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Zhou Z, Zhang R, Zhou A, Lv J, Chen S, Zou H, Zhang G, Lin T, Wang Z, Zhang Y, Weng S, Han X, Liu Z. Proteomics appending a complementary dimension to precision oncotherapy. Comput Struct Biotechnol J 2024; 23:1725-1739. [PMID: 38689716 PMCID: PMC11058087 DOI: 10.1016/j.csbj.2024.04.044] [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: 02/06/2024] [Revised: 04/11/2024] [Accepted: 04/17/2024] [Indexed: 05/02/2024] Open
Abstract
Recent advances in high-throughput proteomic profiling technologies have facilitated the precise quantification of numerous proteins across multiple specimens concurrently. Researchers have the opportunity to comprehensively analyze the molecular signatures in plentiful medical specimens or disease pattern cell lines. Along with advances in data analysis and integration, proteomics data could be efficiently consolidated and employed to recognize precise elementary molecular mechanisms and decode individual biomarkers, guiding the precision treatment of tumors. Herein, we review a broad array of proteomics technologies and the progress and methods for the integration of proteomics data and further discuss how to better merge proteomics in precision medicine and clinical settings.
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Affiliation(s)
- Zhaokai Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Ruiqi Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Aoyang Zhou
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jinxiang Lv
- Department of Gastroenterology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Shuang Chen
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Haijiao Zou
- Center of Reproductive Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ge Zhang
- Department of Cardiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Ting Lin
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Zhan Wang
- Department of Urology, The First Affiliated Hospital of Zhengzhou University, Henan 450052, China
| | - Yuyuan Zhang
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyuan Weng
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xinwei Han
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
| | - Zaoqu Liu
- Department of Interventional Radiology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Institute of Zhengzhou University, Zhengzhou, Henan 450052, China
- Interventional Treatment and Clinical Research Center of Henan Province, Zhengzhou, Henan 450052, China
- Institute of Basic Medical Sciences, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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2
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Nguyen TM, Sreekanth V, Deb A, Kokkonda P, Tiwari PK, Donovan KA, Shoba V, Chaudhary SK, Mercer JAM, Lai S, Sadagopan A, Jan M, Fischer ES, Liu DR, Ebert BL, Choudhary A. Proteolysis-targeting chimeras with reduced off-targets. Nat Chem 2024; 16:218-228. [PMID: 38110475 PMCID: PMC10913580 DOI: 10.1038/s41557-023-01379-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 10/13/2023] [Indexed: 12/20/2023]
Abstract
Proteolysis-targeting chimeras (PROTACs) are molecules that induce proximity between target proteins and E3 ligases triggering target protein degradation. Pomalidomide, a widely used E3 ligase recruiter in PROTACs, can independently degrade other proteins, including zinc-finger (ZF) proteins, with vital roles in health and disease. This off-target degradation hampers the therapeutic applicability of pomalidomide-based PROTACs, requiring development of PROTAC design rules that minimize off-target degradation. Here we developed a high-throughput platform that interrogates off-target degradation and found that reported pomalidomide-based PROTACs induce degradation of several ZF proteins. We generated a library of pomalidomide analogues to understand how functionalizing different positions of the phthalimide ring, hydrogen bonding, and steric and hydrophobic effects impact ZF protein degradation. Modifications of appropriate size on the C5 position reduced off-target ZF degradation, which we validated through target engagement and proteomics studies. By applying these design principles, we developed anaplastic lymphoma kinase oncoprotein-targeting PROTACs with enhanced potency and minimal off-target degradation.
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Affiliation(s)
- Tuan M Nguyen
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA
| | - Vedagopuram Sreekanth
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA
| | - Arghya Deb
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Praveen Kokkonda
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Praveen K Tiwari
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA
| | - Katherine A Donovan
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Veronika Shoba
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Santosh K Chaudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Jaron A M Mercer
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Sophia Lai
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
| | - Ananthan Sadagopan
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Max Jan
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Eric S Fischer
- Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Benjamin L Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Amit Choudhary
- Chemical Biology and Therapeutics Science, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
- Divisions of Renal Medicine and Engineering, Brigham and Women's Hospital, Boston, MA, USA.
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3
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Delafield DG, Miles HN, Ricke WA, Li L. Inclusion of Porous Graphitic Carbon Chromatography Yields Greater Protein Identification and Compartment and Process Coverage and Enables More Reflective Protein-Level Label-Free Quantitation. J Proteome Res 2023; 22:3508-3518. [PMID: 37815119 PMCID: PMC10732698 DOI: 10.1021/acs.jproteome.3c00373] [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] [Indexed: 10/11/2023]
Abstract
The ubiquity of mass spectrometry-based bottom-up proteomic analyses as a component of biological investigation mandates the validation of methodologies that increase acquisition efficiency, improve sample coverage, and enhance profiling depth. Chromatographic separation is often ignored as an area of potential improvement, with most analyses relying on traditional reversed-phase liquid chromatography (RPLC); this consistent reliance on a single chromatographic paradigm fundamentally limits our view of the observable proteome. Herein, we build upon early reports and validate porous graphitic carbon chromatography (PGC) as a facile means to substantially enhance proteomic coverage without changes to sample preparation, instrument configuration, or acquisition methods. Analysis of offline fractionated cell line digests using both separations revealed an increase in peptide and protein identifications by 43% and 24%, respectively. Increased identifications provided more comprehensive coverage of cellular components and biological processes independent of protein abundance, highlighting the substantial quantity of proteomic information that may go undetected in standard analyses. We further utilize these data to reveal that label-free quantitative analyses using RPLC separations alone may not be reflective of actual protein constituency. Together, these data highlight the value and comprehension offered through PGC-MS proteomic analyses. RAW proteomic data have been uploaded to the MassIVE repository with the primary accession code MSV000091495.
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Affiliation(s)
- Daniel G. Delafield
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
| | - Hannah N. Miles
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075
| | - William A. Ricke
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075
- Department of Urology, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
- George M. O’Brien Urology Research Center of Excellence, University of Wisconsin School of Medicine and Public Health, Madison, WI 53705, USA
| | - Lingjun Li
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, WI 53706
- Division of Pharmaceutical Sciences, University of Wisconsin-Madison, 777 Highland Avenue, Madison, WI 53075
- Lachman Institute for Pharmaceutical Development, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Wisconsin Center for NanoBioSystems, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
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4
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Ren AH, Diamandis EP, Kulasingam V. Uncovering the Depths of the Human Proteome: Antibody-based Technologies for Ultrasensitive Multiplexed Protein Detection and Quantification. Mol Cell Proteomics 2021; 20:100155. [PMID: 34597790 PMCID: PMC9357438 DOI: 10.1016/j.mcpro.2021.100155] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 09/01/2021] [Accepted: 09/25/2021] [Indexed: 12/20/2022] Open
Abstract
Probing the human proteome in tissues and biofluids such as plasma is attractive for biomarker and drug target discovery. Recent breakthroughs in multiplex, antibody-based, proteomics technologies now enable the simultaneous quantification of thousands of proteins at as low as sub fg/ml concentrations with remarkable dynamic ranges of up to 10-log. We herein provide a comprehensive guide to the methodologies, performance, technical comparisons, advantages, and disadvantages of established and emerging technologies for the multiplexed ultrasensitive measurement of proteins. Gaining holistic knowledge on these innovations is crucial for choosing the right multiplexed proteomics tool for applications at hand to critically complement traditional proteomics methods. This can bring researchers closer than ever before to elucidating the intricate inner workings and cross talk that spans multitude of proteins in disease mechanisms.
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Affiliation(s)
- Annie H Ren
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada
| | - Eleftherios P Diamandis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada
| | - Vathany Kulasingam
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada; Department of Clinical Biochemistry, University Health Network, Toronto, Canada.
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5
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Glycoproteomic analysis of the changes in protein N-glycosylation during neuronal differentiation in human-induced pluripotent stem cells and derived neuronal cells. Sci Rep 2021; 11:11169. [PMID: 34045517 PMCID: PMC8160270 DOI: 10.1038/s41598-021-90102-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 05/04/2021] [Indexed: 11/09/2022] Open
Abstract
N-glycosylation of glycoproteins, a major post-translational modification, plays a crucial role in various biological phenomena. In central nervous systems, N-glycosylation is thought to be associated with differentiation and regeneration; however, the state and role of N-glycosylation in neuronal differentiation remain unclear. Here, we conducted sequential LC/MS/MS analyses of tryptic digest, enriched glycopeptides, and deglycosylated peptides of proteins derived from human-induced pluripotent stem cells (iPSCs) and iPSC-derived neuronal cells, which were used as a model of neuronal differentiation. We demonstrate that the production profiles of many glycoproteins and their glycoforms were altered during neuronal differentiation. Particularly, the levels of glycoproteins modified with an N-glycan, consisting of five N-acetylhexosamines, three hexoses, and a fucose (HN5H3F), increased in dopaminergic neuron-rich cells (DAs). The N-glycan was deduced to be a fucosylated and bisected biantennary glycan based on product ion spectra. Interestingly, the HN5H3F-modified proteins were predicted to be functionally involved in neural cell adhesion, axon guidance, and the semaphorin-plexin signaling pathway, and protein modifications were site-selective and DA-selective regardless of protein production levels. Our integrated method for glycoproteome analysis and resultant profiles of glycoproteins and their glycoforms provide valuable information for further understanding the role of N-glycosylation in neuronal differentiation and neural regeneration.
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7
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Xiao H, Sun F, Suttapitugsakul S, Wu R. Global and site-specific analysis of protein glycosylation in complex biological systems with Mass Spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:356-379. [PMID: 30605224 PMCID: PMC6610820 DOI: 10.1002/mas.21586] [Citation(s) in RCA: 66] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2018] [Accepted: 11/27/2018] [Indexed: 05/16/2023]
Abstract
Protein glycosylation is ubiquitous in biological systems and plays essential roles in many cellular events. Global and site-specific analysis of glycoproteins in complex biological samples can advance our understanding of glycoprotein functions and cellular activities. However, it is extraordinarily challenging because of the low abundance of many glycoproteins and the heterogeneity of glycan structures. The emergence of mass spectrometry (MS)-based proteomics has provided us an excellent opportunity to comprehensively study proteins and their modifications, including glycosylation. In this review, we first summarize major methods for glycopeptide/glycoprotein enrichment, followed by the chemical and enzymatic methods to generate a mass tag for glycosylation site identification. We next discuss the systematic and quantitative analysis of glycoprotein dynamics. Reversible protein glycosylation is dynamic, and systematic study of glycoprotein dynamics helps us gain insight into glycoprotein functions. The last part of this review focuses on the applications of MS-based proteomics to study glycoproteins in different biological systems, including yeasts, plants, mice, human cells, and clinical samples. Intact glycopeptide analysis is also included in this section. Because of the importance of glycoproteins in complex biological systems, the field of glycoproteomics will continue to grow in the next decade. Innovative and effective MS-based methods will exponentially advance glycoscience, and enable us to identify glycoproteins as effective biomarkers for disease detection and drug targets for disease treatment. © 2019 Wiley Periodicals, Inc. Mass Spec Rev 9999: XX-XX, 2019.
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Affiliation(s)
- Haopeng Xiao
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Fangxu Sun
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Suttipong Suttapitugsakul
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
| | - Ronghu Wu
- School of Chemistry and Biochemistry and the Petit Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta 30332 Georgia
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8
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Giudice G, Petsalaki E. Proteomics and phosphoproteomics in precision medicine: applications and challenges. Brief Bioinform 2019; 20:767-777. [PMID: 29077858 PMCID: PMC6585152 DOI: 10.1093/bib/bbx141] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2017] [Revised: 09/21/2017] [Indexed: 12/11/2022] Open
Abstract
Recent advances in proteomics allow the accurate measurement of abundances for thousands of proteins and phosphoproteins from multiple samples in parallel. Therefore, for the first time, we have the opportunity to measure the proteomic profiles of thousands of patient samples or disease model cell lines in a systematic way, to identify the precise underlying molecular mechanism and discover personalized biomarkers, networks and treatments. Here, we review examples of successful use of proteomics and phosphoproteomics data sets in as well as their integration other omics data sets with the aim of precision medicine. We will discuss the bioinformatics challenges posed by the generation, analysis and integration of such large data sets and present potential reasons why proteomics profiling and biomarkers are not currently widely used in the clinical setting. We will finally discuss ways to contribute to the better use of proteomics data in precision medicine and the clinical setting.
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Affiliation(s)
- Girolamo Giudice
- European Molecular Biology Laboratory European Bioinformatics Institute
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9
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Reis-de-Oliveira G, Fioramonte M, Martins-de-Souza D. A Complete Proteomic Workflow to Study Brain-Related Disorders via Postmortem Tissue. Methods Mol Biol 2019; 1916:319-328. [PMID: 30535709 DOI: 10.1007/978-1-4939-8994-2_31] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Here we describe a mass spectrometry-based proteomics workflow to discovery proteins differentially regulated in brains collected postmortem from mental, neurological, or substance abuse disorders (MNS) patients. One way to maximize protein detection is to carry out enrichment of cellular compartments such as the nucleus, mitochondria and cytosol. Subcellular fractionation improves proteome coverage and may shed light on the role of these organelles in the pathophysiology of MNS.
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Affiliation(s)
- Guilherme Reis-de-Oliveira
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Mariana Fioramonte
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil
| | - Daniel Martins-de-Souza
- Laboratory of Neuroproteomics, Department of Biochemistry and Tissue Biology, Institute of Biology, University of Campinas (UNICAMP), Campinas, Brazil.
- Center for Neurobiology, University of Campinas (UNICAMP), Campinas, Brazil.
- Instituto Nacional de Biomarcadores em Neuropsiquiatria (INBION), Conselho Nacional de Desenvolvimento Cientifico e Tecnologico, Sao Paulo, Brasil.
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10
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Gross JH. Matrix-Assisted Laser Desorption/Ionization. Mass Spectrom (Tokyo) 2017. [DOI: 10.1007/978-3-319-54398-7_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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11
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Abstract
Obesity has emerged as one of the major global epidemics of the 21st century and is now reaching alarming proportions. Obese subjects have an increased morbidity and mortality, decreased quality of life and a major risk of developing pathologies such as diabetes mellitus, insulin resistance and cardiovascular disease. Obesity is a complex disease characterised by an increase in body fat mass resulting from an imbalance between energy intake and expenditure. Signal integration between adipose tissue, other peripheral organs and the CNS seems to regulate energy homeostasis. Proteomics may be useful in unravelling the pathogenesis of obesity, since a combination of genetic predisposition and environmental factors account for its development. Most of the proteomic studies performed to date have focused on protein profiling of adipose tissue in different models of experimental obesity and the study of the adipocyte differentiation process. Another issue that has recently attracted attention is the characterisation of the adipocyte secretome, which may be important in signalling to other organs and in regulating energy balance. Target identification of potential therapies has also been investigated by proteomics. This review focuses on the contributions of proteomics to understanding the molecular mechanisms of obesity and their potential therapies.
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Affiliation(s)
| | - Ramon Gomis
- Diabetes and Obesity Laboratory-Endocrinology and Nutrition Unit, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS)-Hospital Clínic, Universitat de Barcelona, Barcelona, Spain.,CIBER de Diabetes y Enfermedades Metabólicas Asociadas (CIBERDEM), Barcelona, Spain
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12
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Qoronfleh MW. Role and challenges of proteomics in pharma and biotech: technical, scientific and commercial perspective. Expert Rev Proteomics 2014; 3:179-95. [PMID: 16608432 DOI: 10.1586/14789450.3.2.179] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Contemporary proteomics, currently in its exponential growth phase, is a bewildering array of tools. Proteomic methods are the result of a convergence of rapidly improving mass spectrometry technologies, protein chemistry and separation sciences, genomics and bioinformatics. Strides in improving proteomics technologies to map and measure proteomes and subproteomes are being made. However, no single proteomic platform appears ideally suited to address all research needs or accomplish ambitious goals satisfactorily. However, proteomics is in a unique position to contribute to protein discovery and to public health in terms of better biomarkers, diagnostics and treatment of disease. While the potential is great, many challenges and issues remain to be solved. Fundamental issues, such as biological variability, pre-analytic factors and analytical reproducibility, remain to be resolved. Neither an all-genetic approach nor an all-proteomic approach will solve biological complexity. Proteomics will be the foundation for constructing and extracting useful knowledge to pharma and biotech depicted in the following path: data --> structured data --> information --> information architecture --> knowledge --> useful knowledge.
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Affiliation(s)
- M Walid Qoronfleh
- Core Technology Alliance CTA, University of Michigan, Ann Arbor, MI 48109-1274, USA.
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13
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Wheelock AM, Goto S. Effects of post-electrophoretic analysis on variance in gel-based proteomics. Expert Rev Proteomics 2014; 3:129-42. [PMID: 16445357 DOI: 10.1586/14789450.3.1.129] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
2D electrophoresis (2DE) is a prominent separation method for complex proteomes. Although recent advances have increased the utility of this method in quantitative proteomics studies, many sources of variance still exist. This review discusses the post-electrophoretic sources of variance in current 2DE analysis. The essential improvements in protein visualization and software algorithms that have made 2DE a leading quantitative proteomics method are briefly reviewed. A number of shortcomings in the post-electrophoretic analysis of 2DE data that require further attention are highlighted. Topics discussed include protein visualization and image acquisition, internal standards and normalization methods, background subtraction algorithms, normality of distribution, and the need for standardized tests for the evaluation of 2DE analysis software packages.
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Affiliation(s)
- Asa M Wheelock
- Kyoto University, Bioinformatics Center, Institute for Chemical Research, Uji, Kyoto, 611-0011, Japan.
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14
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Abstract
During the last decade, a major breakthrough in the field of proteomics has been achieved. This review describes available techniques for proteomic analyses, both gel and non-gel based, particularly concentrating on relative quantification techniques. The principle of the different techniques is discussed, highlighting the advantages and drawbacks of recently available visualization methods in gel-based assays. In addition, recent developments for quantitative analysis in non-gel-based approaches are summarized. This review focuses on applications in Type 1 diabetes. These mainly include proteomic studies on pancreatic islets in animal models and in the human situation. Also discussed are mass spectrometry-based studies on T-cells, and studies on the development of diagnostic markers for diabetic nephropathology by capillary electrophoresis coupled to mass spectrometry.
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Affiliation(s)
- Wannes D'Hertog
- Laboratory for Experimental Medicine & Endocrinology (LEGENDO), University Hospital Gasthuisberg, Herestraat 49, Catholic University of Leuven, Leuven, Belgium.
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16
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N-glycosidase treatment with 18O labeling and de novo sequencing argues for flagellin FliC glycopolymorphism in Pseudomonas aeruginosa. Anal Bioanal Chem 2013; 405:9835-42. [PMID: 24220757 DOI: 10.1007/s00216-013-7424-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2013] [Revised: 09/27/2013] [Accepted: 10/07/2013] [Indexed: 10/26/2022]
Abstract
In prokaryote organisms, N-glycosylation of proteins is often correlated to cell-cell recognition and extracellular events. Those glycoproteins are potential targets for infection control. To date, many surface-glycosylated proteins from bacterial pathogens have been described. However, N-linked Pseudomonas surface-associated glycoproteins remain underexplored. We report a combined enrichment and labeling strategy to identify major glycoproteins on the outside of microorganisms. More precisely, bacteria were exposed to a mix of biotinylated lectins able to bind with glycoproteins. The latter were then recovered by avidin beads, digested with trypsin, and submitted to mass spectrometry. The targeted mixture of glycoproteins was additionally deglycosylated in the presence of H2(18)O to incorporate (18)O during PNGase F treatment and were also analyzed using mass spectrometry. This approach allowed us to identify a few tens of potential N-glycoproteins, among which flagellin FliC was the most abundant. To detect the possible sites of FliC modifications, a de novo sequencing step was also performed to discriminate between spontaneous deamidation and N-glycan loss. This approach led to the proposal of three potential N-glycosylated sites on the primary sequence of FliC: N26, N69, and N439, with two of these three asparagines belonging to an N-X-(S/T) consensus sequence. These observations suggest that flagellin FliC is a heterogeneous protein mixture containing both O- and N-glycoforms.
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17
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Pasella S, Baralla A, Canu E, Pinna S, Vaupel J, Deiana M, Franceschi C, Baggio G, Zinellu A, Sotgia S, Castaldo G, Carru C, Deiana L. Pre-analytical stability of the plasma proteomes based on the storage temperature. Proteome Sci 2013; 11:10. [PMID: 23518135 PMCID: PMC3658880 DOI: 10.1186/1477-5956-11-10] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2012] [Accepted: 03/18/2013] [Indexed: 12/15/2022] Open
Abstract
Background This study examined the effect of storage temperature on the protein profile of human plasma. Plasma samples were stored for 13 days at -80°C, -20°C, +4°C and room temperature (20-25°C) prior to proteomic analysis. The proteomic comparisons were based on the differences of mean intensity values of protein spots between fresh plasma samples (named “time zero”) and plasma samples stored at different temperatures. To better understand the thermally induced biochemical changes that may affect plasma proteins during storage we identified proteins with different expressions with respect to the time zero sample. Results Using two-dimensional electrophoresis followed by MALDI-TOF MS and /or LC-MS/MS 20 protein spots representing 10 proteins were identified with significant differences in abundance when stored at different temperatures. Our results, in agreement with various authors, indicate that during storage for a short period (13 days) at four different temperatures plasma proteins were more affected by degradation processes at +4°C compared to the other temperatures analysed. However, we founded that numerous protein spots (vitamin D binding protein, alpha-1-antitrypsin, serotransferrin, apoplipoprotein A-I, apolipoprotein E, haptoglobin and complement factor B) decrease in abundance with increasing temperature up to 4°C, but at room temperature their intensity mean values are similar to those of time zero and -80°C. We hypothesize that these proteins are labile at 4°C, but at the same time they are stable at room temperature (20-25°C). Furthermore we have grouped the proteins based on their different sensitivity to the storage temperature. Spots of serum albumin, fibrinogen gamma chain and haptoglobin are more resistant to the higher temperatures tested, as they have undergone changes in abundance only at room temperature; conversely, other spots of serum albumin, fibrinogen beta chain and serotransferrin are more labile as they have undergone changes in abundance at all temperatures except at -80°C. Conclusions Although there are many studies concerning protein stability of clinical samples during storage these findings may help to provide a better understanding of the changes of proteins induced by storage temperature.
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Affiliation(s)
- Sara Pasella
- Biochimica Clinica e Biologia Molecolare Clinica, Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy.
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Kumar V, Calamaras TD, Haeussler D, Colucci WS, Cohen RA, McComb ME, Pimentel D, Bachschmid MM. Cardiovascular redox and ox stress proteomics. Antioxid Redox Signal 2012; 17:1528-59. [PMID: 22607061 PMCID: PMC3448941 DOI: 10.1089/ars.2012.4706] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
SIGNIFICANCE Oxidative post-translational modifications (OPTMs) have been demonstrated as contributing to cardiovascular physiology and pathophysiology. These modifications have been identified using antibodies as well as advanced proteomic methods, and the functional importance of each is beginning to be understood using transgenic and gene deletion animal models. Given that OPTMs are involved in cardiovascular pathology, the use of these modifications as biomarkers and predictors of disease has significant therapeutic potential. Adequate understanding of the chemistry of the OPTMs is necessary to determine what may occur in vivo and which modifications would best serve as biomarkers. RECENT ADVANCES By using mass spectrometry, advanced labeling techniques, and antibody identification, OPTMs have become accessible to a larger proportion of the scientific community. Advancements in instrumentation, database search algorithms, and processing speed have allowed MS to fully expand on the proteome of OPTMs. In addition, the role of enzymatically reversible OPTMs has been further clarified in preclinical models. CRITICAL ISSUES The identification of OPTMs suffers from limitations in analytic detection based on the methodology, instrumentation, sample complexity, and bioinformatics. Currently, each type of OPTM requires a specific strategy for identification, and generalized approaches result in an incomplete assessment. FUTURE DIRECTIONS Novel types of highly sensitive MS instrumentation that allow for improved separation and detection of modified proteins and peptides have been crucial in the discovery of OPTMs and biomarkers. To further advance the identification of relevant OPTMs in advanced search algorithms, standardized methods for sample processing and depository of MS data will be required.
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Affiliation(s)
- Vikas Kumar
- Vascular Biology Section, Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA 02118, USA
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19
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Snégaroff J, Bouchez I, Smaali MEA, Pecquet C, Raison-Peyron N, Jolivet P, Laurière M. Barley γ3-hordein: glycosylation at an atypical site, disulfide bridge analysis, and reactivity with IgE from patients allergic to wheat. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2012; 1834:395-403. [PMID: 22885023 DOI: 10.1016/j.bbapap.2012.07.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Revised: 07/27/2012] [Accepted: 07/28/2012] [Indexed: 10/28/2022]
Abstract
Post translational modifications of a seed storage protein, barley γ3-hordein, were determined using immunochemical and mass spectrometry methods. IgE reactivity towards this protein was measured using sera from patients diagnosed with allergies to wheat. N-glycosylation was found at an atypical Asn-Leu-Cys site. The observed glycan contains xylose. This indicates that at least some γ3-hordein molecules trafficked through the Golgi apparatus. Disulfide bridges in native γ3-hordein were almost the same as those found in wheat γ46-gliadin, except the bridge involving the cysteine included in the glycosylation site. IgE reacted more strongly towards the recombinant than the natural γ3-hordein protein. IgE binding to γ3-hordein increased when the protein sample was reduced. Glycosylation and disulfide bridges therefore decrease epitope accessibility. Thus the IgE from patients sensitized to wheat cross-react with γ3-hordein due to sequence homology with wheat allergens rather than through shared carbohydrate determinants.
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Affiliation(s)
- Jacques Snégaroff
- INRA, UMR1318, Institut Jean-Pierre Bourgin, RD10, F-78000 Versailles, France
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20
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Rivera-Burgos D, Regnier FE. Native protein proteolysis in an immobilized enzyme reactor as a function of temperature. Anal Chem 2012; 84:7021-8. [PMID: 22845770 DOI: 10.1021/ac301114m] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Trypsin concentration and the unmasking of cleavage sites in proteins play important roles in the stoichiometry of peptide production and the number of limit peptides generated during proteolysis. The hypothesis explored in this work was that native proteins could be digested and identified without disulfide reduction by (i) enhancing the unmasking of cleavage sites through elevated reaction temperatures and (ii) increasing trypsin concentration by use of an immobilized enzyme reactor (IMER). Transferrin was chosen as a model protein for these studies on the basis of its resistance to trypsin digestion. Results from this study showed greater than 70% sequence coverage in the peptides identified when nonreduced transferrin was digested at 60 °C. Large numbers of missed cleavages were observed from specific regions in proteins. Proteolysis appeared to start at a small number of high frequency cleavage sites in the cases of both reduced and nonreduced transferrin. Although approximately the same number of peptides were obtained from both structural forms of transferrin, the location of high frequency cleavage sites and the peptides produced were very different. Results from this study suggest that the location of initial cleavage sites along with the path of subsequent digestion depends strongly on the type of treatment used to open protein structures up for proteolysis.
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Affiliation(s)
- Dinelia Rivera-Burgos
- Department of Chemistry, 560 Oval Drive, Purdue University, West Lafayette, Indiana 47906, USA
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21
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Tuzimski T. Application of different modes of thin-layer chromatography and mass spectrometry for the separation and detection of large and small biomolecules. J Chromatogr A 2011; 1218:8799-812. [PMID: 22055526 DOI: 10.1016/j.chroma.2011.10.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2011] [Revised: 09/02/2011] [Accepted: 10/12/2011] [Indexed: 11/28/2022]
Abstract
Biomolecules are widespread throughout the world. A biomolecule is any organic molecule produced by a living organism, including large polymeric molecules such as proteins, polysaccharides and nucleic acids. Many sample preparation techniques are used in biomolecule analysis; the method selected depends on the complexity of the sample, the nature of the matrix and the analytes, and the analytical technique available. This review covers the current state of knowledge on thin-layer chromatography and mass spectrometry for qualitative analysis of biomolecules. In the first part of the paper the reader will gain useful information to avoid some problems about performing various modes of thin-layer chromatography combined with mass spectrometry experiments and in the second part he will find useful information for application of these techniques for separation, detection, and qualitative investigation of structures and quantitative determination of biomolecules such as proteins, peptides, oligonucleotides, amino acids, DNA, RNA, and lipids.
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Affiliation(s)
- Tomasz Tuzimski
- Department of Physical Chemistry, Chair of Chemistry, Faculty of Pharmacy with Medical Analytics Division, Medical University of Lublin, 4A Chodźki Street, 20-093 Lublin, Poland.
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22
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Millón MBB, Delgado MA, Azar NB, Guelbert N, Sturiale L, Garozzo D, Matthijs G, Jaeken J, de Kremer RD, Asteggiano CG. Two Argentinean Siblings with CDG-Ix: A Novel Type of Congenital Disorder of Glycosylation? JIMD Rep 2011; 1:65-72. [PMID: 23430830 DOI: 10.1007/8904_2011_18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Revised: 02/07/2011] [Accepted: 02/21/2011] [Indexed: 01/16/2023] Open
Abstract
Congenital disorders of glycosylation (CDG) are genetic diseases caused by abnormal protein and lipid glycosylation. In this chapter, we report the clinical, biochemical, and molecular findings in two siblings with an unidentified CDG (CDG-Ix). They are the first and the third child of healthy consanguineous Argentinean parents. Patient 1 is now a 11-year-old girl, and patient 2 died at the age of 4 months. Their clinical picture involved liver dysfunction in the neonatal period, psychomotor retardation, microcephaly, seizures, axial hypotonia, feeding difficulties, and hepatomegaly. Patient 1 also developed strabismus and cataract. They showed a type 1 pattern of serum sialotransferrin. Enzymatic analysis for phosphomannomutase and phosphomannose isomerase in leukocytes and fibroblasts excluded PMM2-CDG and MPI-CDG. Lipid-linked oligosaccharide (LLO) analysis showed a normal profile. Therefore, this result could point to a deficiency in the dolichol metabolism. In this context, ALG8-CDG, DPAGT1-CDG, and SRD5A3-CDG were analyzed and no defects were identified. In conclusion, we could not identify the genetic deficiency in these patients yet. Further studies are underway to identify the basic defect in them, taking into account the new CDG types that have been recently described.
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Affiliation(s)
- M B Bistué Millón
- Centro de Estudio Metabolopatías Congénitas (CEMECO), Universidad Nacional de Córdoba, Hospital de Niños de la Santísima Trinidad, Ferroviarios 1250, CP X5014AKN, Cordoba, Argentina
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23
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Kaneshiro K, Fukuyama Y, Iwamoto S, Sekiya S, Tanaka K. Highly Sensitive MALDI Analyses of Glycans by a New Aminoquinoline-Labeling Method Using 3-Aminoquinoline/α-Cyano-4-hydroxycinnamic Acid Liquid Matrix. Anal Chem 2011; 83:3663-7. [DOI: 10.1021/ac103203v] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Kaoru Kaneshiro
- Koichi Tanaka Mass Spectrometry Research Laboratory and Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Yuko Fukuyama
- Koichi Tanaka Mass Spectrometry Research Laboratory and Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Shinichi Iwamoto
- Koichi Tanaka Mass Spectrometry Research Laboratory and Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Sadanori Sekiya
- Koichi Tanaka Mass Spectrometry Research Laboratory and Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory and Koichi Tanaka Laboratory of Advanced Science and Technology, Shimadzu Corporation, 1, Nishinokyo-Kuwabaracho Nakagyo-ku, Kyoto 604-8511, Japan
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24
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Gross JH. Matrix-Assisted Laser Desorption/Ionization. Mass Spectrom (Tokyo) 2011. [DOI: 10.1007/978-3-642-10711-5_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
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25
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Rosenqvist H, Ye J, Jensen ON. Analytical strategies in mass spectrometry-based phosphoproteomics. Methods Mol Biol 2011; 753:183-213. [PMID: 21604124 DOI: 10.1007/978-1-61779-148-2_13] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Phosphoproteomics, the systematic study of protein phosphorylation events and cell signaling networks in cells and tissues, is a rapidly evolving branch of functional proteomics. Current phosphoproteomics research provides a large toolbox of strategies and protocols that may assist researchers to reveal key regulatory events and phosphorylation-mediated processes in the cell and in whole organisms. We present an overview of sensitive and robust analytical methods for phosphopeptide analysis, including calcium phosphate precipitation and affinity enrichment methods such as IMAC and TiO(2). We then discuss various tandem mass spectrometry approaches for phosphopeptide sequencing and quantification, and we consider aspects of phosphoproteome data analysis and interpretation. Efficient integration of these stages of phosphoproteome analysis is highly important to ensure a successful outcome of large-scale experiments for studies of phosphorylation-mediated protein regulation.
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Affiliation(s)
- Heidi Rosenqvist
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow G4 0RE, Scotland, UK
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26
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Osiri JK, Shadpour H, Witek MA, Soper SA. Integrated multifunctional microfluidics for automated proteome analyses. Top Curr Chem (Cham) 2011; 304:261-94. [PMID: 21678138 DOI: 10.1007/128_2011_152] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Proteomics is a challenging field for realizing totally integrated microfluidic systems for complete proteome processing due to several considerations, including the sheer number of different protein types that exist within most proteomes, the large dynamic range associated with these various protein types, and the diverse chemical nature of the proteins comprising a typical proteome. For example, the human proteome is estimated to have >10(6) different components with a dynamic range of >10(10). The typical processing pipeline for proteomics involves the following steps: (1) selection and/or extraction of the particular proteins to be analyzed; (2) multidimensional separation; (3) proteolytic digestion of the protein sample; and (4) mass spectral identification of either intact proteins (top-down proteomics) or peptide fragments generated from proteolytic digestions (bottom-up proteomics). Although a number of intriguing microfluidic devices have been designed, fabricated and evaluated for carrying out the individual processing steps listed above, work toward building fully integrated microfluidic systems for protein analysis has yet to be realized. In this chapter, information will be provided on the nature of proteomic analysis in terms of the challenges associated with the sample type and the microfluidic devices that have been tested to carry out individual processing steps. These include devices such as those for multidimensional electrophoretic separations, solid-phase enzymatic digestions, and solid-phase extractions, all of which have used microfluidics as the functional platform for their implementation. This will be followed by an in-depth review of microfluidic systems, which are defined as units possessing two or more devices assembled into autonomous systems for proteome processing. In addition, information will be provided on the challenges involved in integrating processing steps into a functional system and the approaches adopted for device integration. In this chapter, we will focus exclusively on the front-end processing microfluidic devices and systems for proteome processing, and not on the interface technology of these platforms to mass spectrometry due to the extensive reviews that already exist on these types of interfaces.
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Affiliation(s)
- John K Osiri
- Department of Chemistry, Louisiana State University, Baton Rouge, LA 70817, USA
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27
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Novotna L, Emmerova T, Horak D, Kucerova Z, Ticha M. Iminodiacetic acid-modified magnetic poly(2-hydroxyethyl methacrylate)-based microspheres for phosphopeptide enrichment. J Chromatogr A 2010; 1217:8032-40. [DOI: 10.1016/j.chroma.2010.08.058] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2010] [Revised: 08/06/2010] [Accepted: 08/23/2010] [Indexed: 11/25/2022]
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Abstract
Abstract
Immunophenotyping by flow cytometry or immunohistochemistry is a clinical standard procedure for diagnosis, classification, and monitoring of hematologic malignancies. Antibody-based cell surface phenotyping is commonly limited to cell surface proteins for which specific antibodies are available and the number of parallel measurements is limited. The resulting limited knowledge about cell surface protein markers hampers early clinical diagnosis and subclassification of hematologic malignancies. Here, we describe the mass spectrometry based phenotyping of 2 all-trans retinoic acid treated acute myeloid leukemia model systems at an unprecedented level to a depth of more than 500 membrane proteins, including 137 bona fide cell surface exposed CD proteins. This extensive view of the leukemia surface proteome was achieved by developing and applying new implementations of the Cell Surface Capturing (CSC) technology. Bioinformatic and hierarchical cluster analysis showed that the applied strategy reliably revealed known differentiation-induced abundance changes of cell surface proteins in HL60 and NB4 cells and it also identified cell surface proteins with very little prior information. The extensive and quantitative analysis of the cell surface protein landscape from a systems biology perspective will be most useful in the clinic for the improved subclassification of hematologic malignancies and the identification of new drug targets.
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29
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Gou LT, Tong AP, Yan F, Yuan Z, He F, Wang W, Zhou Y, Chen LJ, Tang MH, Yang JL. Altered protein-expressing profile in hPNAS4-induced apoptosis in A549 human lung adenocarcinoma cells. J Cell Biochem 2010; 108:1211-9. [PMID: 19795389 DOI: 10.1002/jcb.22353] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Human PNAS4 (hPNAS4) is a recently identified pro-apoptosis gene, which is able to induce apoptosis in A549 human lung adenocarcinoma cells following its overexpression. In this work, we investigated the changes of protein profile in hPNAS4-induced apoptosis in A549 cells through proteomic strategy consisting of two-dimensional electrophoresis (2-DE) coupled with MALDI-Q-TOF mass spectrometry. A total of 20 different proteins with more than 3.0-fold change in expression, including 5 up-regulated and 15 down-regulated proteins were successfully identified by database search. The mRNA transcription levels of the different proteins were further examined by RT-PCT. Functional analyses showed these different proteins are involved in diverse biological processes including metabolism, proteolysis, signal transduction, apoptosis, and redox regulation. Two essential apoptosis-associated protein, annexin A1 and prothymosin alpha, were confirmed by Western blot and showed consistent changes with proteomic detection. Our data provide molecular evidence and possible associated pathway in hPNAS4-induced apoptosis through proteomic strategy, which should be contributed to further investigation on biological function of hPNAS4.
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Affiliation(s)
- Lan-Tu Gou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, West China Medical School, Sichuan University, Chengdu 610041, Sichuan Province, China
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30
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Chang YC, Huang CN, Lin CH, Chang HC, Wu CC. Mapping protein cysteine sulfonic acid modifications with specific enrichment and mass spectrometry: An integrated approach to explore the cysteine oxidation. Proteomics 2010; 10:2961-71. [DOI: 10.1002/pmic.200900850] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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31
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Yan J, Li X, Yu L, Jin Y, Zhang X, Xue X, Ke Y, Liang X. Selective enrichment of glycopeptides/phosphopeptides using porous titania microspheres. Chem Commun (Camb) 2010; 46:5488-90. [PMID: 20442969 DOI: 10.1039/c000094a] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Titanium dioxide (TiO(2)) microspheres synthesized by sol-gel method showed high affinity to glycopeptides and were successfully used for simultaneous enrichment of glycopeptides and phosphopeptides.
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Affiliation(s)
- Jingyu Yan
- Key Lab of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Science, 457 Zhongshan Road, Dalian 116023, China
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32
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Wu Y, Mechref Y, Klouckova I, Mayampurath A, Novotny MV, Tang H. Mapping site-specific protein N-glycosylations through liquid chromatography/mass spectrometry and targeted tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:965-972. [PMID: 20209665 DOI: 10.1002/rcm.4474] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Glycosylation is one of the most common posttranslational modifications (PTMs) of proteins, the characterization of which is commonly achieved through proteomic protocol, involving trypsin digestion followed by liquid chromatography/tandem mass spectrometry (LC/MS/MS). However, it is often not possible to characterize all glycopeptides in a complex sample because of the high complexity of glycoproteomic samples, and the relative lower abundances of glycopeptides in comparison to the unmodified peptides. We present here a targeted MS/MS analysis approach, which utilizes a previously developed computational tool, GlyPID, to guide multiple experiments, thus permitting a complete characterization of all N-glycosylation sites of glycoproteins present in a complex sample. We have tested our approach using model glycoproteins analyzed by high-resolution LTQ-FT MS. The results demonstrate a potential use of our method for a high-throughput characterization of complex mixtures of glycosylated proteins.
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Affiliation(s)
- Yin Wu
- School of Informatics and Computing, Indiana University, Bloomington, IN 47408, USA
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Advance of Peptide Detectability Prediction on Mass Spectrometry Platform in Proteomics. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.3724/sp.j.1096.2010.00286] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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34
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Kwon KH. Analytical methods for proteome data obtained from SDS-PAGE multi-dimensional separation and mass spectrometry. J Anal Sci Technol 2010. [DOI: 10.5355/jast.2010.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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XU CM, ZHANG JY, LIU H, SUN HC, ZHU YP, XIE HW. Advance of Peptide Detectability Prediction on Mass Spectrometry Platform in Proteomics. CHINESE JOURNAL OF ANALYTICAL CHEMISTRY 2010. [DOI: 10.1016/s1872-2040(09)60023-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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36
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Heal WP, Tate EW. Getting a chemical handle on proteinpost-translational modification. Org Biomol Chem 2010; 8:731-8. [DOI: 10.1039/b917894e] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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37
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Songping L. Protocols for peptidomic analysis of spider venoms. Methods Mol Biol 2010; 615:75-85. [PMID: 20013201 DOI: 10.1007/978-1-60761-535-4_6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Spider venom contains a complex mixture of components with a large range of molecular masses (0.1-60 kDa) exhibiting a diverse array of actions. Most of these components are proteinaceous molecules - biologically active proteins and peptides. Proteomics profiling of spider venoms (the components with MW >10 kDa) could be achieved through conventional 2-DE-based proteomics methods combined with MS or MS/MS detection. Peptidomic profiling (of the components with MW below ~10 kDa) is usually achieved through off-line separation by a combination of ion-exchange and reverse-phase chromatography, and it relies more heavily on de novo sequencing by Edman degradation or MS/MS for peptide identification.
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Affiliation(s)
- Liang Songping
- College of Life Sciences, Hunan Normal University, Changsha, China
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38
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Abstract
The review describes methods of de novo sequencing of peptides by mass spectrometry. De novo methods utilize computational approaches to deduce the sequence or partial sequence of peptides directly from the experimental MS/MS spectra. The concepts behind a number of de novo sequencing methods are discussed. The other approach to identify peptides by tandem mass spectrometry is to match the fragment ions with virtual peptide ions generated from a genomic or protein database. De novo methods are essential to identify proteins when the genomes are not known but they are also extremely useful even when the genomes are known since they are not affected by errors in a search database. Another advantage of de novo methods is that the partial sequence can be used to search for posttranslation modifications or for the identification of mutations by homology based software.
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Affiliation(s)
- Christopher Hughes
- Department of Biochemistry, University of Western Ontario, London, ON, Canada
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Mandal N, Heegaard S, Prause JU, Honoré B, Vorum H. Ocular proteomics with emphasis on two-dimensional gel electrophoresis and mass spectrometry. Biol Proced Online 2009; 12:56-88. [PMID: 21406065 PMCID: PMC3055252 DOI: 10.1007/s12575-009-9019-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2009] [Accepted: 09/28/2009] [Indexed: 01/30/2023] Open
Abstract
The intention of this review is to provide an overview of current methodologies employed in the rapidly developing field of ocular proteomics with emphasis on sample preparation, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) and mass spectrometry (MS). Appropriate sample preparation for the diverse range of cells and tissues of the eye is essential to ensure reliable results. Current methods of protein staining for 2D-PAGE, protein labelling for two-dimensional difference gel electrophoresis, gel-based expression analysis and protein identification by MS are summarised. The uses of gel-free MS-based strategies (MuDPIT, iTRAQ, ICAT and SILAC) are also discussed. Proteomic technologies promise to shed new light onto ocular disease processes that could lead to the discovery of strong novel biomarkers and therapeutic targets useful in many ophthalmic conditions.
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Affiliation(s)
- Nakul Mandal
- Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
- Department of Medical Biochemistry, Aarhus University, Aarhus, Denmark
| | - Steffen Heegaard
- Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Jan Ulrik Prause
- Eye Pathology Section, Department of Neuroscience and Pharmacology, University of Copenhagen, Copenhagen, Denmark
| | - Bent Honoré
- Department of Medical Biochemistry, Aarhus University, Aarhus, Denmark
| | - Henrik Vorum
- Department of Medical Biochemistry, Aarhus University, Aarhus, Denmark
- Department of Ophthalmology, Aalborg Hospital, Aarhus University Hospital, Aalborg, Denmark
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40
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Wagner V, Gessner G, Mittag M. Functional Proteomics: A Promising Approach to Find Novel Components of the Circadian System. Chronobiol Int 2009; 22:403-15. [PMID: 16076645 DOI: 10.1081/cbi-200062348] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
In the postgenome era, the analysis of entire subproteomes in correlation with their function has emerged due to high throughput technologies. Early approaches have been initiated to identify novel components of the circadian system. For example, in the marine dinoflagellate Lingulodinium polyedra, a chronobiological proteome assay was performed, which resulted in the identification of already known circadian expressed proteins as well as novel temporal controlled proteins involved in metabolic pathways. In the green alga Chlamydomonas reinhardtii, two circadian expressed proteins (a protein disulfide isomerase and a tetratricopeptide repeat protein) were identified by functional proteomics. Also, the first hints of temporal control within chloroplast proteins of Arabidopsis thaliana were identified by proteome analysis.
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Affiliation(s)
- Volker Wagner
- Institut für Allgemeine Botanik, Friedrich-Schiller-Universität-Jena, Germany
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41
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Root BE, Zhang B, Barron AE. Size-based protein separations by microchip electrophoresis using an acid-labile surfactant as a replacement for SDS. Electrophoresis 2009; 30:2117-22. [DOI: 10.1002/elps.200800771] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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42
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Rosenfeld H, Lassen S, Prange A. Characterization of Haptoglobin in the Blood Plasma of Harbor Seals (Phoca vitulina). J Proteome Res 2009; 8:2923-32. [DOI: 10.1021/pr900035s] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Henning Rosenfeld
- GKSS Research Centre, Institute for Coastal Research, Department for Marine Bioanalytical Chemistry, Max-Planck-Strasse 1, D-21502 Geesthacht, Germany
| | - Stephan Lassen
- GKSS Research Centre, Institute for Coastal Research, Department for Marine Bioanalytical Chemistry, Max-Planck-Strasse 1, D-21502 Geesthacht, Germany
| | - Andreas Prange
- GKSS Research Centre, Institute for Coastal Research, Department for Marine Bioanalytical Chemistry, Max-Planck-Strasse 1, D-21502 Geesthacht, Germany
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43
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Barone R, Sturiale L, Garozzo D. Mass spectrometry in the characterization of human genetic N-glycosylation defects. MASS SPECTROMETRY REVIEWS 2009; 28:517-542. [PMID: 18844296 DOI: 10.1002/mas.20201] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Human genetic diseases that affect N-glycosylation result from the defective synthesis of the N-linked sugar moiety (glycan) of glycoproteins. The role of glycans for proper protein folding and biological functions is illustrated in the variety and severity of clinical manifestations shared by congenital disorders of glycosylation (CDG). This family of inherited metabolic disorders includes defects in the assembly of the oligosaccharide precursor that lead to an under-occupancy of N-glycosylation sites (CDG-I), and defects of glycan remodeling (CDG-II). Mass spectrometry constitutes a key tool for characterization of CDG-I defects by mass resolution of native protein glycoforms that differ for glycosylation-site occupancy. Glycan MS analyses in CDG-II is mandatory to detect whenever possible a repertoire of structures to pinpoint candidate enzymes and genes responsible for the abnormal N-glycan synthesis. In this manuscript, we review the MS applications in the area of CDG and related disorders with a special emphasis on those techniques that have been already applied or might become functional for diagnosis, characterization, and treatment monitoring in some specific conditions.
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Affiliation(s)
- Rita Barone
- Institute of Chemistry and Technology of Polymers, CNR, Catania, Italy
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44
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Yu YQ, Fournier J, Gilar M, Gebler JC. Phosphopeptide enrichment using microscale titanium dioxide solid phase extraction. J Sep Sci 2009; 32:1189-99. [DOI: 10.1002/jssc.200800652] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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45
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Perdivara I, Deterding LJ, Cozma C, Tomer KB, Przybylski M. Glycosylation profiles of epitope-specific anti-beta-amyloid antibodies revealed by liquid chromatography-mass spectrometry. Glycobiology 2009; 19:958-70. [PMID: 19318519 DOI: 10.1093/glycob/cwp038] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Alzheimer's disease (AD) is the most prevalent form of age-related neurodementia. The accumulation of beta-amyloid polypeptide (Abeta) in brain is generally believed to be a key event in AD. The recent discovery of physiological beta-amyloid autoantibodies represents a promising perspective for treatment and early diagnosis of AD. The mechanisms by which natural beta-amyloid autoantibodies prevent neurodegeneration are currently unknown. The aim of the present study was to analyze the N-linked glycosylation of a plaque-specific, monoclonal antibody (clone 6E10) relevant for immunotherapy of AD, in comparison with the glycosylation pattern of an Abeta autoantibody isolated from an IgG source. Liquid chromatography in combination with tandem mass spectrometry was used to analyze the glycopeptides generated by enzymatic degradation of the antibodies reduced and alkylated heavy chains. The oligosaccharide pattern of the 6E10 antibody shows primarily core-fucosylated biantennary complex structures and, to a low extent, tri- and tetragalactosyl glycoforms, with or without terminal sialic acids. The glycans associated with the serum anti-Abeta autoantibodies are of the complex, biantennary-type, fucosylated at the first N-acetyl glucosamine residue of the trimannosyl chitobiose core and contain zero to two galactose residues, and zero to one terminal sialic acid, with or without bisecting N-acetyl glucosamine. Glycosylation analysis of the Abeta-autoantibody performed at the peptide level revealed all four human IgG subclasses, with IgG(1) and IgG(2) as the dominant subclasses.
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Affiliation(s)
- Irina Perdivara
- Department of Chemistry, Laboratory of Analytical Chemistry and Biopolymer Structure Analysis, University of Konstanz, 78457 Konstanz, Germany
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Wagner V, Boesger J, Mittag M. Sub-proteome analysis in the green flagellate alga Chlamydomonas reinhardtii. J Basic Microbiol 2009; 49:32-41. [PMID: 19253330 DOI: 10.1002/jobm.200800292] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
In the past years, research on the flagellate unicellular alga Chlamydomonas reinhardtii has entered a new era based on the availability of its complete genome. Since this green alga can be grown relatively easy in a short time-range, sufficient biological material is available to efficiently establish biochemical purification procedures of sub-cellular fractions. Combined with the available genome sequences, this paved the way to perform analysis of specific sub-proteomes by mass spectrometry. In this review, several approaches that provided comprehensive lists of components of certain sub-cellular compartments and their biological relevance will be described. These include proteins of chloroplast ribosomes, of flagella, of the eyespot as well as posttranslational and environmentally modified sub-proteomes. The power of such proteome approaches lies in the identification of novel components and modifications of a given sub-proteome that have not been discovered before. Information is usually gained at a large scale and is very valuable to further understand biological processes of a given cellular sub-compartment. But clearly the arduous task has then to be performed to further analyze the function of specific proteins/genes by RNA interference technology, mutant analyses or methods for identifying the protein interaction network within a sub-proteome.
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Affiliation(s)
- Volker Wagner
- Institute of General Botany and Plant Physiology, Friedrich-Schiller-University Jena, 07743 Jena, Germany
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Xue Y, Wei J, Han H, Zhao L, Cao D, Wang J, Yang X, Zhang Y, Qian X. Application of open tubular capillary columns coated with zirconium phosphonate for enrichment of phosphopeptides. J Chromatogr B Analyt Technol Biomed Life Sci 2009; 877:757-64. [DOI: 10.1016/j.jchromb.2009.02.020] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2008] [Revised: 02/05/2009] [Accepted: 02/05/2009] [Indexed: 11/17/2022]
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48
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YUN D, LU H, WANG H, ZHANG Y, CHENG G, JIN H, YU Y, XU Y, YANG P, HE F. Iterative Non- m/ z-sharing Rule for Confident and Sensitive Protein Identification of Non-shotgun Proteomics. CHINESE J CHEM 2009. [DOI: 10.1002/cjoc.200990053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ek P, Schönberg T, Sjödahl J, Jacksén J, Vieider C, Emmer A, Roeraade J. Electrospray ionization from an adjustable gap between two silicon chips. JOURNAL OF MASS SPECTROMETRY : JMS 2009; 44:171-181. [PMID: 18946877 DOI: 10.1002/jms.1478] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
In this paper, a silicon chip-based electrospray emitter with a variable orifice size is presented. The device consists of two chips, with a thin beam elevating from the center of each of the chips. The chips are individually mounted to form an open gap of a narrow, uniform width between the top areas of the beams. The electrospray is generated at the endpoint of the gap, where the spray point is formed by the very sharp intersection between the crystal planes of the <100> silicon chips. Sample solution is applied to the rear end of the gap from a capillary via a liquid bridge, and capillary forces ensure a spontaneous imbibition of the gap. The sample solution is confined to the gap by means of a hydrophobic treatment of the surfaces surrounding the gap, as well as the geometrical boundaries formed by the edges of the gap walls. The gap width could be adjusted between 1 and 25 microm during electrospray experiments without suffering from any interruption of the electrospray process. Using a peptide sample solution, a shift toward higher charge states and increased signal-to-noise ratios was observed when the gap width was decreased. The limit of detection for the peptide insulin (chain B, oxidized) was approximately 4 nM. We also show a successful interfacing of the electrospray setup with capillary electrophoresis.
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Affiliation(s)
- Patrik Ek
- School of Chemical Science and Engineering, Department of Analytical Chemistry, Royal Institute of Technology, SE-100 44 Stockholm, Sweden
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50
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Bi H, Qiao L, Busnel JM, Devaud V, Liu B, Girault HH. TiO2 Printed Aluminum Foil: Single-Use Film for a Laser Desorption/Ionization Target Plate. Anal Chem 2009; 81:1177-83. [DOI: 10.1021/ac8024448] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Hongyan Bi
- Laboratoire d’Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland, and Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Liang Qiao
- Laboratoire d’Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland, and Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Jean-Marc Busnel
- Laboratoire d’Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland, and Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Valerie Devaud
- Laboratoire d’Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland, and Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Baohong Liu
- Laboratoire d’Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland, and Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P.R. China
| | - Hubert H. Girault
- Laboratoire d’Electrochimie Physique et Analytique, Ecole Polytechnique Fédérale de Lausanne, Station 6, CH-1015 Lausanne, Switzerland, and Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, P.R. China
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