1
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Downard KM. 25 Years Responding to Respiratory and Other Viruses with Mass Spectrometry. Mass Spectrom (Tokyo) 2023; 12:A0136. [PMID: 38053835 PMCID: PMC10694638 DOI: 10.5702/massspectrometry.a0136] [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: 10/12/2023] [Accepted: 10/24/2023] [Indexed: 12/07/2023] Open
Abstract
This review article presents the development and application of mass spectrometry (MS) approaches, developed in the author's laboratory over the past 25 years, to detect; characterise, type and subtype; and distinguish major variants and subvariants of respiratory viruses such as influenza and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). All features make use of matrix-assisted laser desorption ionisation (MALDI) mass maps, recorded for individual viral proteins or whole virus digests. A MALDI-based immunoassay in which antibody-peptide complexes were preserved on conventional MALDI targets without their immobilisation led to an approach that enabled their indirect detection. The site of binding, and thus the molecular antigenicity of viruses, could be determined. The same approach was employed to study antivirals bound to their target viral protein, the nature of the binding residues, and relative binding affinities. The benefits of high-resolution MS were exploited to detect sequence-conserved signature peptides of unique mass within whole virus and single protein digests. These enabled viruses to be typed, subtyped, their lineage determined, and variants and subvariants to be distinguished. Their detection using selected ion monitoring improved analytical sensitivity limits to aid the identification of viruses in clinical specimens. The same high-resolution mass map data, for a wide range of viral strains, were input into a purpose-built algorithm (MassTree) in order to both chart and interrogate viral evolution. Without the need for gene or protein sequences, or any sequence alignment, this phylonumerics approach also determines and displays single-point mutations associated with viral protein evolution in a single-tree building step.
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Affiliation(s)
- Kevin M. Downard
- Infectious Disease Responses Laboratory, Prince of Wales Clinical Research Sciences, Sydney, NSW, Australia
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2
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Walter J, Eludin Z, Drabovich AP. Redefining serological diagnostics with immunoaffinity proteomics. Clin Proteomics 2023; 20:42. [PMID: 37821808 PMCID: PMC10568870 DOI: 10.1186/s12014-023-09431-y] [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: 04/20/2023] [Accepted: 09/19/2023] [Indexed: 10/13/2023] Open
Abstract
Serological diagnostics is generally defined as the detection of specific human immunoglobulins developed against viral, bacterial, or parasitic diseases. Serological tests facilitate the detection of past infections, evaluate immune status, and provide prognostic information. Serological assays were traditionally implemented as indirect immunoassays, and their design has not changed for decades. The advantages of straightforward setup and manufacturing, analytical sensitivity and specificity, affordability, and high-throughput measurements were accompanied by limitations such as semi-quantitative measurements, lack of universal reference standards, potential cross-reactivity, and challenges with multiplexing the complete panel of human immunoglobulin isotypes and subclasses. Redesign of conventional serological tests to include multiplex quantification of immunoglobulin isotypes and subclasses, utilize universal reference standards, and minimize cross-reactivity and non-specific binding will facilitate the development of assays with higher diagnostic specificity. Improved serological assays with higher diagnostic specificity will enable screenings of asymptomatic populations and may provide earlier detection of infectious diseases, autoimmune disorders, and cancer. In this review, we present the major clinical needs for serological diagnostics, overview conventional immunoassay detection techniques, present the emerging immunoassay detection technologies, and discuss in detail the advantages and limitations of mass spectrometry and immunoaffinity proteomics for serological diagnostics. Finally, we explore the design of novel immunoaffinity-proteomic assays to evaluate cell-mediated immunity and advance the sequencing of clinically relevant immunoglobulins.
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Affiliation(s)
- Jonathan Walter
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Zicki Eludin
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada
| | - Andrei P Drabovich
- Division of Analytical and Environmental Toxicology, Department of Laboratory Medicine and Pathology, Faculty of Medicine and Dentistry, University of Alberta, 10-102 Clinical Sciences Building, Edmonton, AB, T6G 2G3, Canada.
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3
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Liu M, Miao D, Qin S, Liu H, Bai Y. Mass tags-based mass spectrometric immunoassay and its bioanalysis applications. Trends Analyt Chem 2022. [DOI: 10.1016/j.trac.2022.116745] [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]
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4
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Xu S, Liu H, Bai Y. Highly sensitive and multiplexed mass spectrometric immunoassay techniques and clinical applications. Anal Bioanal Chem 2022; 414:5121-5138. [PMID: 35165779 DOI: 10.1007/s00216-022-03945-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 01/17/2022] [Accepted: 01/31/2022] [Indexed: 11/29/2022]
Abstract
Immunoassay is one of the most important clinical techniques for disease/pathological diagnosis. Mass spectrometry (MS) has been a popular and powerful readout technique for immunoassays, generating the mass spectrometric immunoassays (MSIAs) with unbeatable channels for multiplexed detection. The sensitivity of MSIAs has been greatly improved with the development of mass labels from element labels to small-molecular labels. MSIAs are also expended from the representative element MS-based methods to the laser-based organic MS and latest ambient MS, improving in both technology and methodology. Various MSIAs present high potential for clinical applications, including the biomarker screening, the immunohistochemistry, and the advanced single-cell analysis. Here, we give an overall review of the development of MSIAs in recent years, highlighting the latest improvement of mass labels and MS techniques for clinical immunoassays.
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Affiliation(s)
- Shuting Xu
- State Key Laboratory of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China.,Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.,Institute of Analytical Food Safety, School of Food Science and Technology, Jiangnan University, Wuxi, 214122, Jiangsu, China
| | - Huwei Liu
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China
| | - Yu Bai
- Beijing National Laboratory for Molecular Sciences, Key Laboratory of Bioorganic Chemistry and Molecular Engineering of Ministry of Education, College of Chemistry and Molecular Engineering, Peking University, Beijing, 100871, China.
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5
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Stevens KG, Pukala TL. Conjugating immunoassays to mass spectrometry: Solutions to contemporary challenges in clinical diagnostics. Trends Analyt Chem 2020; 132:116064. [PMID: 33046944 PMCID: PMC7539833 DOI: 10.1016/j.trac.2020.116064] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Developments in immunoassays and mass spectrometry have independently influenced diagnostic technology. However, both techniques possess unique strengths and limitations, which define their ability to meet evolving requirements for faster, more affordable and more accurate clinical tests. In response, hybrid techniques, which combine the accessibility and ease-of-use of immunoassays with the sensitivity, high throughput and multiplexing capabilities of mass spectrometry are continually being explored. Developments in antibody conjugation methodology have expanded the role of these biomolecules to applications outside of conventional colorimetric assays and histology. Furthermore, the range of different mass spectrometry ionisation and analysis technologies has enabled its successful adaptation as a detection method for numerous clinically relevant immunological assays. Several recent examples of combined mass spectrometry-immunoassay techniques demonstrate the potential of these methods as improved diagnostic tests for several important human diseases. The present challenges are to continue technological advancements in mass spectrometry instrumentation and develop improved bioconjugation methods, which can overcome their existing limitations and demonstrate the clinical significance of these hybrid approaches.
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6
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Ibrahim S, Froehlich BC, Aguilar-Mahecha A, Aloyz R, Poetz O, Basik M, Batist G, Zahedi RP, Borchers CH. Using Two Peptide Isotopologues as Internal Standards for the Streamlined Quantification of Low-Abundance Proteins by Immuno-MRM and Immuno-MALDI. Anal Chem 2020; 92:12407-12414. [DOI: 10.1021/acs.analchem.0c02157] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Sahar Ibrahim
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Bjoern C. Froehlich
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria V8Z 7X8, Canada
| | - Adriana Aguilar-Mahecha
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Raquel Aloyz
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Oliver Poetz
- NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
- SIGNATOPE GmbH, Reutlingen 72770, Germany
| | - Mark Basik
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montréal, Québec H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - Gerald Batist
- Segal Cancer Center, Lady Davis Institute for Medical Research, Sir Mortimer B. Davis Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
| | - René P. Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
| | - Christoph H. Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria V8Z 7X8, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Québec H3T 1E2, Canada
- Center for Computational and Data-Intensive Science and Engineering, Skolkovo Institute of Science and Technology, Moscow 121205, Russia
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7
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Neubert H, Shuford CM, Olah TV, Garofolo F, Schultz GA, Jones BR, Amaravadi L, Laterza OF, Xu K, Ackermann BL. Protein Biomarker Quantification by Immunoaffinity Liquid Chromatography–Tandem Mass Spectrometry: Current State and Future Vision. Clin Chem 2020; 66:282-301. [DOI: 10.1093/clinchem/hvz022] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/12/2019] [Indexed: 12/19/2022]
Abstract
Abstract
Immunoaffinity–mass spectrometry (IA-MS) is an emerging analytical genre with several advantages for profiling and determination of protein biomarkers. Because IA-MS combines affinity capture, analogous to ligand binding assays (LBAs), with mass spectrometry (MS) detection, this platform is often described using the term hybrid methods. The purpose of this report is to provide an overview of the principles of IA-MS and to demonstrate, through application, the unique power and potential of this technology. By combining target immunoaffinity enrichment with the use of stable isotope-labeled internal standards and MS detection, IA-MS achieves high sensitivity while providing unparalleled specificity for the quantification of protein biomarkers in fluids and tissues. In recent years, significant uptake of IA-MS has occurred in the pharmaceutical industry, particularly in the early stages of clinical development, enabling biomarker measurement previously considered unattainable. By comparison, IA-MS adoption by CLIA laboratories has occurred more slowly. Current barriers to IA-MS use and opportunities for expanded adoption are discussed. The path forward involves identifying applications for which IA-MS is the best option compared with LBA or MS technologies alone. IA-MS will continue to benefit from advances in reagent generation, more sensitive and higher throughput MS technologies, and continued growth in use by the broader analytical community. Collectively, the pursuit of these opportunities will secure expanded long-term use of IA-MS for clinical applications.
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8
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Abstract
The apolipoproteins are well known for their roles in both health and disease, as components of plasma lipoprotein particles, such as high-density lipoprotein (HDL), low-density lipoprotein (LDL), very-low-density lipoprotein (VLDL), chylomicrons, and metabolic, vascular- and inflammation-related disorders, such as cardiovascular disease, atherosclerosis, metabolic syndrome, and diabetes. Increasingly, their roles in neurovascular and neurodegenerative disorders are also being elucidated. They play major roles in lipid and cholesterol transport between blood and organs and are, therefore, critical to maintenance and homeostasis of the lipidome, with apolipoprotein-lipid interactions, including cholesterol, fatty acids, triglycerides, phospholipids, and isoprostanes. Further, they have important pleiotropic roles related to aging and longevity, which are largely managed through their many structural variants, including multiple isoforms, and a diversity of post-translational modifications. Consequently, tools for the characterization and accurate quantification of apolipoproteins, including their diverse array of variant forms, are required to understand their salutary and disease related roles. In this chapter we outline three distinct quantitative approaches suitable for targeting apolipoproteins: (1) multiplex immunoassays, (2) mass spectrometric immunoassay, and (3) multiple reaction monitoring, mass spectrometric quantification. We also discuss management of pre-analytical and experimental design variables.
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9
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Lee MJ, Lee ES, Kim TH, Jeon JW, Kim Y, Oh BK. Detection of thioredoxin-1 using ultra-sensitive ELISA with enzyme-encapsulated human serum albumin nanoparticle. NANO CONVERGENCE 2019; 6:37. [PMID: 31814041 PMCID: PMC6900377 DOI: 10.1186/s40580-019-0210-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 10/18/2019] [Indexed: 06/10/2023]
Abstract
Many methods for early diagnosis of the disease use biomarker tests, which measure indicators of biological state in body fluids or blood. However, a limitation of these methods is their low sensitivity to biomarkers. In this study, human serum albumin (HSA) based nanoparticles capable of encapsulating excess horseradish peroxidase (HRP) are synthesized and applied to the development of enzyme-linked immunosorbent assay (ELISA) kit with ultra-high sensitivity. The size of the nanoparticles and the amount of encapsulated enzyme are controlled by varying the synthesis conditions of pH and protein concentration, and the surface of the nanoparticles is modified with protein A (proA) to immobilize antibodies to the nanoparticles by self-assembly. Using the synthesized nanoparticles, the biomarker of breast cancer, thioredoxin-1, can be measured in the range of 10 fM to 100 pM by direct sandwich ELISA, which is 105 times more sensitive than conventional methods.
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Affiliation(s)
- Myeong-Jun Lee
- Department of Chemical & Biomolecular Engineering, Sogang University, Mapo-Gu, Seoul, 04170, South Korea
| | - Eun-Sol Lee
- Department of Chemical & Biomolecular Engineering, Sogang University, Mapo-Gu, Seoul, 04170, South Korea
| | - Tae-Hwan Kim
- Department of Chemical & Biomolecular Engineering, Sogang University, Mapo-Gu, Seoul, 04170, South Korea
| | - Ju-Won Jeon
- Department of Applied Chemistry, Kookmin University, Seoungbuk-Gu, Seoul, 02707, South Korea
| | - YongTae Kim
- George W. Woodruff School of Mechanical Engineering, Wallace H. Coulter Department of Biomedical Engineering, Parker H. Petit Institute for Bioengineering and Bioscience, Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Byung-Keun Oh
- Department of Chemical & Biomolecular Engineering, Sogang University, Mapo-Gu, Seoul, 04170, South Korea.
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10
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A Simple Liquid Crystal-based Aptasensor Using a Hairpin-shaped Aptamer for the Bare-Eye Detection of Carcinoembryonic Antigen. BIOCHIP JOURNAL 2019. [DOI: 10.1007/s13206-019-3406-1] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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11
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Yuan M, Ismaiel O, Mylott W. Hybrid Ligand Binding Immunoaffinity-Liquid Chromatography/Mass Spectrometry for Biotherapeutics and Biomarker Quantitation: How to develop a hybrid LBA-LC-MS/MS method for a protein? ACTA ACUST UNITED AC 2019. [DOI: 10.17145/rss.19.005] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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12
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Jin K, Hu S, Su Y, Yang C, Li J, Ma H. Disposable impedance-based immunosensor array with direct-laser writing platform. Anal Chim Acta 2019; 1067:48-55. [PMID: 31047148 DOI: 10.1016/j.aca.2019.03.053] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2018] [Revised: 03/18/2019] [Accepted: 03/28/2019] [Indexed: 11/28/2022]
Abstract
Immunoassay is a powerful technique to identify and quantify biological molecules, which base on the specificity and selectivity of antigen-antibody interaction. Impedance-based immunosensor has recently shown a great potential to provide rapid and label-free detections. However, the conventional impedance-based immunosensors rely on dedicated electrochemical measurement interface which involves expensive fabrication procedures such as gold deposition and photolithography. In this work, we propose an ultra-low-cost and high processing efficiency platform for impedance-based immunosensing. With effortless operations of direct-laser-writing, an impedance-based immunoassay can be fabricated within 5 min in standard laboratories. The as-fabricated devices have shown great stability and a high device-to-device uniformity. In order to further validate impedance sensing system's performance, finite element analysis and impedance equivalent model analysis were performed. The measured data was consistent with the simulation results. With the standard gold electrodes surface bio-functionalization procedures, the disposable immunoassay can detect anti-IgG down to 10 ng/ml.
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Affiliation(s)
- Kai Jin
- International Joint Research Center for Nanophotonics and Biophotonics, School of Science, Changchun University of Science and Technology, Changchun, Jilin province, 130022, PR China; CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, No.88 Keling Road, Suzhou, Jiangsu province, 215163, PR China
| | - Siyi Hu
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, No.88 Keling Road, Suzhou, Jiangsu province, 215163, PR China
| | - Yang Su
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, No.88 Keling Road, Suzhou, Jiangsu province, 215163, PR China; ACXEL TECH LTD, Unit 184 Cambridge Science Park, Cambridge, CB4 0GA, UK
| | - Chao Yang
- ACXEL TECH LTD, Unit 184 Cambridge Science Park, Cambridge, CB4 0GA, UK
| | - Jinhua Li
- International Joint Research Center for Nanophotonics and Biophotonics, School of Science, Changchun University of Science and Technology, Changchun, Jilin province, 130022, PR China.
| | - Hanbin Ma
- CAS Key Laboratory of Bio-medical Diagnostics, Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, No.88 Keling Road, Suzhou, Jiangsu province, 215163, PR China; ACXEL TECH LTD, Unit 184 Cambridge Science Park, Cambridge, CB4 0GA, UK.
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13
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Abstract
Crosslinking of proteins for their irreversible immobilization on surfaces is a proven and popular method. However, many protocols lead to random orientation and the formation of undefined or even inactive by-products. Most concepts to obtain a more targeted conjugation or immobilization requires the recombinant modification of at least one binding partner, which is often impractical or prohibitively expensive. Here a novel method is presented, which is based on the chemical preactivation of Protein A or G with selected conventional crosslinkers. In a second step, the antibody is added, which is subsequently crosslinked in the Fc part. This leads to an oriented and covalent immobilization of the immunoglobulin with a very high yield. Protocols for Protein A and Protein G with murine and human IgG are presented. This method may be useful for the preparation of columns for affinity chromatography, immunoprecipitation, antibodies conjugated to magnetic particles, permanent and oriented immobilization of antibodies in biosensor systems, microarrays, microtitration plates or any other system, where the loss of antibodies needs to be avoided, and maximum binding capacity is desired. This method is directly applicable even to antibodies in crude cell culture supernatants, raw sera or protein-stabilized antibody preparations without any purification nor enrichment of the IgG. This new method delivered much higher signals as a traditional method and, hence, seems to be preferable in many applications.
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14
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Ruhaak LR, Xu G, Li Q, Goonatilleke E, Lebrilla CB. Mass Spectrometry Approaches to Glycomic and Glycoproteomic Analyses. Chem Rev 2018; 118:7886-7930. [PMID: 29553244 PMCID: PMC7757723 DOI: 10.1021/acs.chemrev.7b00732] [Citation(s) in RCA: 253] [Impact Index Per Article: 42.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycans are produced through a complicated nontemplate driven process involving the competition of enzymes that extend the nascent chain. The large diversity of structures, the variations in polarity of the individual saccharide residues, and the poor ionization efficiencies of glycans all conspire to make the analysis arguably much more difficult than any other biopolymer. Furthermore, the large number of glycoforms associated with a specific protein site makes it more difficult to characterize than any post-translational modification. Nonetheless, there have been significant progress, and advanced separation and mass spectrometry methods have been at its center and the main reason for the progress. While glycomic and glycoproteomic analyses are still typically available only through highly specialized laboratories, new software and workflow is making it more accessible. This review focuses on the role of mass spectrometry and separation methods in advancing glycomic and glycoproteomic analyses. It describes the current state of the field and progress toward making it more available to the larger scientific community.
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Affiliation(s)
- L. Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, 2333 ZA Leiden, The Netherlands
| | - Gege Xu
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Qiongyu Li
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Elisha Goonatilleke
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
| | - Carlito B. Lebrilla
- Department of Chemistry, University of California, Davis, One Shields Avenue, Davis, California 95616, United States
- Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California 95616, United States
- Foods for Health Institute, University of California, Davis, Davis, California 95616, United States
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15
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Zahedi RP, Parker CE, Borchers CH. Immuno-MALDI-TOF-MS in the Clinic. Clin Chem 2018; 64:1271-1272. [PMID: 30018057 DOI: 10.1373/clinchem.2018.292136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 06/25/2018] [Indexed: 01/17/2023]
Affiliation(s)
- René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Carol E Parker
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada; .,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Quebec, Canada.,University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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16
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Van Raemdonck GA, Osbak KK, Van Ostade X, Kenyon CR. Needle lost in the haystack: multiple reaction monitoring fails to detect Treponema pallidum candidate protein biomarkers in plasma and urine samples from individuals with syphilis. F1000Res 2018; 7:336. [PMID: 30519456 PMCID: PMC6248270 DOI: 10.12688/f1000research.13964.2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/04/2018] [Indexed: 12/13/2022] Open
Abstract
Background: Current syphilis diagnostic strategies are lacking a sensitive manner of directly detecting
Treponema pallidum antigens. A diagnostic test that could directly detect
T. pallidum antigens in individuals with syphilis would be of considerable clinical utility, especially for the diagnosis of reinfections and for post-treatment serological follow-up. Methods: In this study, 11 candidate
T. pallidum biomarker proteins were chosen according to their physiochemical characteristics,
T. pallidum specificity and predicted abundance. Thirty isotopically labelled proteotypic surrogate peptides (hPTPs) were synthesized and incorporated into a scheduled multiple reaction monitoring assay. Protein extracts from undepleted/unenriched plasma (N = 18) and urine (N = 4) samples from 18 individuals with syphilis in various clinical stages were tryptically digested, spiked with the hPTP mixture and analysed with a triple quadruple mass spectrometer. Results: No endogenous PTPs corresponding to the eleven candidate biomarkers were detected in any samples analysed. To estimate the Limit of Detection (LOD) of a comparably sensitive mass spectrometer (LTQ-Orbitrap), two dilution series of rabbit cultured purified
T. pallidum were prepared in PBS. Polyclonal anti-
T. pallidum antibodies coupled to magnetic Dynabeads were used to enrich one sample series; no LOD improvement was found compared to the unenriched series. The estimated LOD of MS instruments is 300
T. pallidum/ml in PBS. Conclusions: Biomarker protein detection likely failed due to the low (femtomoles/liter) predicted concentration of
T. pallidum proteins. Alternative sample preparation strategies may improve the detectability of
T. pallidum proteins in biofluids.
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Affiliation(s)
- Geert A Van Raemdonck
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, 2000, Belgium.,Laboratory for Protein Science, Proteomics and Epigenetic Signalling (PPES) and Centre for Proteomics (CFP), University of Antwerp, Wilrijk, 2610, Belgium
| | - Kara K Osbak
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, 2000, Belgium
| | - Xaveer Van Ostade
- Laboratory for Protein Science, Proteomics and Epigenetic Signalling (PPES) and Centre for Proteomics (CFP), University of Antwerp, Wilrijk, 2610, Belgium
| | - Chris R Kenyon
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, 2000, Belgium.,Division of Infectious Diseases and HIV Medicine, University of Cape Town, Cape Town, 7925, South Africa
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17
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Top-down mass spectrometric immunoassay for human insulin and its therapeutic analogs. J Proteomics 2018; 175:27-33. [DOI: 10.1016/j.jprot.2017.08.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 07/24/2017] [Accepted: 08/01/2017] [Indexed: 01/08/2023]
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18
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Gao J, Meyer K, Borucki K, Ueland PM. Multiplex Immuno-MALDI-TOF MS for Targeted Quantification of Protein Biomarkers and Their Proteoforms Related to Inflammation and Renal Dysfunction. Anal Chem 2018; 90:3366-3373. [DOI: 10.1021/acs.analchem.7b04975] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jie Gao
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
| | - Klaus Meyer
- Bevital AS, Jonas Lies veg 87, Laboratory Building, Ninth Floor, 5021 Bergen, Norway
| | - Katrin Borucki
- Institute for Clinical Chemistry and Pathobiochemistry, Otto-von-Guericke University Magdeburg, Leipziger Strasse 44 , 39120 Magdeburg, Germany
| | - Per Magne Ueland
- Department of Clinical Science, University of Bergen, 5021 Bergen, Norway
- Laboratory of Clinical Biochemistry, Haukeland University Hospital, 5021 Bergen, Norway
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Quantitation of saxitoxin in human urine using immunocapture extraction and LC–MS. Bioanalysis 2018; 10:229-239. [DOI: 10.4155/bio-2017-0156] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Aim: An immunomagnetic capture protocol for use with LC–MS was developed for the quantitation of saxitoxin (STX) in human urine. Materials & methods: This method uses monoclonal antibodies coupled to magnetic beads. STX was certified reference material grade from National Research Council, Canada. Analysis was carried out using LC–MS. Results: With an extraction efficiency of 80%, accuracy and precision of 93.0–100.2% and 5.3–12.6%, respectively, and a dynamic range of 1.00–100 ng/ml, the method is well suited to quantify STX exposures based on previously reported cases. Conclusion: Compared with our previously published protocols, this method has improved selectivity, a fivefold increase in sensitivity and uses only a third of the sample volume. This method can diagnose future toxin exposures and may complement the shellfish monitoring programs worldwide.
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Mass Spectrometry Immuno Assay (MSIA™) Streptavidin Disposable Automation Research Tips (D.A.R.T's ®) Antibody Phage Display Biopanning. Methods Mol Biol 2017. [PMID: 29116511 DOI: 10.1007/978-1-4939-7447-4_15] [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: 09/09/2023]
Abstract
Antibody phage display has been widely established as the method of choice to generate monoclonal antibodies with various efficacies post hybridoma technology. This technique is a popular method which takes precedence over ease of methodology, time- and cost-savings with comparable outcomes to conventional methods. Phage display technology manipulates the genome of M13 bacteriophage to display large diverse collection of antibodies that is capable of binding to various targets (nucleic acids, peptides, proteins, and carbohydrates). This subsequently leads to the discovery of target-related antibody binders. There have been several different approaches adapted for antibody phage display over the years. This chapter focuses on the semi-automated phage display antibody biopanning method utilizing the MSIA™ streptavidin D.A.R.T's® system. The system employs the use of electronic multichannel pipettes with predefined programs to carry out the panning process. The method should also be adaptable to larger liquid handling instrumentations for higher throughput.
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Li S, Wan Y, Su Y, Fan C, Bhethanabotla VR. Gold nanoparticle-based low limit of detection Love wave biosensor for carcinoembryonic antigens. Biosens Bioelectron 2017; 95:48-54. [DOI: 10.1016/j.bios.2017.04.012] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2016] [Revised: 03/28/2017] [Accepted: 04/11/2017] [Indexed: 01/06/2023]
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22
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Nedelkov D. Human proteoforms as new targets for clinical mass spectrometry protein tests. Expert Rev Proteomics 2017; 14:691-699. [DOI: 10.1080/14789450.2017.1362337] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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23
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Zhang C, Glaros T, Manicke NE. Targeted Protein Detection Using an All-in-One Mass Spectrometry Cartridge. J Am Chem Soc 2017; 139:10996-10999. [DOI: 10.1021/jacs.7b05571] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Chengsen Zhang
- Department
of Chemistry and Chemical Biology, Indiana University—Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Trevor Glaros
- BioSciences
Division, BioDefense Branch, US Army Edgewood Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
| | - Nicholas E. Manicke
- Department
of Chemistry and Chemical Biology, Indiana University—Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
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24
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Li H, Popp R, Borchers CH. Affinity-mass spectrometric technologies for quantitative proteomics in biological fluids. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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25
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Abstract
Since the sequence of the human genome is complete, the main issue is how to understand the information written in the DNA sequence. Despite numerous genome-wide studies that have already been performed, the challenge to determine the function of genes, gene products, and also their interaction is still open. As changes in the human genome are highly likely to cause pathological conditions, functional analysis is vitally important for human health. For many years there have been a variety of technologies and tools used in functional genome analysis. However, only in the past decade there has been rapid revolutionizing progress and improvement in high-throughput methods, which are ranging from traditional real-time polymerase chain reaction to more complex systems, such as next-generation sequencing or mass spectrometry. Furthermore, not only laboratory investigation, but also accurate bioinformatic analysis is required for reliable scientific results. These methods give an opportunity for accurate and comprehensive functional analysis that involves various fields of studies: genomics, epigenomics, proteomics, and interactomics. This is essential for filling the gaps in the knowledge about dynamic biological processes at both cellular and organismal level. However, each method has both advantages and limitations that should be taken into account before choosing the right method for particular research in order to ensure successful study. For this reason, the present review paper aims to describe the most frequent and widely-used methods for the comprehensive functional analysis.
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Affiliation(s)
- Evelina Gasperskaja
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University Vilnius, Lithuania
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Vilnius University Vilnius, Lithuania
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26
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Biron D, Nedelkov D, Missé D, Holzmuller P. Proteomics and Host–Pathogen Interactions. GENETICS AND EVOLUTION OF INFECTIOUS DISEASES 2017. [PMCID: PMC7149668 DOI: 10.1016/b978-0-12-799942-5.00011-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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27
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Development of a mass spectrometry immunoassay for unambiguous detection of egg allergen traces in wines. Anal Bioanal Chem 2016; 409:1581-1589. [DOI: 10.1007/s00216-016-0099-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2016] [Revised: 11/04/2016] [Accepted: 11/14/2016] [Indexed: 02/05/2023]
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Tran JC, Tran D, Hilderbrand A, Andersen N, Huang T, Reif K, Hotzel I, Stefanich EG, Liu Y, Wang J. Automated Affinity Capture and On-Tip Digestion to Accurately Quantitate in Vivo Deamidation of Therapeutic Antibodies. Anal Chem 2016; 88:11521-11526. [PMID: 27797494 DOI: 10.1021/acs.analchem.6b02766] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Deamidation of therapeutic antibodies may result in decreased drug activity and undesirable changes in pharmacokinetics and immunogenicity. Therefore, it is necessary to monitor the deamidation levels [during storage] and after in vivo administration. Because of the complexity of in vivo samples, immuno-affinity capture is widely used for specific enrichment of the target antibody prior to LC-MS. However, the conventional use of bead-based methods requires large sample volumes and extensive processing steps. Furthermore, with automation difficulties and extended sample preparation time, bead-based approaches may increase artificial deamidation. To overcome these challenges, we developed an automated platform to perform tip-based affinity capture of antibodies from complex matrixes with rapid digestion and peptide elution into 96-well microtiter plates followed by LC-MS analysis. Detailed analyses showed that the new method presents high repeatability and reproducibility with both intra and inter assay CVs < 8%. Using the automated platform, we successfully quantified the levels of deamidation of a humanized monoclonal antibody in cynomolgus monkeys over a time period of 12 weeks after administration. Moreover, we found that deamidation kinetics between in vivo samples and samples stressed in vitro at neutral pH were consistent, suggesting that the in vitro stress test may be used as a method to predict the liability to deamidation of therapeutic antibodies in vivo.
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Affiliation(s)
- John C Tran
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Daniel Tran
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Amy Hilderbrand
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Nisana Andersen
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Tao Huang
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Karin Reif
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Isidro Hotzel
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Eric G Stefanich
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Yichin Liu
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
| | - Jianyong Wang
- Biochemical and Cellular Pharmacology, ‡Protein Analytical Chemistry, §Immunology, ∥Antibody Engineering, and ⊥Preclinical and Translational Pharmacokinetics, Genentech, Inc. , South San Francisco, California 94080-4990, United States
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Downard KM. Indirect study of non-covalent protein complexes by MALDI mass spectrometry: Origins, advantages, and applications of the "intensity-fading" approach. MASS SPECTROMETRY REVIEWS 2016; 35:559-573. [PMID: 26250984 DOI: 10.1002/mas.21480] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2015] [Revised: 07/07/2015] [Accepted: 07/07/2015] [Indexed: 06/04/2023]
Abstract
This review article describes the origins, advantages, and application of an indirect approach with which to study protein and other macromolecular complexes and identify the nature and site of interaction interfaces by means of conventional matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS). First reported in 1999, it involves the detection of ion depletion or the absence of ions associated with a binding partner or domain in the MALDI mass spectrum of a mixture of interacting components compared to that for an untreated control. Later referred to as intensity-fading in some applications, the method offers numerous advantages over the direct detection of protein and other macromolecule complexes by MALDI-MS and even electrospray ionization (ESI) MS. The origins of this indirect method, its development for use with gel-separated components, validation using companion biochemical assays, and application to a range of protein-antibody and protein-drug complexes are reviewed together with software specifically developed to aid with data interpretation. The sensitivity of the approach for revealing how subtle differences in the structure of the binding partners can be detected by MALDI-MS is also demonstrated. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 35:559-573, 2016.
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Azizkhanian I, Trenchevska O, Bashawri Y, Hu J, Koska J, Reaven PD, Nelson RW, Nedelkov D, Yassine HN. Posttranslational modifications of apolipoprotein A-II proteoforms in type 2 diabetes. J Clin Lipidol 2016; 10:808-815. [PMID: 27578111 PMCID: PMC5195850 DOI: 10.1016/j.jacl.2016.03.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Revised: 02/25/2016] [Accepted: 03/01/2016] [Indexed: 01/04/2023]
Abstract
BACKGROUND Apolipoprotein A-II (apoA-II) is the second most abundant protein in high-density lipoprotein particles. However, it exists in plasma in multiple forms. The effect of diabetes on apoA-II proteoforms is not known. OBJECTIVE Our objective was to characterize plasma apoA-II proteoforms in participants with and without type 2 diabetes. METHODS Using a novel mass spectrometric immunoassay, the relative abundance of apoA-II proteoforms was examined in plasma of 30 participants with type 2 diabetes and 25 participants without diabetes. RESULTS Six apoA-II proteoforms (monomer, truncated TQ monomer, truncated Q monomer, dimer, truncated Q dimer, and truncated 2Qs dimer) and their oxidized proteoforms were identified. The ratios of oxidized monomer and all oxidized proteoforms to the native apoA-II were significantly greater in the diabetic group (P = .004 and P = .005, respectively) compared with the nondiabetic group. CONCLUSION The relative abundance of oxidized apoA-II is significantly increased in type 2 diabetes.
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Affiliation(s)
- Ida Azizkhanian
- Department of Medicine, University of Southern California, Los Angeles, CA, USA
| | | | - Yara Bashawri
- Department of Medicine, University of Southern California, Los Angeles, CA, USA; King Fahad Medical City, Riyadh, Saudi Arabia
| | - Jiaqi Hu
- Department of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Juraj Koska
- Department of Medicine, Phoenix VA Health Care System, Phoenix, AZ, USA
| | - Peter D Reaven
- Department of Medicine, Phoenix VA Health Care System, Phoenix, AZ, USA
| | | | | | - Hussein N Yassine
- Department of Medicine, University of Southern California, Los Angeles, CA, USA.
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Trenchevska O, Yassine HN, Borges CR, Nelson RW, Nedelkov D. Development of quantitative mass spectrometric immunoassay for serum amyloid A. Biomarkers 2016; 21:743-751. [PMID: 27308834 DOI: 10.1080/1354750x.2016.1201533] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
OBJECTIVE Proteins can exist as multiple proteoforms in vivo that can have important roles in physiological and pathological states. METHODS We present the development and characterization of mass spectrometric immunoassay (MSIA) for quantitative determination of serum amyloid A (SAA) proteoforms. RESULTS Intra- and inter-day precision revealed CVs <10%. Against existing SAA ELISA, the developed MSIA showed good correlation according to the Altman-Bland plot. Individual concentrations of the SAA proteoforms across a cohort of 170 samples revealed 7 diverse SAA polymorphic types and 12 different proteoforms. CONCLUSION The new SAA MSIA enables parallel analysis of SAA polymorphisms and quantification of all expressed SAA proteoforms, in a high-throughput and time-efficient manner.
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Affiliation(s)
| | - Hussein N Yassine
- b Department of Medicine , University of Southern California , Los Angeles , CA , USA
| | - Chad R Borges
- a The Biodesign Institute, Arizona State University , Tempe , AZ , USA
| | - Randall W Nelson
- a The Biodesign Institute, Arizona State University , Tempe , AZ , USA
| | - Dobrin Nedelkov
- a The Biodesign Institute, Arizona State University , Tempe , AZ , USA
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33
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Trenchevska O, Nelson RW, Nedelkov D. Mass Spectrometric Immunoassays in Characterization of Clinically Significant Proteoforms. Proteomes 2016; 4:proteomes4010013. [PMID: 28248223 PMCID: PMC5217360 DOI: 10.3390/proteomes4010013] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Revised: 03/10/2016] [Accepted: 03/14/2016] [Indexed: 02/07/2023] Open
Abstract
Proteins can exist as multiple proteoforms in vivo, as a result of alternative splicing and single-nucleotide polymorphisms (SNPs), as well as posttranslational processing. To address their clinical significance in a context of diagnostic information, proteoforms require a more in-depth analysis. Mass spectrometric immunoassays (MSIA) have been devised for studying structural diversity in human proteins. MSIA enables protein profiling in a simple and high-throughput manner, by combining the selectivity of targeted immunoassays, with the specificity of mass spectrometric detection. MSIA has been used for qualitative and quantitative analysis of single and multiple proteoforms, distinguishing between normal fluctuations and changes related to clinical conditions. This mini review offers an overview of the development and application of mass spectrometric immunoassays for clinical and population proteomics studies. Provided are examples of some recent developments, and also discussed are the trends and challenges in mass spectrometry-based immunoassays for the next-phase of clinical applications.
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Affiliation(s)
- Olgica Trenchevska
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Randall W Nelson
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
| | - Dobrin Nedelkov
- The Biodesign Institute, Arizona State University, Tempe, AZ 85287, USA.
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Knoop A, Thomas A, Fichant E, Delahaut P, Schänzer W, Thevis M. Qualitative identification of growth hormone-releasing hormones in human plasma by means of immunoaffinity purification and LC-HRMS/MS. Anal Bioanal Chem 2016; 408:3145-53. [PMID: 26879649 PMCID: PMC4830873 DOI: 10.1007/s00216-016-9377-3] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/18/2016] [Accepted: 01/28/2016] [Indexed: 11/24/2022]
Abstract
The use of growth hormone-releasing hormones (GHRHs) is prohibited in sports according to the regulations of the World Anti-Doping Agency (WADA). The aim of the present study was to develop a method for the simultaneous detection of four different GHRHs and respective metabolites from human plasma by means of immunoaffinity purification and subsequent nano-ultrahigh performance liquid chromatography-high resolution/high accuracy (tandem) mass spectrometry. The target analytes included Geref (Sermorelin), CJC-1293, CJC-1295, and Egrifta (Tesamorelin) as well as two metabolites of Geref and CJC-1293, which were captured from plasma samples using a polyclonal GHRH antibody in concert with protein A/G monolithic MSIA™ D.A.R.T.'S® (Disposable Automation Research Tips) prior to separation and detection. The method was fully validated and found to be fit for purpose considering the parameters specificity, linearity, recovery (19-37%), lower limit of detection (<50 pg/mL), imprecision (<20%), and ion suppression/enhancement effects. The analytes' stability and metabolism were elucidated using in vitro and in vivo approaches. EDTA blood samples were collected from rats 2, 4, and 8 h after intravenous administration of GHRH (one compound per test animal). All intact substances were detected for at least 4 h but no anticipated metabolite was confirmed in laboratory rodents' samples; conversely, a Geref metabolite (GHRH3-29) was found in a human plasma sample collected after subcutaneous injection of the drug to a healthy male volunteer. The obtained results demonstrate that GHRHs are successfully detected in plasma using an immunoaffinity-mass spectrometry-based method, which can be applied to sports drug testing samples. Further studies are however required and warranted to account for potential species-related differences in metabolism and elimination of the target analytes.
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Affiliation(s)
- Andre Knoop
- Institute for Biochemistry-Center for Preventive Doping Research, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany
| | - Andreas Thomas
- Institute for Biochemistry-Center for Preventive Doping Research, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany
| | - Eric Fichant
- Laboratoire d'Hormonologie, C.E.R. Groupe-Département Santé, Rue du Point du jour 8, 6900, Marloie, Belgium
| | - Philippe Delahaut
- Laboratoire d'Hormonologie, C.E.R. Groupe-Département Santé, Rue du Point du jour 8, 6900, Marloie, Belgium
| | - Wilhelm Schänzer
- Institute for Biochemistry-Center for Preventive Doping Research, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany
| | - Mario Thevis
- Institute for Biochemistry-Center for Preventive Doping Research, German Sport University Cologne, Am Sportpark Müngersdorf 6, 50933, Cologne, Germany. .,European Monitoring Center for Emerging Doping Agents (EuMoCEDA), Cologne/Bonn, Germany.
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Wu C, Duan J, Liu T, Smith RD, Qian WJ. Contributions of immunoaffinity chromatography to deep proteome profiling of human biofluids. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1021:57-68. [PMID: 26868616 DOI: 10.1016/j.jchromb.2016.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 01/06/2016] [Accepted: 01/08/2016] [Indexed: 02/07/2023]
Abstract
Human biofluids, especially blood plasma or serum, hold great potential as the sources of candidate biomarkers for various diseases; however, the enormous dynamic range of protein concentrations in biofluids represents a significant analytical challenge for detecting promising low-abundance proteins. Over the last decade, various immunoaffinity chromatographic methods have been developed and routinely applied for separating low-abundance proteins from the high- and moderate-abundance proteins, thus enabling much more effective detection of low-abundance proteins. Herein, we review the advances of immunoaffinity separation methods and their contributions to the proteomic applications in human biofluids. The limitations and future perspectives of immunoaffinity separation methods are also discussed.
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Affiliation(s)
- Chaochao Wu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Jicheng Duan
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Richard D Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States.
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Application of streptavidin mass spectrometric immunoassay tips for immunoaffinity based antibody phage display panning. J Microbiol Methods 2016; 120:6-14. [DOI: 10.1016/j.mimet.2015.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/09/2015] [Accepted: 11/09/2015] [Indexed: 11/21/2022]
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37
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Pompach P, Nováková J, Kavan D, Benada O, Růžička V, Volný M, Novák P. Planar Functionalized Surfaces for Direct Immunoaffinity Desorption/Ionization Mass Spectrometry. Clin Chem 2016; 62:270-8. [DOI: 10.1373/clinchem.2015.244004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 08/25/2015] [Indexed: 01/21/2023]
Abstract
Abstract
BACKGROUND
Recent studies show that the haptoglobin phenotype in individuals with diabetes mellitus is an important factor for predicting the risk of myocardial infarction, cardiovascular death, and stroke. Current methods for haptoglobin phenotyping include PCR and gel electrophoresis. A need exists for a reliable method for high-throughput clinical applications. Mass spectrometry (MS) can in principle provide fast phenotyping because haptoglobin α 1 and α 2, which define the phenotype, have different molecular masses. Because of the complexity of the serum matrix, an efficient and fast enrichment technique is necessary for an MS-based assay.
METHODS
MALDI plates were functionalized by ambient ion landing of electrosprayed antihaptoglobin antibody. The array was deposited on standard indium tin oxide slides. Fast immunoaffinity enrichment was performed in situ on the plate, which was further analyzed by MALDI-TOF MS. The haptoglobin phenotype was determined from the spectra by embedded software script.
RESULTS
The MALDI mass spectra showed ion signals of haptoglobin α subunits at m/z 9192 and at m/z 15 945. A cohort of 116 sera was analyzed and the reliability of the method was confirmed by analyzing the identical samples by Western blot. One hundred percent overlap of results between the direct immunoaffinity desorption/ionization MS and Western Blot analysis was found.
CONCLUSIONS
MALDI plates modified by antihaptoglobin antibody using ambient ion landing achieve low nonspecific interactions and efficient MALDI ionization and are usable for quick haptoglobin phenotyping.
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Affiliation(s)
- Petr Pompach
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
- AffiPro, s.r.o., Mratin, Czech Republic
| | - Jana Nováková
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
| | - Daniel Kavan
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
| | - Oldřich Benada
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
| | | | - Michael Volný
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
- AffiPro, s.r.o., Mratin, Czech Republic
| | - Petr Novák
- Institute of Microbiology, v.v.i., Czech Academy of Sciences, Prague, Czech Republic
- Faculty of Science, Charles University in Prague, Prague, Czech Republic
- AffiPro, s.r.o., Mratin, Czech Republic
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The Association of Human Apolipoprotein C-III Sialylation Proteoforms with Plasma Triglycerides. PLoS One 2015; 10:e0144138. [PMID: 26633899 PMCID: PMC4669142 DOI: 10.1371/journal.pone.0144138] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 11/14/2015] [Indexed: 11/19/2022] Open
Abstract
Introduction Apolipoprotein C-III (apoC-III) regulates triglyceride (TG) metabolism. In plasma, apoC-III exists in non-sialylated (apoC-III0a without glycosylation and apoC-III0b with glycosylation), monosialylated (apoC-III1) or disialylated (apoC-III2) proteoforms. Our aim was to clarify the relationship between apoC-III sialylation proteoforms with fasting plasma TG concentrations. Methods In 204 non-diabetic adolescent participants, the relative abundance of apoC-III plasma proteoforms was measured using mass spectrometric immunoassay. Results Compared with the healthy weight subgroup (n = 16), the ratios of apoC-III0a, apoC-III0b, and apoC-III1 to apoC-III2 were significantly greater in overweight (n = 33) and obese participants (n = 155). These ratios were positively correlated with BMI z-scores and negatively correlated with measures of insulin sensitivity (Si). The relationship of apoC-III1 / apoC-III2 with Si persisted after adjusting for BMI (p = 0.02). Fasting TG was correlated with the ratio of apoC-III0a / apoC-III2 (r = 0.47, p<0.001), apoC-III0b / apoC-III2 (r = 0.41, p<0.001), apoC-III1 / apoC-III2 (r = 0.43, p<0.001). By examining apoC-III concentrations, the association of apoC-III proteoforms with TG was driven by apoC-III0a (r = 0.57, p<0.001), apoC-III0b (r = 0.56. p<0.001) and apoC-III1 (r = 0.67, p<0.001), but not apoC-III2 (r = 0.006, p = 0.9) concentrations, indicating that apoC-III relationship with plasma TG differed in apoC-III2 compared with the other proteoforms. Conclusion We conclude that apoC-III0a, apoC-III0b, and apoC-III1, but not apoC- III2 appear to be under metabolic control and associate with fasting plasma TG. Measurement of apoC-III proteoforms can offer insights into the biology of TG metabolism in obesity.
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Duncan MW, Nedelkov D, Walsh R, Hattan SJ. Applications of MALDI Mass Spectrometry in Clinical Chemistry. Clin Chem 2015; 62:134-43. [PMID: 26585930 DOI: 10.1373/clinchem.2015.239491] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 11/02/2015] [Indexed: 02/02/2023]
Abstract
BACKGROUND MALDI-TOF mass spectrometry (MS) is set to make inroads into clinical chemistry because it offers advantages over other analytical platforms. These advantages include low acquisition and operating costs, ease of use, ruggedness, and high throughput. When coupled with innovative front-end strategies and applied to important clinical problems, it can deliver rapid, sensitive, and cost-effective assays. CONTENT This review describes the general principles of MALDI-TOF MS, highlights the unique features of the platform, and discusses some practical methods based upon it. There is substantial potential for MALDI-TOF MS to make further inroads into clinical chemistry because of the selectivity of mass detection and its ability to independently quantify proteoforms. SUMMARY MALDI-TOF MS has already transformed the practice of clinical microbiology and this review illustrates how and why it is now set to play an increasingly important role in in vitro diagnostics in particular, and clinical chemistry in general.
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Affiliation(s)
- Mark W Duncan
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO; Obesity Research Center, College of Medicine, King Saud University, Riyadh 11461, Saudi Arabia;
| | - Dobrin Nedelkov
- Molecular Biomarkers Laboratory, Biodesign Institute, Arizona State University, Tempe, AZ
| | - Ryan Walsh
- Division of Endocrinology, Diabetes & Metabolism, Department of Medicine, School of Medicine, University of Colorado Denver, Anschutz Medical Campus, Aurora, CO
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Boström T, Takanen JO, Hober S. Antibodies as means for selective mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1021:3-13. [PMID: 26565067 DOI: 10.1016/j.jchromb.2015.10.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/15/2015] [Accepted: 10/23/2015] [Indexed: 01/21/2023]
Abstract
For protein analysis of biological samples, two major strategies are used today; mass spectrometry (MS) and antibody-based methods. Each strategy offers advantages and drawbacks. However, combining the two using an immunoenrichment step with MS analysis brings together the benefits of each method resulting in increased sensitivity, faster analysis and possibility of higher degrees of multiplexing. The immunoenrichment can be performed either on protein or peptide level and quantification standards can be added in order to enable determination of the absolute protein concentration in the sample. The combination of immunoenrichment and MS holds great promise for the future in both proteomics and clinical diagnostics. This review describes different setups of immunoenrichment coupled to mass spectrometry and how these can be utilized in various applications.
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Affiliation(s)
- Tove Boström
- School of Biotechnology, Division of Protein Technology, KTH-Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Jenny Ottosson Takanen
- School of Biotechnology, Division of Proteomics and Nanobiotechnology, KTH-Royal Institute ofTechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Sophia Hober
- School of Biotechnology, Division of Protein Technology, KTH-Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden.
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Park MH, Lee MW, Shin YG. Qualification and application of a liquid chromatography-quadrupole time-of-flight mass spectrometric method for the determination of trastuzumab in rat plasma. Biomed Chromatogr 2015; 30:625-31. [DOI: 10.1002/bmc.3606] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Revised: 06/30/2015] [Accepted: 08/24/2015] [Indexed: 11/08/2022]
Affiliation(s)
- Min-Ho Park
- College of Pharmacy; Chungnam National University; Daejeon 305-764 South Korea
| | - Min-Woo Lee
- College of Pharmacy; Chungnam National University; Daejeon 305-764 South Korea
| | - Young G. Shin
- College of Pharmacy; Chungnam National University; Daejeon 305-764 South Korea
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LC–MS-based quantification of intact proteins: perspective for clinical and bioanalytical applications. Bioanalysis 2015; 7:1943-58. [DOI: 10.4155/bio.15.113] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bioanalytical LC–MS for protein quantification is traditionally based on enzymatic digestion of the target protein followed by absolute quantification of a specific signature peptide relative to a stable-isotope labeled analog. The enzymatic digestion, nonetheless, limits rapid method development, sample throughput and turnaround time, and, moreover, makes that essential information regarding the biological function of the intact protein is lost. The recent advancements in high-resolution MS instrumentation and improved sample preparation techniques dedicated to protein clean-up raise the question to what extent LC–MS can be applied for quantitative bioanalysis of intact proteins. This review provides an overview of current and potential applications of LC–MS for intact protein quantification as well as the main limitations and challenges for broad application.
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Trenchevska O, Schaab MR, Nelson RW, Nedelkov D. Development of multiplex mass spectrometric immunoassay for detection and quantification of apolipoproteins C-I, C-II, C-III and their proteoforms. Methods 2015; 81:86-92. [PMID: 25752847 PMCID: PMC4574700 DOI: 10.1016/j.ymeth.2015.02.020] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2014] [Revised: 02/23/2015] [Accepted: 02/27/2015] [Indexed: 01/11/2023] Open
Abstract
The impetus for discovery and evaluation of protein biomarkers has been accelerated by recent development of advanced technologies for rapid and broad proteome analyses. Mass spectrometry (MS)-based protein assays hold great potential for in vitro biomarker studies. Described here is the development of a multiplex mass spectrometric immunoassay (MSIA) for quantification of apolipoprotein C-I (apoC-I), apolipoprotein C-II (apoC-II), apolipoprotein C-III (apoC-III) and their proteoforms. The multiplex MSIA assay was fast (∼ 40 min) and high-throughput (96 samples at a time). The assay was applied to a small cohort of human plasma samples, revealing the existence of multiple proteoforms for each apolipoprotein C. The quantitative aspect of the assay enabled determination of the concentration for each proteoform individually. Low-abundance proteoforms, such as fucosylated apoC-III, were detected in less than 20% of the samples. The distribution of apoC-III proteoforms varied among samples with similar total apoC-III concentrations. The multiplex analysis of the three apolipoproteins C and their proteoforms using quantitative MSIA represents a significant step forward toward better understanding of their physiological roles in health and disease.
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Affiliation(s)
- Olgica Trenchevska
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
| | - Matthew R Schaab
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
| | - Randall W Nelson
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
| | - Dobrin Nedelkov
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States.
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Liang B, Ju Y, Joubert JR, Kaleta EJ, Lopez R, Jones IW, Hall HK, Ratnayaka SN, Wysocki VH, Saavedra SS. Label-free detection and identification of protein ligands captured by receptors in a polymerized planar lipid bilayer using MALDI-TOF MS. Anal Bioanal Chem 2015; 407:2777-89. [PMID: 25694144 PMCID: PMC4417943 DOI: 10.1007/s00216-015-8508-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/10/2015] [Accepted: 01/21/2015] [Indexed: 01/27/2023]
Abstract
Matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) coupled with affinity capture is a well-established method to extract biological analytes from complex samples followed by label-free detection and identification. Many bioanalytes of interest bind to membrane-associated receptors; however, the matrices and high-vacuum conditions inherent to MALDI-TOF MS make it largely incompatible with the use of artificial lipid membranes with incorporated receptors as platforms for detection of captured proteins and peptides. Here we show that cross-linking polymerization of a planar supported lipid bilayer (PSLB) provides the stability needed for MALDI-TOF MS analysis of proteins captured by receptors embedded in the membrane. PSLBs composed of poly(bis-sorbylphosphatidylcholine) (poly(bis-SorbPC)) and doped with the ganglioside receptors GM1 and GD1a were used for affinity capture of the B subunits of cholera toxin, heat-labile enterotoxin, and pertussis toxin. The three toxins were captured simultaneously, then detected and identified by MS on the basis of differences in their molecular weights. Poly(bis-SorbPC) PSLBs are inherently resistant to nonspecific protein adsorption, which allowed selective toxin detection to be achieved in complex matrices (bovine serum and shrimp extract). Using GM1-cholera toxin subunit B as a model receptor-ligand pair, we estimated the minimal detectable concentration of toxin to be 4 nM. On-plate tryptic digestion of bound cholera toxin subunit B followed by MS/MS analysis of digested peptides was performed successfully, demonstrating the feasibility of using the PSLB-based affinity capture platform for identification of unknown, membrane-associated proteins. Overall, this work demonstrates that combining a poly(lipid) affinity capture platform with MALDI-TOF MS detection is a viable approach for capture and proteomic characterization of membrane-associated proteins in a label-free manner.
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Affiliation(s)
- Boying Liang
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | | | - James R. Joubert
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | - Erin J. Kaleta
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | - Rodrigo Lopez
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | - Ian W. Jones
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | - Henry K. Hall
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | - Saliya N. Ratnayaka
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
| | | | - S. Scott Saavedra
- Department of Chemistry and Biochemistry, University of Arizona, 1306 East University Boulevard, Tucson, AZ 85721, USA
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Lesur A, Ancheva L, Kim YJ, Berchem G, van Oostrum J, Domon B. Screening protein isoforms predictive for cancer using immunoaffinity capture and fast LC-MS in PRM mode. Proteomics Clin Appl 2015; 9:695-705. [PMID: 25656350 DOI: 10.1002/prca.201400158] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2014] [Revised: 12/19/2014] [Accepted: 02/02/2015] [Indexed: 01/11/2023]
Abstract
PURPOSE We report an immunocapture strategy to extract proteins known to harbor driver mutations for a defined cancer type before the simultaneous assessment of their mutational status by MS. Such a method bypasses the sensitivity and selectivity issues encountered during the analysis of unfractionated complex biological samples. EXPERIMENTAL DESIGN Fast LC separations using short nanobore columns hyphenated with a high-resolution quadrupole-orbitrap mass spectrometer have been devised to take advantage of fast MS cycle times in conjunction with sharp chromatographic peak widths to accelerate the sample analysis throughput. Such an analytical platform is well suited to analyze simple protein mixtures obtained after immunoaffinity enrichment. RESULTS After establishing the technical performance of the platform, the method was applied to the quantitative profiling of cellular Ras and EGFR protein isoforms, as well as serum amyloid A isoforms in plasma. CONCLUSIONS AND CLINICAL RELEVANCE Immunoaffinity purification combined with fast LC-MS detection for the detection of driver mutations in tissue and tumor biomarkers in plasma samples can assist clinicians to select an optimal therapeutic intervention for patients.
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Affiliation(s)
- Antoine Lesur
- Luxembourg Clinical Proteomics Center (LCP), CRP-Santé, Strassen, Luxembourg
| | - Lina Ancheva
- Luxembourg Clinical Proteomics Center (LCP), CRP-Santé, Strassen, Luxembourg
| | - Yeoun Jin Kim
- Luxembourg Clinical Proteomics Center (LCP), CRP-Santé, Strassen, Luxembourg
| | - Guy Berchem
- Laboratory of Experimental Hemato-Oncology, CRP-Santé, Strassen, Luxembourg.,Centre Hospitalier Luxembourg (CHL), Strassen, Luxembourg
| | - Jan van Oostrum
- Luxembourg Clinical Proteomics Center (LCP), CRP-Santé, Strassen, Luxembourg
| | - Bruno Domon
- Luxembourg Clinical Proteomics Center (LCP), CRP-Santé, Strassen, Luxembourg
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Heegaard NHH, Østergaard O, Bahl JMC, Overgaard M, Beck HC, Rasmussen LM, Larsen MR. Important options available--from start to finish--for translating proteomics results to clinical chemistry. Proteomics Clin Appl 2015; 9:235-52. [PMID: 25472910 DOI: 10.1002/prca.201400137] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2014] [Revised: 11/11/2014] [Accepted: 11/26/2014] [Indexed: 12/20/2022]
Abstract
In the realm of clinical chemistry, the field of clinical proteomics, that is, the application of proteomic methods for understanding mechanisms and enabling diagnosis, prediction, measurement of activity, and treatment response in disease, is first and foremost a discovery and research tool that feeds assay development downstream. Putative new assay candidates generated by proteomics discovery projects compete with well-established assays with known indications, well-described performance, and of known value in specific clinical settings. Careful attention to the many options available in the design, execution, and interpretation of clinical proteomics studies is thus necessary for translation into clinical practice. We here review and discuss important options associated with clinical proteomics endeavors stretching from the planning phases to the final use in clinical chemistry.
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Affiliation(s)
- Niels H H Heegaard
- Department of Clinical Biochemistry, Immunology & Genetics, Statens Serum Institut, Copenhagen, Denmark; Department of Clinical Biochemistry and Pharmacology, Odense University Hospital, Odense, Denmark
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Yassine HN, Trenchevska O, He H, Borges CR, Nedelkov D, Mack W, Kono N, Koska J, Reaven PD, Nelson RW. Serum amyloid a truncations in type 2 diabetes mellitus. PLoS One 2015; 10:e0115320. [PMID: 25607823 PMCID: PMC4301920 DOI: 10.1371/journal.pone.0115320] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2014] [Accepted: 11/21/2014] [Indexed: 12/16/2022] Open
Abstract
Serum Amyloid A (SAA) is an acute phase protein complex consisting of several abundant isoforms. The N- terminus of SAA is critical to its function in amyloid formation. SAA is frequently truncated, either missing an arginine or an arginine-serine dipeptide, resulting in isoforms that may influence the capacity to form amyloid. However, the relative abundance of truncated SAA in diabetes and chronic kidney disease is not known.
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Affiliation(s)
- Hussein N Yassine
- University of Southern California, Los Angeles, CA, United States of America
| | | | - Huijuan He
- University of Southern California, Los Angeles, CA, United States of America
| | - Chad R Borges
- Arizona State University, Tempe, AZ, United States of America
| | - Dobrin Nedelkov
- Arizona State University, Tempe, AZ, United States of America
| | - Wendy Mack
- University of Southern California, Los Angeles, CA, United States of America
| | - Naoko Kono
- University of Southern California, Los Angeles, CA, United States of America
| | - Juraj Koska
- Phoenix VA Health Care System, Phoenix, AZ, United States of America
| | - Peter D Reaven
- Phoenix VA Health Care System, Phoenix, AZ, United States of America
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Lopez MF, Krastins B, Sarracino DA, Byram G, Vogelsang MS, Prakash A, Peterman S, Ahmad S, Vadali G, Deng W, Inglessis I, Wickham T, Feeney K, Dec GW, Palacios I, Buonanno FS, Lo EH, Ning M. Proteomic signatures of serum albumin-bound proteins from stroke patients with and without endovascular closure of PFO are significantly different and suggest a novel mechanism for cholesterol efflux. Clin Proteomics 2015; 12:2. [PMID: 25678897 PMCID: PMC4305391 DOI: 10.1186/1559-0275-12-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2014] [Accepted: 12/23/2014] [Indexed: 01/13/2023] Open
Abstract
BACKGROUND The anatomy of PFO suggests that it can allow thrombi and potentially harmful circulatory factors to travel directly from the venous to the arterial circulation - altering circulatory phenotype. Our previous publication using high-resolution LC-MS/MS to profile protein and peptide expression patterns in plasma showed that albumin was relatively increased in donor samples from PFO-related than other types of ischemic strokes. Since albumin binds a host of molecules and acts as a carrier for lipoproteins, small molecules and drugs, we decided to investigate the albumin-bound proteins (in a similar sample cohort) in an effort to unravel biological changes and potentially discover biomarkers related to PFO-related stroke and PFO endovascular closure. METHODS The method used in this study combined albumin immuno-enrichment with high resolution LC-MS in order to specifically capture and quantify the albumin-bound proteins. Subsequently, we measured cholesterol and HDL in a larger, separate cohort of PFO stroke patients, pre and post closure. RESULTS The results demonstrated that a number of proteins were specifically associated with albumin in samples with and without endovascular closure of the PFO, and that the protein profiles were very different. Eight proteins, typically associated with HDL were common to both sample sets and quantitatively differently abundant. Pathway analysis of the MS results suggested that enhanced cholesterol efflux and reduced lipid oxidation were associated with PFO closure. Measurement of total cholesterol and HDL in a larger cohort of PFO closure samples using a colorimetric assay was consistent with the proteomic predictions. CONCLUSIONS The collective data presented in this study demonstrate that analysis of albumin-bound proteins could provide a valuable tool for biomarker discovery on the effects of PFO endovascular closure. In addition, the results suggest that PFO endovascular closure can potentially have effects on HDL, cholesterol and albumin-bound ApoA-I abundance, therefore possibly providing benefits in cardioprotective functions.
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Affiliation(s)
- Mary F Lopez
- Thermo Scientific BRIMS, 790 Memorial Dr, Cambridge, MA 02139 UK
| | - Bryan Krastins
- Thermo Scientific BRIMS, 790 Memorial Dr, Cambridge, MA 02139 UK
| | | | - Gregory Byram
- Thermo Scientific BRIMS, 790 Memorial Dr, Cambridge, MA 02139 UK
| | | | - Amol Prakash
- Thermo Scientific BRIMS, 790 Memorial Dr, Cambridge, MA 02139 UK
| | - Scott Peterman
- Thermo Scientific BRIMS, 790 Memorial Dr, Cambridge, MA 02139 UK
| | - Shadab Ahmad
- Thermo Scientific BRIMS, 790 Memorial Dr, Cambridge, MA 02139 UK
| | - Gouri Vadali
- Thermo Scientific BRIMS, 790 Memorial Dr, Cambridge, MA 02139 UK
| | - Wenjun Deng
- Clinical Proteomics Research Center and Cardio-Neurology Clinic, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Ignacio Inglessis
- Clinical Proteomics Research Center and Cardio-Neurology Clinic, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Tom Wickham
- Clinical Proteomics Research Center and Cardio-Neurology Clinic, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Kathleen Feeney
- Clinical Proteomics Research Center and Cardio-Neurology Clinic, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - G William Dec
- Clinical Proteomics Research Center and Cardio-Neurology Clinic, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Igor Palacios
- Clinical Proteomics Research Center and Cardio-Neurology Clinic, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Ferdinando S Buonanno
- Clinical Proteomics Research Center and Cardio-Neurology Clinic, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - Eng H Lo
- Clinical Proteomics Research Center and Cardio-Neurology Clinic, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
| | - MingMing Ning
- Clinical Proteomics Research Center and Cardio-Neurology Clinic, Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston, MA USA
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Gregorich ZR, Ge Y. Top-down proteomics in health and disease: challenges and opportunities. Proteomics 2014; 14:1195-210. [PMID: 24723472 DOI: 10.1002/pmic.201300432] [Citation(s) in RCA: 147] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 03/10/2014] [Accepted: 03/24/2014] [Indexed: 01/06/2023]
Abstract
Proteomics is essential for deciphering how molecules interact as a system and for understanding the functions of cellular systems in human disease; however, the unique characteristics of the human proteome, which include a high dynamic range of protein expression and extreme complexity due to a plethora of PTMs and sequence variations, make such analyses challenging. An emerging "top-down" MS-based proteomics approach, which provides a "bird's eye" view of all proteoforms, has unique advantages for the assessment of PTMs and sequence variations. Recently, a number of studies have showcased the potential of top-down proteomics for the unraveling of disease mechanisms and discovery of new biomarkers. Nevertheless, the top-down approach still faces significant challenges in terms of protein solubility, separation, and the detection of large intact proteins, as well as underdeveloped data analysis tools. Consequently, new technological developments are urgently needed to advance the field of top-down proteomics. Herein, we intend to provide an overview of the recent applications of top-down proteomics in biomedical research. Moreover, we will outline the challenges and opportunities facing top-down proteomics strategies aimed at understanding and diagnosing human diseases.
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Affiliation(s)
- Zachery R Gregorich
- Molecular and Cellular Pharmacology Training Program, University of Wisconsin-Madison, Madison, WI, USA; Department of Cell and Regenerative Biology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA
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Trenchevska O, Sherma ND, Oran PE, Reaven PD, Nelson RW, Nedelkov D. Quantitative mass spectrometric immunoassay for the chemokine RANTES and its variants. J Proteomics 2014; 116:15-23. [PMID: 25549571 DOI: 10.1016/j.jprot.2014.12.011] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2014] [Revised: 12/12/2014] [Accepted: 12/19/2014] [Indexed: 01/27/2023]
Abstract
UNLABELLED The chemokine RANTES plays a key role in inflammation, cell recruitment and T cell activation. RANTES is heterogenic and exists as multiple variants in vivo. Herein we describe the development and characterization of a fully quantitative mass spectrometric immunoassay (MSIA) for analysis of intact RANTES and its proteoforms in human serum and plasma samples. The assay exhibits linearity over a wide concentration range (1.56-200ng/mL), intra- and inter-assay precision with CVs <10%, and good linearity and recovery correlations. The assay was tested in different biological matrices, and it was benchmarked against an existing RANTES ELISA. The new RANTES MSIA was used to analyze RANTES and its proteoforms in a small clinical cohort, revealing the quantitative distribution and frequency of the native and truncated RANTES proteoforms. BIOLOGICAL SIGNIFICANCE In the last two decades, RANTES has been studied extensively due to its association with numerous clinical conditions, including kidney-related, autoimmune, cardiovascular, viral and metabolic pathologies. Although a single gene product, RANTES is expressed in a range of cells and tissues presenting with different endogenously produced variants and PTMs. The structural variety and population diversity that has been identified for RANTES necessitate developing advanced methodologies that can provide insight into the protein heterogeneity and its function and regulation in disease. In this work we present a simple, efficient and high-throughput mass spectrometric immunoassay (MSIA) method for analysis of RANTES proteoforms. RANTES MSIA can detect and analyze RANTES proteoforms and provide an insight into the endogenous protein modifications.
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Affiliation(s)
- Olgica Trenchevska
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States.
| | - Nisha D Sherma
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
| | - Paul E Oran
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
| | | | - Randall W Nelson
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
| | - Dobrin Nedelkov
- The Biodesign Institute at Arizona State University, Tempe, AZ 85287, United States
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