PMCID: PMC9926160 DOI: 10.1007/978-1-0716-2445-6_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The development of mass spectrometry (MS)-based proteomics methods has been critical in providing new insight about cellular processes and adaptations in all domains of life. While traditional MS-based methods are not inherently quantitative, technologies are now available to overcome this limitation. Of note, stable isotope labeling of amino acids in cell culture (SILAC) is reported as a reliable tool to label proteomes for quantitative MS-based proteomics that is accurate and flexible for multiplexing. The isotopically labeled lysine and arginine are easily incorporated into the proteome of cells auxotrophic for these amino acids. Microorganisms of the domain Archaea provide a fascinating alternative to understanding cellular adaptations and responses to environmental stresses. However, the availability of preferred SILAC-based quantitative analyses is limited. This protocol describes the use of SILAC to quantitatively analyze the proteome of Haloferax volcanii, a mesophilic halophilic archaeon that is easy to grow and requires no special equipment to maintain.
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Dimethylcysteine (DiCys)/ o-Phthalaldehyde Derivatization for Chiral Metabolite Analyses: Cross-Comparison of Six Chiral Thiols. Molecules 2021; 26:molecules26247416. [PMID: 34946495 PMCID: PMC8707109 DOI: 10.3390/molecules26247416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 10/24/2021] [Accepted: 10/25/2021] [Indexed: 11/16/2022] Open
Abstract
Metabolomics profiling using liquid chromatography-mass spectrometry (LC-MS) has become an important tool in biomedical research. However, resolving enantiomers still represents a significant challenge in the metabolomics study of complex samples. Here, we introduced N,N-dimethyl-l-cysteine (dimethylcysteine, DiCys), a chiral thiol, for the o-phthalaldehyde (OPA) derivatization of enantiomeric amine metabolites. We took interest in DiCys because of its potential for multiplex isotope-tagged quantification. Here, we characterized the usefulness of DiCys in reversed-phase LC-MS analyses of chiral metabolites, compared against five commonly used chiral thiols: N-acetyl-l-cysteine (NAC); N-acetyl-d-penicillamine (NAP); isobutyryl-l-cysteine (IBLC); N-(tert-butoxycarbonyl)-l-cysteine methyl ester (NBC); and N-(tert-butylthiocarbamoyl)-l-cysteine ethyl ester (BTCC). DiCys and IBLC showed the best overall performance in terms of chiral separation, fluorescence intensity, and ionization efficiency. For chiral separation of amino acids, DiCys/OPA also outperformed Marfey’s reagents: 1-fluoro-2-4-dinitrophenyl-5-l-valine amide (FDVA) and 1-fluoro-2-4-dinitrophenyl-5-l-alanine amide (FDAA). As proof of principle, we compared DiCys and IBLC for detecting chiral metabolites in aqueous extracts of rice. By LC–MS analyses, both methods detected twenty proteinogenic l-amino acids and seven d-amino acids (Ala, Arg, Lys, Phe, Ser, Tyr, and Val), but DiCys showed better analyte separation. We conclude that DiCys/OPA is an excellent amine-derivatization method for enantiomeric metabolite detection in LC-MS analyses.
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8
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Global Proteome Profiling to Assess Changes in Protein Abundance Using Isobaric Labeling and Liquid Chromatography-Tandem Mass Spectrometry. Methods Mol Biol 2021. [PMID: 34432251 DOI: 10.1007/978-1-0716-1665-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Protein degradation is a critical component of all facets of cell biology, and recently methods have been developed to make use of targeted protein degradation as both an investigative tool and a potential therapeutic avenue. Mass spectrometry-based proteomic studies have allowed detailed characterization of changes in protein level and the biology underlying growth, development, and disease. Current methods and instrumentation allow identification and quantitative analysis of thousands of proteins in a single assay. The method described here involves cell lysis and digestion to peptides, labeling peptides with isobaric tagging TMT reagents, basic reversed phase fractionation, and liquid chromatography-tandem mass spectrometry analysis of the enriched peptides.
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9
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Theodorakis E, Antonakis AN, Baltsavia I, Pavlopoulos GA, Samiotaki M, Amoutzias GD, Theodosiou T, Acuto O, Efstathiou G, Iliopoulos I. ProteoSign v2: a faster and evolved user-friendly online tool for statistical analyses of differential proteomics. Nucleic Acids Res 2021; 49:W573-W577. [PMID: 33963869 PMCID: PMC8262687 DOI: 10.1093/nar/gkab329] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 04/08/2021] [Accepted: 04/21/2021] [Indexed: 12/30/2022] Open
Abstract
Bottom-up proteomics analyses have been proved over the last years to be a powerful tool in the characterization of the proteome and are crucial for understanding cellular and organism behaviour. Through differential proteomic analysis researchers can shed light on groups of proteins or individual proteins that play key roles in certain, normal or pathological conditions. However, several tools for the analysis of such complex datasets are powerful, but hard-to-use with steep learning curves. In addition, some other tools are easy to use, but are weak in terms of analytical power. Previously, we have introduced ProteoSign, a powerful, yet user-friendly open-source online platform for protein differential expression/abundance analysis designed with the end-proteomics user in mind. Part of Proteosign's power stems from the utilization of the well-established Linear Models For Microarray Data (LIMMA) methodology. Here, we present a substantial upgrade of this computational resource, called ProteoSign v2, where we introduce major improvements, also based on user feedback. The new version offers more plot options, supports additional experimental designs, analyzes updated input datasets and performs a gene enrichment analysis of the differentially expressed proteins. We also introduce the deployment of the Docker technology and significantly increase the speed of a full analysis. ProteoSign v2 is available at http://bioinformatics.med.uoc.gr/ProteoSign.
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Affiliation(s)
- Evangelos Theodorakis
- Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece.,Department of Informatics, Technical University of Munich, Boltzmannstr. 3, 85748 Garching, Germany
| | - Andreas N Antonakis
- Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece
| | - Ismini Baltsavia
- Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece
| | - Georgios A Pavlopoulos
- Institute for Fundamental Biomedical Research, BSRC "Alexander Fleming", 34 Fleming Street, 16672 Vari, Greece
| | - Martina Samiotaki
- Institute for Bioinnovation, BSRC "Alexander Fleming", 34 Fleming Street, 16672 Vari, Greece
| | - Grigoris D Amoutzias
- Bioinformatics Laboratory, Department of Biochemistry and Biotechnology, University of Thessaly, Larisa 41500, Greece
| | - Theodosios Theodosiou
- Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece
| | - Oreste Acuto
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX13RE, UK
| | - Georgios Efstathiou
- Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece.,Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX13RE, UK
| | - Ioannis Iliopoulos
- Division of Basic Sciences, University of Crete Medical School, Heraklion 71110, Greece
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10
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Sauer CS, Phetsanthad A, Riusech OL, Li L. Developing mass spectrometry for the quantitative analysis of neuropeptides. Expert Rev Proteomics 2021; 18:607-621. [PMID: 34375152 PMCID: PMC8522511 DOI: 10.1080/14789450.2021.1967146] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Accepted: 08/09/2021] [Indexed: 12/22/2022]
Abstract
INTRODUCTION Neuropeptides are signaling molecules originating in the neuroendocrine system that can act as neurotransmitters and hormones in many biochemical processes. Their exact function is difficult to characterize, however, due to dependence on concentration, post-translational modifications, and the presence of other comodulating neuropeptides. Mass spectrometry enables sensitive, accurate, and global peptidomic analyses that can profile neuropeptide expression changes to understand their roles in many biological problems, such as neurodegenerative disorders and metabolic function. AREAS COVERED We provide a brief overview of the fundamentals of neuropeptidomic research, limitations of existing methods, and recent progress in the field. This review is focused on developments in mass spectrometry and encompasses labeling strategies, post-translational modification analysis, mass spectrometry imaging, and integrated multi-omic workflows, with discussion emphasizing quantitative advancements. EXPERT OPINION Neuropeptidomics is critical for future clinical research with impacts in biomarker discovery, receptor identification, and drug design. While advancements are being made to improve sensitivity and accuracy, there is still room for improvement. Better quantitative strategies are required for clinical analyses, and these methods also need to be amenable to mass spectrometry imaging, post-translational modification analysis, and multi-omics to facilitate understanding and future treatment of many diseases.
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Affiliation(s)
- Christopher S. Sauer
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Ashley Phetsanthad
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Olga L. Riusech
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706, USA
- School of Pharmacy, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075, USA
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11
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Michalak M, Kalteis MS, Ahadova A, Kloor M, Kriegsmann M, Kriegsmann K, Warnken U, Helm D, Kopitz J. Differential Glycosite Profiling-A Versatile Method to Compare Membrane Glycoproteomes. Molecules 2021; 26:molecules26123564. [PMID: 34200965 PMCID: PMC8230608 DOI: 10.3390/molecules26123564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 06/03/2021] [Accepted: 06/07/2021] [Indexed: 11/16/2022] Open
Abstract
Glycosylation is the most prevalent and varied form of post-translational protein modifications. Protein glycosylation regulates multiple cellular functions, including protein folding, cell adhesion, molecular trafficking and clearance, receptor activation, signal transduction, and endocytosis. In particular, membrane proteins are frequently highly glycosylated, which is both linked to physiological processes and of high relevance in various disease mechanisms. The cellular glycome is increasingly considered to be a therapeutic target. Here we describe a new strategy to compare membrane glycoproteomes, thereby identifying proteins with altered glycan structures and the respective glycosites. The workflow started with an optimized procedure for the digestion of membrane proteins followed by the lectin-based isolation of glycopeptides. Since alterations in the glycan part of a glycopeptide cause mass alterations, analytical size exclusion chromatography was applied to detect these mass shifts. N-glycosidase treatment combined with nanoUPLC-coupled mass spectrometry identified the altered glycoproteins and respective glycosites. The methodology was established using the colon cancer cell line CX1, which was treated with 2-deoxy-glucose-a modulator of N-glycosylation. The described methodology is not restricted to cell culture, as it can also be adapted to tissue samples or body fluids. Altogether, it is a useful module in various experimental settings that target glycan functions.
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Affiliation(s)
- Malwina Michalak
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.S.K.); (A.A.); (M.K.)
- Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Correspondence: (M.M.); (J.K.); Tel.: +49-6221-56-6167 (M.M.)
| | - Martin Simon Kalteis
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.S.K.); (A.A.); (M.K.)
- Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Aysel Ahadova
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.S.K.); (A.A.); (M.K.)
- Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Matthias Kloor
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.S.K.); (A.A.); (M.K.)
- Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
| | - Mark Kriegsmann
- Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany;
| | - Katharina Kriegsmann
- Department of Hematology, Oncology and Rheumatology, Heidelberg University Hospital, Im Neuenheimer Feld 410, 69120 Heidelberg, Germany;
| | - Uwe Warnken
- Clinical Cooperation Unit Neurooncology, DKFZ (German Cancer Research Center), Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;
| | - Dominic Helm
- Genomics and Proteomics Core Facility, MS-based Protein Analysis Unit, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany;
| | - Jürgen Kopitz
- Department of Applied Tumor Biology, Institute of Pathology, Heidelberg University Hospital, Im Neuenheimer Feld 224, 69120 Heidelberg, Germany; (M.S.K.); (A.A.); (M.K.)
- Clinical Cooperation Unit Applied Tumor Biology, DKFZ (German Cancer Research Center) Heidelberg, Im Neuenheimer Feld 280, 69120 Heidelberg, Germany
- Correspondence: (M.M.); (J.K.); Tel.: +49-6221-56-6167 (M.M.)
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12
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Moyer TB, Parsley NC, Sadecki PW, Schug WJ, Hicks LM. Leveraging orthogonal mass spectrometry based strategies for comprehensive sequencing and characterization of ribosomal antimicrobial peptide natural products. Nat Prod Rep 2021; 38:489-509. [PMID: 32929442 PMCID: PMC7956910 DOI: 10.1039/d0np00046a] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Covering: Up to July 2020Ribosomal antimicrobial peptide (AMP) natural products, also known as ribosomally synthesized and post-translationally modified peptides (RiPPs) or host defense peptides, demonstrate potent bioactivities and impressive complexity that complicate molecular and biological characterization. Tandem mass spectrometry (MS) has rapidly accelerated bioactive peptide sequencing efforts, yet standard workflows insufficiently address intrinsic AMP diversity. Herein, orthogonal approaches to accelerate comprehensive and accurate molecular characterization without the need for prior isolation are reviewed. Chemical derivatization, proteolysis (enzymatic and chemical cleavage), multistage MS fragmentation, and separation (liquid chromatography and ion mobility) strategies can provide complementary amino acid composition and post-translational modification data to constrain sequence solutions. Examination of two complex case studies, gomesin and styelin D, highlights the practical implementation of the proposed approaches. Finally, we emphasize the importance of heterogeneous AMP peptidoforms that confer varying biological function, an area that warrants significant further development.
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Affiliation(s)
- Tessa B Moyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
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13
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Zaikin VG, Borisov RS. Options of the Main Derivatization Approaches for Analytical ESI and MALDI Mass Spectrometry. Crit Rev Anal Chem 2021; 52:1287-1342. [PMID: 33557614 DOI: 10.1080/10408347.2021.1873100] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The inclusion of preliminary chemical labeling (derivatization) in the analysis process by such powerful and widespread methods as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) is a popular and widely used methodological approach. This is due to the need to remove some fundamental limitations inherent in these powerful analytic methods. Although a number of special reviews has been published discussing the utilization of derivatization approaches, the purpose of the present critical review is to comprehensively summarize, characterize and evaluate most of the previously developed and practically applied, as well as recently proposed representative derivatization reagents for ESI-MS and MALDI-MS platforms in their mostly sensitive positive ion mode and frequently hyphenated with separation techniques. The review is focused on the use of preliminary chemical labeling to facilitate the detection, identification, structure elucidation, quantification, profiling or MS imaging of compounds within complex matrices. Two main derivatization approaches, namely the introduction of permanent charge-fixed or highly proton affinitive residues into analytes are critically evaluated. In situ charge-generation, charge-switch and charge-transfer derivatizations are considered separately. The potential of using reactive matrices in MALDI-MS and chemical labeling in MS-based omics sciences is given.
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Affiliation(s)
- Vladimir G Zaikin
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
| | - Roman S Borisov
- A.V. Topchiev Institute of Petrochemical Synthesis, Russian Academy of Sciences, Moscow, Russian Federation
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14
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Sequeira VM, Vermeulen M. Identifying Protein-(Hydroxy)Methylated DNA Interactions Using Quantitative Interaction Proteomics. Methods Mol Biol 2021; 2272:209-224. [PMID: 34009616 DOI: 10.1007/978-1-0716-1294-1_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
In recent years, workflows coupling DNA affinity purifications from crude nuclear extracts with quantitative mass spectrometry-based proteomics have enabled comprehensive mapping of protein-DNA interactions in an unbiased manner. Here, we describe a detailed protocol for one such method in which affinity purifications with extracts from cells or tissues of interest are combined with a chemical stable isotope labeling method, dimethyl labeling, to identify specific interaction partners for (hydroxy)methylated and non-methylated DNA sequences of interest.
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Affiliation(s)
- Velin Marita Sequeira
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands
| | - Michiel Vermeulen
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Oncode Institute, Radboud University Nijmegen, Nijmegen, The Netherlands.
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15
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Chen SH, Lin YC, Shih MK, Wang LF, Liu SS, Hsu JL. LC-MS Quantification of Site-Specific Phosphorylation Degree by Stable-Isotope Dimethyl Labeling Coupled with Phosphatase Dephosphorylation. Molecules 2020; 25:molecules25225316. [PMID: 33202651 PMCID: PMC7697701 DOI: 10.3390/molecules25225316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 11/03/2020] [Accepted: 11/12/2020] [Indexed: 11/16/2022] Open
Abstract
Protein phosphorylation is a crucial post-translational modification that plays an important role in the regulation of cellular signaling processes. Site-specific quantitation of phosphorylation levels can help decipher the physiological functions of phosphorylation modifications under diverse physiological statuses. However, quantitative analysis of protein phosphorylation degrees is still a challenging task due to its dynamic nature and the lack of an internal standard simultaneously available for the samples differently prepared for various phosphorylation extents. In this study, stable-isotope dimethyl labeling coupled with phosphatase dephosphorylation (DM + deP) was tried to determine the site-specific degrees of phosphorylation in proteins. Firstly, quantitation accuracy of the (DM + deP) approach was confirmed using synthetic peptides of various simulated phosphorylation degrees. Afterwards, it was applied to evaluate the phosphorylation stoichiometry of milk caseins. The phosphorylation degree of Ser130 on α-S1-casein was also validated by absolute quantification with the corresponding synthetic phosphorylated and nonphosphorylated peptides under a selected reaction monitoring (SRM) mode. Moreover, this (DM + deP) method was used to detect the phosphorylation degree change of Ser82 on the Hsp27 protein of HepG2 cells caused by tert-butyl hydroperoxide (t-BHP) treatment. The results showed that the absolute phosphorylation degree obtained from the (DM + deP) approach was comparable with the relative quantitation resulting from stable-isotope dimethyl labeling coupled with TiO2 enrichment. This study suggested that the (DM + deP) approach is promising for absolute quantification of site-specific degrees of phosphorylation in proteins, and it may provide more convincing information than the relative quantification method.
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Affiliation(s)
- Sin-Hong Chen
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| | - Ya-Chi Lin
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
| | - Ming-Kuei Shih
- Graduate Institute of Food Culture and Innovation, National Kaohsiung University of Hospitality and Tourism, Kaohsiung 81271, Taiwan;
| | - Li-Fei Wang
- Hospitality and Tourism Research Center, National Kaohsiung University of Hospitality and Tourism, Kaohsiung 81271, Taiwan;
| | - Shyh-Shyan Liu
- Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
- Correspondence: (S.-S.L.); (J.-L.H.); Tel.: +886-8-7703202 (ext. 5075) (S.-S.L.); +886-8-7703202 (ext. 5197) (J.-L.H.); Fax: +886-8-7740178 (S.-S.L.); +886-8-7740550 (J.-L.H.)
| | - Jue-Liang Hsu
- Department of Biological Science and Technology, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan;
- Research Center for Tropic Agriculture, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
- Research Center for Animal Biologics, National Pingtung University of Science and Technology, Pingtung 91201, Taiwan
- Correspondence: (S.-S.L.); (J.-L.H.); Tel.: +886-8-7703202 (ext. 5075) (S.-S.L.); +886-8-7703202 (ext. 5197) (J.-L.H.); Fax: +886-8-7740178 (S.-S.L.); +886-8-7740550 (J.-L.H.)
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16
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Liu D, Yang S, Kavdia K, Sifford JM, Wu Z, Xie B, Wang Z, Pagala VR, Wang H, Yu K, Dey KK, High AA, Serrano GE, Beach TG, Peng J. Deep Profiling of Microgram-Scale Proteome by Tandem Mass Tag Mass Spectrometry. J Proteome Res 2020; 20:337-345. [PMID: 33175545 DOI: 10.1021/acs.jproteome.0c00426] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Tandem mass tag (TMT)-based mass spectrometry (MS) enables deep proteomic profiling of more than 10,000 proteins in complex biological samples but requires up to 100 μg protein in starting materials during a standard analysis. Here, we present a streamlined protocol to quantify more than 9000 proteins with 0.5 μg protein per sample by 16-plex TMT coupled with two-dimensional liquid chromatography and tandem mass spectrometry (LC/LC-MS/MS). In this protocol, we optimized multiple conditions to reduce sample loss, including processing each sample in a single tube to minimize surface adsorption, increasing digestion enzymes to shorten proteolysis and function as carriers, eliminating a desalting step between digestion and TMT labeling, and developing miniaturized basic pH LC for prefractionation. By profiling 16 identical human brain tissue samples of Alzheimer's disease (AD), vascular dementia (VaD), and non-dementia controls, we directly compared this new microgram-scale protocol to the standard-scale protocol, quantifying 9116 and 10,869 proteins, respectively. Importantly, bioinformatics analysis indicated that the microgram-scale protocol had adequate sensitivity and reproducibility to detect differentially expressed proteins in disease-related pathways. Thus, this newly developed protocol is of general application for deep proteomics analysis of biological and clinical samples at sub-microgram levels.
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Affiliation(s)
- Danting Liu
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Shu Yang
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kanisha Kavdia
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Jeffrey M Sifford
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhiping Wu
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Boer Xie
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Zhen Wang
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Vishwajeeth R Pagala
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Hong Wang
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kaiwen Yu
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Kaushik Kumar Dey
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Anthony A High
- Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
| | - Geidy E Serrano
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Thomas G Beach
- Banner Sun Health Research Institute, Sun City, Arizona 85351, United States
| | - Junmin Peng
- Departments of Structural Biology and Developmental Neurobiology, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States.,Center for Proteomics and Metabolomics, Saint Jude Children's Research Hospital, 262 Danny Thomas Place, Memphis, Tennessee 38105, United States
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17
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Yuan W, Wang J, Zhang Y, Lu H. Sample preparation approaches for qualitative and quantitative analysis of lipid-derived electrophile modified proteomes by mass spectrometry. Mol Omics 2020; 16:511-520. [PMID: 33079115 DOI: 10.1039/d0mo00099j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Lipid-derived electrophile (LDE) modifications, which are covalent modifications of proteins by endogenous LDEs, are essential types of protein posttranslational modifications. LDE modifications alter the protein structure and regulate their biological processes in cells. LDE modifications of proteins are also closely associated with several diseases and function as potential biomarkers for clinical diagnosis. The crucial step in studying the LDE modifications is to enrich the LDE modified proteins/peptides from complex biological samples with high efficiency and high selectivity and quantify modified proteins/peptides with high accuracy. In this review, we summarize the recent progress in MS-based proteomic technologies to globally identify and quantify LDE modified proteomes, mainly focusing on discussing the qualitative and quantitative technologies.
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Affiliation(s)
- Wenjuan Yuan
- Shanghai Cancer Center and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200032, P. R. China.
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18
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Itze-Mayrhofer C, Brem G. Quantitative proteomic strategies to study reproduction in farm animals: Female reproductive fluids. J Proteomics 2020; 225:103884. [PMID: 32593762 DOI: 10.1016/j.jprot.2020.103884] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 06/10/2020] [Accepted: 06/21/2020] [Indexed: 02/06/2023]
Abstract
Reproductive fluids from the female reproductive tract are gaining attention for their potential to support and optimize reproductive processes, including gamete maturation and embryo culture in vitro. Quantitative proteomics is a powerful way to decipher the proteome of reproductive tract fluids and to identify biologically relevant proteins. The present review describes proteomic strategies for analysing female reproductive fluid proteins. In addition, it considers the strategies for the preparation of oviductal, uterine and follicular fluid samples. Finally, it highlights the main results of quantitative proteomic studies, providing insights into the biological processes related to reproductive biology in farm animals. SIGNIFICANCE: Assisted reproductive technologies (ARTs) have become vitally important for farm animal breeding and much effort is going into the optimization and refinement of the techniques. There are also attempts to imitate physiological conditions by adding reproductive fluids or individual fluid proteins to improve in vitro procedures. A detailed knowledge of the reproductive fluid proteomes is indispensable. The present review summarizes the most widely used quantitative proteomic approaches for the analysis of fluids from the female reproductive tract and highlights the potential of quantitative proteomics to delineate reproductive processes and identify candidate proteins for ARTs in farm animals.
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Affiliation(s)
- Corina Itze-Mayrhofer
- Institute of Animal Breeding and Genetics, Group Molecular Reproduction IFA-Tulln, University of Veterinary Medicine, Vienna, Austria.
| | - Gottfried Brem
- Institute of Animal Breeding and Genetics, Department of Biomedical Sciences, University of Veterinary Medicine, Vienna, Austria
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19
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Parthasarathy A, Kalesh K. Defeating the trypanosomatid trio: proteomics of the protozoan parasites causing neglected tropical diseases. RSC Med Chem 2020; 11:625-645. [PMID: 33479664 PMCID: PMC7549140 DOI: 10.1039/d0md00122h] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 05/12/2020] [Indexed: 12/20/2022] Open
Abstract
Mass spectrometry-based proteomics enables accurate measurement of the modulations of proteins on a large scale upon perturbation and facilitates the understanding of the functional roles of proteins in biological systems. It is a particularly relevant methodology for studying Leishmania spp., Trypanosoma cruzi and Trypanosoma brucei, as the gene expression in these parasites is primarily regulated by posttranscriptional mechanisms. Large-scale proteomics studies have revealed a plethora of information regarding modulated proteins and their molecular interactions during various life processes of the protozoans, including stress adaptation, life cycle changes and interactions with the host. Important molecular processes within the parasite that regulate the activity and subcellular localisation of its proteins, including several co- and post-translational modifications, are also accurately captured by modern proteomics mass spectrometry techniques. Finally, in combination with synthetic chemistry, proteomic techniques facilitate unbiased profiling of targets and off-targets of pharmacologically active compounds in the parasites. This provides important data sets for their mechanism of action studies, thereby aiding drug development programmes.
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Affiliation(s)
- Anutthaman Parthasarathy
- Rochester Institute of Technology , Thomas H. Gosnell School of Life Sciences , 85 Lomb Memorial Dr , Rochester , NY 14623 , USA
| | - Karunakaran Kalesh
- Department of Chemistry , Durham University , Lower Mount Joy, South Road , Durham DH1 3LE , UK .
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20
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Dimethyl Labeling-Based Quantitative Proteomics of Recalcitrant Cocoa Pod Tissue. Methods Mol Biol 2020. [PMID: 32462583 DOI: 10.1007/978-1-0716-0528-8_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Dimethyl labeling is a type of stable-isotope labeling suitable for creating isotopic variants of peptides and thus be utilized for quantitative proteomics experiments. Labeling is achieved through a reductive amination/alkylation reaction using the low-cost reagents formaldehyde and cyanoborohydride, resulting in dimethylation of free amine groups of Lys and N-termini. Availability of isotopomeric forms of these reagents allows for the generation of up to six different isotopic variants. Here we describe the application of dimethylation to create two isotopic variants, light and heavy, differing in 4 Da, to label the total tryptic digest peptides of cocoa pod extracted from healthy pods from cultivars susceptible and resistant to the fungal disease called "frosty pod" caused by Moniliophthora roreri.
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21
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Moyer TB, Heil LR, Kirkpatrick CL, Goldfarb D, Lefever WA, Parsley NC, Wommack AJ, Hicks LM. PepSAVI-MS Reveals a Proline-rich Antimicrobial Peptide in Amaranthus tricolor. JOURNAL OF NATURAL PRODUCTS 2019; 82:2744-2753. [PMID: 31557021 PMCID: PMC6874829 DOI: 10.1021/acs.jnatprod.9b00352] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Traditional medicinal plants are a rich source of antimicrobials; however, the bioactive peptide constituents of most ethnobotanical species remain largely unexplored. Herein, PepSAVI-MS, a mass spectrometry-based peptidomics pipeline, was implemented for antimicrobial peptide (AMP) discovery in the medicinal plant Amaranthus tricolor. This investigation revealed a novel 1.7 kDa AMP with strong activity against Escherichia coli ATCC 25922, deemed Atr-AMP1. Initial efforts to determine the sequence of Atr-AMP1 utilized chemical derivatization and enzymatic digestion to provide information about specific residues and post-translational modifications. EThcD (electron-transfer/higher-energy collision dissociation) produced extensive backbone fragmentation and facilitated de novo sequencing, the results of which were consistent with orthogonal characterization experiments. Additionally, multistage HCD (higher-energy collisional dissociation) facilitated discrimination between isobaric leucine and isoleucine. These results revealed a positively charged proline-rich peptide present in a heterogeneous population of multiple peptidoforms, possessing several post-translational modifications including a disulfide bond, methionine oxidation, and proline hydroxylation. Additional bioactivity screening of a simplified fraction containing Atr-AMP1 revealed activity against Staphylococcus aureus LAC, demonstrating activity against both a Gram-negative and a Gram-positive bacterial species unlike many known short chain proline-rich antimicrobial peptides.
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Affiliation(s)
- Tessa B. Moyer
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina United States
| | - Lilian R. Heil
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina United States
| | - Christine L. Kirkpatrick
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina United States
| | - Dennis Goldfarb
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina United States
| | - William A. Lefever
- Department of Chemistry, High Point University, High Point, North Carolina United States
| | - Nicole C. Parsley
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina United States
| | - Andrew J. Wommack
- Department of Chemistry, High Point University, High Point, North Carolina United States
| | - Leslie M. Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina United States
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22
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23
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Miao M, Yu F, Wang D, Tong Y, Yang L, Xu J, Qiu Y, Zhou X, Zhao X. Proteomics Profiling of Host Cell Response via Protein Expression and Phosphorylation upon Dengue Virus Infection. Virol Sin 2019; 34:549-562. [PMID: 31134586 DOI: 10.1007/s12250-019-00131-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Accepted: 04/08/2019] [Indexed: 12/26/2022] Open
Abstract
Dengue virus (DENV) infection is a worldwide public health threat. To date, the knowledge about the pathogenesis and progression of DENV infection is still limited. Combining global profiling based on proteomic analysis together with functional verification analysis is a powerful strategy to investigate the interplay between the virus and host cells. In the present study, quantitative proteomics has been applied to evaluate host responses (as indicated by altered proteins and modifications) in human cells (using K562 cell line) upon DENV-2 infection, as DENV-2 spreads most widely among all DENV serotypes. Comparative analysis was performed to define differentially expressed proteins in the infected cells compared to the mock-control, and it revealed critical pathogen-induced changes covering a broad spectrum of host cellular compartments and processes. We also discovered more dramatic changes (> 20%, 160 regulated phosphoproteins) in protein phosphorylation compared to protein expression (14%, 321 regulated proteins). Most of these proteins/phosphoproteins were involved in transcription regulation, RNA splicing and processing, immune system, cellular response to stimulus, and macromolecule biosynthesis. Western blot analysis was also performed to confirm the proteomic data. Potential roles of these altered proteins were discussed. The present study provides valuable large-scale protein-related information for elucidating the functional emphasis of host cell proteins and their post-translational modifications in virus infection, and also provides insight and protein evidence for understanding the general pathogenesis and pathology of DENV.
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Affiliation(s)
- Meng Miao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Fei Yu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Danya Wang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Yongjia Tong
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Liuting Yang
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China.,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Jiuyue Xu
- Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, China
| | - Yang Qiu
- Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, China
| | - Xi Zhou
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China. .,Laboratory of RNA Virology, Wuhan Institute of Virology, Chinese Academy of Science, Wuhan, 430071, China.
| | - Xiaolu Zhao
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China. .,Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, 430072, China.
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24
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Feasibility of Utilizing Stable-Isotope Dimethyl Labeling in Liquid Chromatography⁻Tandem Mass Spectrometry-Based Determination for Food Allergens-Case of Kiwifruit. Molecules 2019; 24:molecules24101920. [PMID: 31109069 PMCID: PMC6571768 DOI: 10.3390/molecules24101920] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 05/17/2019] [Accepted: 05/17/2019] [Indexed: 12/28/2022] Open
Abstract
Stable-isotope dimethyl labeling is a highly reactive and cost-effective derivatization procedure that could be utilized in proteomics analysis. In this study, a liquid chromatography- tandem mass spectrometry in multiple reaction monitoring mode (LC-MS-MRM) platform for the quantification of kiwi allergens was first developed using this strategy. Three signature peptides for target allergens Act d 1, Act d 5, and Act d 11 were determined and were derivatized with normal and deuterated formaldehyde as external calibrants and internal standards, respectively. The results showed that sample preparation with the phenol method provided comprehensive protein populations. Recoveries at four different levels ranging from 72.5-109.3% were achieved for the H-labeled signature peptides of Act d 1 (SPA1-H) and Act d 5 (SPA5-H) with precision ranging from 1.86-9.92%. The limit of quantification (LOQ) was set at 8 pg mL-1 for SPA1-H and at 8 ng mL-1 for SPA5-H. The developed procedure was utilized to analyze seven kinds of hand-made kiwi foods containing 0.0175-0.0515 mg g-1 of Act d 1 and 0.0252-0.0556 mg g-1 of Act d 5. This study extended the applicability of stable-isotope dimethyl labeling to the economical and precise determination of food allergens and peptides.
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25
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An Y, Zhou L, Huang Z, Nice EC, Zhang H, Huang C. Molecular insights into cancer drug resistance from a proteomics perspective. Expert Rev Proteomics 2019; 16:413-429. [PMID: 30925852 DOI: 10.1080/14789450.2019.1601561] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
INTRODUCTION Resistance to chemotherapy and development of specific and effective molecular targeted therapies are major obstacles facing current cancer treatment. Comparative proteomic approaches have been employed for the discovery of putative biomarkers associated with cancer drug resistance and have yielded a number of candidate proteins, showing great promise for both novel drug target identification and personalized medicine for the treatment of drug-resistant cancer. Areas covered: Herein, we review the recent advances and challenges in proteomics studies on cancer drug resistance with an emphasis on biomarker discovery, as well as understanding the interconnectivity of proteins in disease-related signaling pathways. In addition, we highlight the critical role that post-translational modifications (PTMs) play in the mechanisms of cancer drug resistance. Expert opinion: Revealing changes in proteome profiles and the role of PTMs in drug-resistant cancer is key to deciphering the mechanisms of treatment resistance. With the development of sensitive and specific mass spectrometry (MS)-based proteomics and related technologies, it is now possible to investigate in depth potential biomarkers and the molecular mechanisms of cancer drug resistance, assisting the development of individualized therapeutic strategies for cancer patients.
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Affiliation(s)
- Yao An
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Li Zhou
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Zhao Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China
| | - Edouard C Nice
- c Department of Biochemistry and Molecular Biology , Monash University , Clayton , Australia
| | - Haiyuan Zhang
- b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
| | - Canhua Huang
- a West China School of Basic Medical Sciences & Forensic Medicine , Sichuan University , Chengdu , PR China.,b Department of Oncology , The Second Affiliated Hospital of Hainan Medical University , Haikou , P.R. China
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26
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Sheng Y, Capri J, Waring A, Valentine JS, Whitelegge J. Exposure of Solvent-Inaccessible Regions in the Amyloidogenic Protein Human SOD1 Determined by Hydroxyl Radical Footprinting. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:218-226. [PMID: 30328005 PMCID: PMC6347482 DOI: 10.1007/s13361-018-2075-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/18/2018] [Accepted: 09/22/2018] [Indexed: 06/08/2023]
Abstract
Solvent-accessibility change plays a critical role in protein misfolding and aggregation, the culprit for several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS). Mass spectrometry-based hydroxyl radical (·OH) protein footprinting has evolved as a powerful and fast tool in elucidating protein solvent accessibility. In this work, we used fast photochemical oxidation of protein (FPOP) hydroxyl radical (·OH) footprinting to investigate solvent accessibility in human copper-zinc superoxide dismutase (SOD1), misfolded or aggregated forms of which underlie a portion of ALS cases. ·OH-mediated modifications to 56 residues were detected with locations largely as predicted based on X-ray crystallography data, while the interior of SOD1 β-barrel is hydrophobic and solvent-inaccessible and thus protected from modification. There were, however, two notable exceptions-two closely located residues inside the β-barrel, predicted to have minimal or no solvent accessibility, that were found modified by FPOP (Phe20 and Ile112). Molecular dynamics (MD) simulations were consistent with differential access of peroxide versus quencher to SOD1's interior complicating surface accessibility considerations. Modification of these two residues could potentially be explained either by local motions of the β-barrel that increased peroxide/solvent accessibility to the interior or by oxidative events within the interior that might include long-distance radical transfer to buried sites. Overall, comparison of modification patterns for the metal-free apoprotein versus zinc-bound forms demonstrated that binding of zinc protected the electrostatic loop and organized the copper-binding site. Our study highlights SOD1 hydrophobic groups that may contribute to early events in aggregation and discusses caveats to surface accessibility conclusions. Graphical Abstract.
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Affiliation(s)
- Yuewei Sheng
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Joseph Capri
- The Pasarow Mass Spectrometry Laboratory, University of California, Los Angeles, CA, USA
| | - Alan Waring
- Department of Medicine, University of California, Los Angeles, CA, USA
| | | | - Julian Whitelegge
- The Pasarow Mass Spectrometry Laboratory, University of California, Los Angeles, CA, USA.
- The Brain Research Institute, University of California, Los Angeles, CA, USA.
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27
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Affiliation(s)
- Albert B. Arul
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Renã A. S. Robinson
- Department of Chemistry, Vanderbilt University, Nashville, Tennessee 37235, United States
- Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee 37212, United States
- Vanderbilt Brain Institute, Vanderbilt University Medical Center, Nashville, Tennessee 37232, United States
- Vanderbilt Institute of Chemical Biology, Vanderbilt University Medical Center, Nashville, Tennessee 37235, United States
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28
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Yang F, Gao J, Che J, Jia G, Wang C. A Dimethyl-Labeling-Based Strategy for Site-Specifically Quantitative Chemical Proteomics. Anal Chem 2018; 90:9576-9582. [PMID: 29989794 DOI: 10.1021/acs.analchem.8b02426] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Activity-based protein profiling (ABPP) has emerged as a powerful functional chemoproteomic strategy which enables global profiling of proteome reactivity toward bioactive small molecules in complex biological and/or pathological processes. To quantify the degree of reactivity in a site-specific manner, an isotopic tandem orthogonal proteolysis (isoTOP)-ABPP strategy has been developed; however, the high cost and long workflow associated with the synthesis of isotopically labeled cleavable tags limit its wide use. Herein, we combined reductive dimethyl labeling with TOP-ABPP to develop a fast, affordable, and efficient method, termed "rdTOP-ABPP", for quantitative chemical proteomics with site-specific precision and triplex quantification. The rdTOP-ABPP method shows high accuracy and precision, good reproducibility, and better capacity for site identification and quantification and is highly compatible with many commercially available cleavable tags. We demonstrated the power of rdTOP-ABPP by profiling the target of (1 S,3 R)-RSL3, a canonical inducer for cell ferroptosis, and provided the first global portrait of its proteome reactivity in a quantitative and site-specific manner.
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29
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Leitner A. A review of the role of chemical modification methods in contemporary mass spectrometry-based proteomics research. Anal Chim Acta 2018; 1000:2-19. [DOI: 10.1016/j.aca.2017.08.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Revised: 07/11/2017] [Accepted: 08/15/2017] [Indexed: 12/20/2022]
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Zhang S, Yuan H, Zhao B, Zhang L, Zhang Y. Integrated platform with combination of on-line protein digestion, isotope dimethyl labeling and multidimensional peptide separation for high-throughput proteome quantification. Anal Chim Acta 2018; 1000:172-179. [DOI: 10.1016/j.aca.2017.10.023] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 10/20/2017] [Accepted: 10/23/2017] [Indexed: 02/08/2023]
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