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Van Puyvelde B, Hunter CL, Zhgamadze M, Savant S, Wang YO, Hoedt E, Raedschelders K, Pope M, Huynh CA, Ramanujan VK, Tourtellotte W, Razavi M, Anderson NL, Martens G, Deforce D, Fu Q, Dhaenens M, Van Eyk JE. Acoustic ejection mass spectrometry empowers ultra-fast protein biomarker quantification. Nat Commun 2024; 15:5114. [PMID: 38879593 PMCID: PMC11180209 DOI: 10.1038/s41467-024-48563-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 05/07/2024] [Indexed: 06/19/2024] Open
Abstract
The global scientific response to COVID 19 highlighted the urgent need for increased throughput and capacity in bioanalytical laboratories, especially for the precise quantification of proteins that pertain to health and disease. Acoustic ejection mass spectrometry (AEMS) represents a much-needed paradigm shift for ultra-fast biomarker screening. Here, a quantitative AEMS assays is presented, employing peptide immunocapture to enrich (i) 10 acute phase response (APR) protein markers from plasma, and (ii) SARS-CoV-2 NCAP peptides from nasopharyngeal swabs. The APR proteins were quantified in 267 plasma samples, in triplicate in 4.8 h, with %CV from 4.2% to 10.5%. SARS-CoV-2 peptides were quantified in triplicate from 145 viral swabs in 10 min. This assay represents a 15-fold speed improvement over LC-MS, with instrument stability demonstrated across 10,000 peptide measurements. The combination of speed from AEMS and selectivity from peptide immunocapture enables ultra-high throughput, reproducible quantitative biomarker screening in very large cohorts.
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Affiliation(s)
- Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Ghent, Belgium
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | | | - Maxim Zhgamadze
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | | | - Y Oliver Wang
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Esthelle Hoedt
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Koen Raedschelders
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Matt Pope
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC, 20009, USA
| | - Carissa A Huynh
- Cedars Sinai Biobank & Research Pathology Resource, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - V Krishnan Ramanujan
- Cedars Sinai Biobank & Research Pathology Resource, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Warren Tourtellotte
- Cedars Sinai Biobank & Research Pathology Resource, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Morteza Razavi
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC, 20009, USA
| | - N Leigh Anderson
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC, 20009, USA
| | - Geert Martens
- AZ Delta Medical Laboratories, AZ Delta General Hospital, 8800, Roeselare, Belgium
| | - Dieter Deforce
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Ghent, Belgium
| | - Qin Fu
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000, Ghent, Belgium.
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, CA, 90048, USA.
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Lane D, Allsopp R, Holmes CW, Slingsby OC, Jukes-Jones R, Bird P, Anderson NL, Razavi M, Yip R, Pearson TW, Pope M, Khunti K, Doykov I, Hällqvist J, Mills K, Skipp P, Carling R, Ng L, Shaw J, Gupta P, Jones DJL. A high throughput immuno-affinity mass spectrometry method for detection and quantitation of SARS-CoV-2 nucleoprotein in human saliva and its comparison with RT-PCR, RT-LAMP, and lateral flow rapid antigen test. Clin Chem Lab Med 2024; 62:1206-1216. [PMID: 38253336 DOI: 10.1515/cclm-2023-0243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 12/12/2023] [Indexed: 01/24/2024]
Abstract
OBJECTIVES Many reverse transcription polymerase chain reaction (RT-PCR) methods exist that can detect SARS-CoV-2 RNA in different matrices. RT-PCR is highly sensitive, although viral RNA may be detected long after active infection has taken place. SARS-CoV-2 proteins have shorter detection windows hence their detection might be more meaningful. Given salivary droplets represent a main source of transmission, we explored the detection of viral RNA and protein using four different detection platforms including SISCAPA peptide immunoaffinity liquid chromatography-mass spectrometry (SISCAPA-LC-MS) using polyclonal capture antibodies. METHODS The SISCAPA-LC MS method was compared to RT-PCR, RT-loop-mediated isothermal amplification (RT-LAMP), and a lateral flow rapid antigen test (RAT) for the detection of virus material in the drool saliva of 102 patients hospitalised after infection with SARS-CoV-2. Cycle thresholds (Ct) of RT-PCR (E gene) were compared to RT-LAMP time-to-positive (TTP) (NE and Orf1a genes), RAT optical densitometry measurements (test line/control line ratio) and to SISCAPA-LC-MS for measurements of viral protein. RESULTS SISCAPA-LC-MS showed low sensitivity (37.7 %) but high specificity (89.8 %). RAT showed lower sensitivity (24.5 %) and high specificity (100 %). RT-LAMP had high sensitivity (83.0 %) and specificity (100.0 %). At high initial viral RNA loads (<20 Ct), results obtained using SISCAPA-LC-MS correlated with RT-PCR (R2 0.57, p-value 0.002). CONCLUSIONS Detection of SARS-CoV-2 nucleoprotein in saliva was less frequent than the detection of viral RNA. The SISCAPA-LC-MS method allowed processing of multiple samples in <150 min and was scalable, enabling high throughput.
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Affiliation(s)
- Dan Lane
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, University Hospitals of Leicester, Leicester, UK
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Rebecca Allsopp
- Department of Genetics and Genome Biology, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Christopher W Holmes
- Clinical Microbiology, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | | | - Rebekah Jukes-Jones
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, University Hospitals of Leicester, Leicester, UK
| | - Paul Bird
- Clinical Microbiology, Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | | | | | - Richard Yip
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
| | | | - Matt Pope
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
| | - Kamlesh Khunti
- Leicester Diabetes Centre, Leicester General Hospital, University of Leicester, Leicester, UK
| | - Ivan Doykov
- Genetics & Genomic Medicine Department, Translational Mass Spectrometry Research Group, UCL Institute of Child Health, London, UK
- Great Ormond Street Biomedical Research Centre, UCL Institute of Child Health, London, UK
| | - Jenny Hällqvist
- Genetics & Genomic Medicine Department, Translational Mass Spectrometry Research Group, UCL Institute of Child Health, London, UK
- Great Ormond Street Biomedical Research Centre, UCL Institute of Child Health, London, UK
| | - Kevin Mills
- Genetics & Genomic Medicine Department, Translational Mass Spectrometry Research Group, UCL Institute of Child Health, London, UK
- Great Ormond Street Biomedical Research Centre, UCL Institute of Child Health, London, UK
| | - Paul Skipp
- Centre for Proteomic Research, University of Southampton, Southampton, UK
| | - Rachel Carling
- Biochemical Sciences, Synnovis, Guys & St Thomas' NHSFT, London, UK
- GKT School Medical Education, Kings College London, London, UK
| | - Leong Ng
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
| | - Jacqui Shaw
- Department of Genetics and Genome Biology, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
| | - Pankaj Gupta
- The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, University Hospitals of Leicester, Leicester, UK
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Donald J L Jones
- Department of Genetics and Genome Biology, Leicester Cancer Research Centre, University of Leicester, Leicester, UK
- van Geest MS-OMICS Facility, University of Leicester, Leicester, UK
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Wenk D, Zuo C, Kislinger T, Sepiashvili L. Recent developments in mass-spectrometry-based targeted proteomics of clinical cancer biomarkers. Clin Proteomics 2024; 21:6. [PMID: 38287260 PMCID: PMC10826105 DOI: 10.1186/s12014-024-09452-1] [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: 11/10/2023] [Accepted: 01/14/2024] [Indexed: 01/31/2024] Open
Abstract
Routine measurement of cancer biomarkers is performed for early detection, risk classification, and treatment monitoring, among other applications, and has substantially contributed to better clinical outcomes for patients. However, there remains an unmet need for clinically validated assays of cancer protein biomarkers. Protein tumor markers are of particular interest since proteins carry out the majority of biological processes and thus dynamically reflect changes in cancer pathophysiology. Mass spectrometry-based targeted proteomics is a powerful tool for absolute peptide and protein quantification in biological matrices with numerous advantages that make it attractive for clinical applications in oncology. The use of liquid chromatography-tandem mass spectrometry (LC-MS/MS) based methodologies has allowed laboratories to overcome challenges associated with immunoassays that are more widely used for tumor marker measurements. Yet, clinical implementation of targeted proteomics methodologies has so far been limited to a few cancer markers. This is due to numerous challenges associated with paucity of robust validation studies of new biomarkers and the labor-intensive and operationally complex nature of LC-MS/MS workflows. The purpose of this review is to provide an overview of targeted proteomics applications in cancer, workflows used in targeted proteomics, and requirements for clinical validation and implementation of targeted proteomics assays. We will also discuss advantages and challenges of targeted MS-based proteomics assays for clinical cancer biomarker analysis and highlight some recent developments that will positively contribute to the implementation of this technique into clinical laboratories.
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Affiliation(s)
- Deborah Wenk
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Charlotte Zuo
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Thomas Kislinger
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada.
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada.
- Princess Margaret Cancer Research Tower, Room 9-807, 101 College Street, Toronto, ON, M5G 1L7, Canada.
| | - Lusia Sepiashvili
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, 555 University Ave, Rm 3606, Toronto, ON, M5G 1X8, Canada.
- Department of Laboratory Medicine & Pathobiology, University of Toronto, Toronto, ON, Canada.
- Sickkids Research Institute, Toronto, ON, Canada.
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4
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Zhu Y. Plasma/Serum Proteomics based on Mass Spectrometry. Protein Pept Lett 2024; 31:192-208. [PMID: 38869039 PMCID: PMC11165715 DOI: 10.2174/0109298665286952240212053723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/22/2024] [Accepted: 01/31/2024] [Indexed: 06/14/2024]
Abstract
Human blood is a window of physiology and disease. Examination of biomarkers in blood is a common clinical procedure, which can be informative in diagnosis and prognosis of diseases, and in evaluating treatment effectiveness. There is still a huge demand on new blood biomarkers and assays for precision medicine nowadays, therefore plasma/serum proteomics has attracted increasing attention in recent years. How to effectively proceed with the biomarker discovery and clinical diagnostic assay development is a question raised to researchers who are interested in this area. In this review, we comprehensively introduce the background and advancement of technologies for blood proteomics, with a focus on mass spectrometry (MS). Analyzing existing blood biomarkers and newly-built diagnostic assays based on MS can shed light on developing new biomarkers and analytical methods. We summarize various protein analytes in plasma/serum which include total proteome, protein post-translational modifications, and extracellular vesicles, focusing on their corresponding sample preparation methods for MS analysis. We propose screening multiple protein analytes in the same set of blood samples in order to increase success rate for biomarker discovery. We also review the trends of MS techniques for blood tests including sample preparation automation, and further provide our perspectives on their future directions.
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Affiliation(s)
- Yiying Zhu
- Department of Chemistry, Tsinghua University, Beijing, China
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Tominari T, Takatoya M, Matsubara T, Matsunobe M, Arai D, Matsumoto C, Hirata M, Yoshinouchi S, Miyaura C, Itoh Y, Komaki H, Takeda S, Aoki Y, Inada M. Establishment of a Triple Quadrupole HPLC-MS Quantitation Method for Dystrophin Protein in Mouse and Human Skeletal Muscle. Int J Mol Sci 2023; 25:303. [PMID: 38203473 PMCID: PMC10779312 DOI: 10.3390/ijms25010303] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2023] [Revised: 12/19/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Duchenne muscular dystrophy (DMD) is the most common type of neuromuscular disease caused by mutations in the DMD gene encoding dystrophin protein. To quantitively assess human dystrophin protein in muscle biopsy samples, it is imperative to consistently detect as low as 0.003% of the dystrophin protein relative to the total muscle protein content. The quantitation of dystrophin protein has traditionally been conducted using semiquantitative immunoblotting or immunohistochemistry; however, there is a growing need to establish a more precise quantitative method by employing liquid chromatography-mass spectrometry (LC-MS) to measure dystrophin protein. In this study, a novel quantification method was established using a mouse experiment platform applied to the clinical quantification of human dystrophin protein. The method using a spike-in approach with a triple quadrupole LC-MS quantitated the amount of dystrophin in wild-type and human DMD transgenic mice but not in DMD-null mice. In conclusion, we established a quantitating method of dystrophin using HPLC-LC-MS with a novel spike-in approach. These results indicate that our methodology could be applied to several LC-MS devices to enable the accurate measurement of dystrophin protein in patients with DMD.
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Affiliation(s)
- Tsukasa Tominari
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Masaru Takatoya
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Toshiya Matsubara
- Life Science Research Center, Shimadzu Corporation, Nakagyo, Kyoto 604-8511, Japan
| | - Michio Matsunobe
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Daichi Arai
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Chiho Matsumoto
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Michiko Hirata
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Shosei Yoshinouchi
- Cooperative Major of Advanced Health Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Chisato Miyaura
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
| | - Yoshifumi Itoh
- Inada Research Unit, Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- Kennedy Institute of Rheumatology, Nuffield Department of Orthopaedics, Rheumatology and Musculoskeletal Sciences, University of Oxford, Oxford OX3 7FY, UK
| | - Hirofumi Komaki
- Translational Medical Center, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8551, Japan
| | - Shin’ichi Takeda
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Yoshitsugu Aoki
- Department of Molecular Therapy, National Institute of Neuroscience, National Center of Neurology and Psychiatry, Kodaira, Tokyo 187-8502, Japan
| | - Masaki Inada
- Department of Biotechnology and Life Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- Cooperative Major of Advanced Health Science, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
- Inada Research Unit, Institute of Global Innovation Research, Tokyo University of Agriculture and Technology, Koganei, Tokyo 184-8588, Japan
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Fu Q, Murray CI, Karpov OA, Van Eyk JE. Automated proteomic sample preparation: The key component for high throughput and quantitative mass spectrometry analysis. MASS SPECTROMETRY REVIEWS 2023; 42:873-886. [PMID: 34786750 PMCID: PMC10339360 DOI: 10.1002/mas.21750] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 10/11/2021] [Accepted: 10/27/2021] [Indexed: 06/13/2023]
Abstract
Sample preparation for mass spectrometry-based proteomics has many tedious and time-consuming steps that can introduce analytical errors. In particular, the steps around the proteolytic digestion of protein samples are prone to inconsistency. One route for reliable sample processing is the development and optimization of a workflow utilizing an automated liquid handling workstation. Diligent assessment of the sample type, protocol design, reagents, and incubation conditions can significantly improve the speed and consistency of preparation. When combining robust liquid chromatography-mass spectrometry with either discovery or targeted methods, automated sample preparation facilitates increased throughput and reproducible quantitation of biomarker candidates. These improvements in analysis are also essential to process the large patient cohorts necessary to validate a candidate biomarker for potential clinical use. This article reviews the steps in the workflow, optimization strategies, and known applications in clinical, pharmaceutical, and research fields that demonstrate the broad utility for improved automation of sample preparation in the proteomic field.
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Affiliation(s)
- Qin Fu
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Christopher I Murray
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Oleg A Karpov
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
| | - Jennifer E Van Eyk
- Smidt Heart Institute, Advanced Clinical Biosystems Research Institute, Cedars-Sinai Medical Center, Los Angeles, California, USA
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Abstract
A new protocol step improves robustness and ease-of-use for mass spectrometry in the clinic, opening the door to mass deployment to monitor infectious agents.
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Affiliation(s)
- Bart Van Puyvelde
- Laboratory of Pharmaceutical Biotechnology, Ghent UniversityGhentBelgium
- ProGenTomicsGhentBelgium
| | - Maarten Dhaenens
- Laboratory of Pharmaceutical Biotechnology, Ghent UniversityGhentBelgium
- ProGenTomicsGhentBelgium
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8
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Shu Q, Kenny T, Fan J, Lyon CJ, Cazares LH, Hu TY. Species-specific quantification of circulating ebolavirus burden using VP40-derived peptide variants. PLoS Pathog 2021; 17:e1010039. [PMID: 34748613 PMCID: PMC8601621 DOI: 10.1371/journal.ppat.1010039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 11/18/2021] [Accepted: 10/14/2021] [Indexed: 11/18/2022] Open
Abstract
Six ebolavirus species are reported to date, including human pathogens Bundibugyo virus (BDBV), Ebola virus (EBOV), Sudan virus (SUDV), and Taï Forest virus (TAFV); non-human pathogen Reston virus (RESTV); and the plausible Bombali virus (BOMV). Since there are differences in the disease severity caused by different species, species identification and viral burden quantification are critical for treating infected patients timely and effectively. Here we developed an immunoprecipitation-coupled mass spectrometry (IP-MS) assay for VP40 antigen detection and quantification. We carefully selected two regions of VP40, designated as peptide 8 and peptide12 from the protein sequence that showed minor variations among Ebolavirus species through MS analysis of tryptic peptides and antigenicity prediction based on available bioinformatic tools, and generated high-quality capture antibodies pan-specific for these variant peptides. We applied this assay to human plasma spiked with recombinant VP40 protein from EBOV, SUDV, and BDBV and virus-like particles (VLP), as well as EBOV infected NHP plasma. Sequence substitutions between EBOV and SUDV, the two species with highest lethality, produced affinity variations of 2.6-fold for p8 and 19-fold for p12. The proposed IP-MS assay differentiates four of the six known EBV species in one assay, through a combination of p8 and p12 data. The IP-MS assay limit of detection (LOD) using multiple reaction monitoring (MRM) as signal readout was determined to be 28 ng/mL and 7 ng/mL for EBOV and SUDV respectively, equivalent to ~1.625-6.5×105 Geq/mL, and comparable to the LOD of lateral flow immunoassays currently used for Ebola surveillance. The two peptides of the IP-MS assay were also identified by their tandem MS spectra using a miniature MALDI-TOF MS instrument, greatly increasing the feasibility of high specificity assay in a decentralized laboratory.
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Affiliation(s)
- Qingbo Shu
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Tara Kenny
- Systems and Structural Biology Division, Protein Sciences Branch, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Jia Fan
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Christopher J. Lyon
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
| | - Lisa H. Cazares
- Systems and Structural Biology Division, Protein Sciences Branch, U.S. Army Medical Research Institute of Infectious Diseases, Frederick, Maryland, United States of America
| | - Tony Y. Hu
- Center for Cellular and Molecular Diagnostics, Department of Biochemistry and Molecular Biology, School of Medicine, Tulane University, New Orleans, Louisiana, United States of America
- * E-mail:
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van Bentum M, Selbach M. An Introduction to Advanced Targeted Acquisition Methods. Mol Cell Proteomics 2021; 20:100165. [PMID: 34673283 PMCID: PMC8600983 DOI: 10.1016/j.mcpro.2021.100165] [Citation(s) in RCA: 57] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 01/13/2023] Open
Abstract
Targeted proteomics via selected reaction monitoring (SRM) or parallel reaction monitoring (PRM) enables fast and sensitive detection of a preselected set of target peptides. However, the number of peptides that can be monitored in conventional targeting methods is usually rather small. Recently, a series of methods has been described that employ intelligent acquisition strategies to increase the efficiency of mass spectrometers to detect target peptides. These methods are based on one of two strategies. First, retention time adjustment-based methods enable intelligent scheduling of target peptide retention times. These include Picky, iRT, as well as spike-in free real-time adjustment methods such as MaxQuant.Live. Second, in spike-in triggered acquisition methods such as SureQuant, Pseudo-PRM, TOMAHAQ, and Scout-MRM, targeted scans are initiated by abundant labeled synthetic peptides added to samples before the run. Both strategies enable the mass spectrometer to better focus data acquisition time on target peptides. This either enables more sensitive detection or a higher number of targets per run. Here, we provide an overview of available advanced targeting methods and highlight their intrinsic strengths and weaknesses and compatibility with specific experimental setups. Our goal is to provide a basic introduction to advanced targeting methods for people starting to work in this field.
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Affiliation(s)
- Mirjam van Bentum
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany
| | - Matthias Selbach
- Proteome Dynamics, Max Delbrück Center for Molecular Medicine, Berlin, Germany; Charité-Universitätsmedizin Berlin, Berlin, Germany.
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10
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Affinity capture in bottom-up protein analysis - Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers. Anal Chim Acta 2021; 1182:338714. [PMID: 34602193 DOI: 10.1016/j.aca.2021.338714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022]
Abstract
Antibody-based affinity capture has become the gold standard in sample preparation for determination of low-abundance protein biomarkers in biological matrices prior to liquid chromatography-mass spectrometry (LC-MS) determination. This comprises both capture of intact proteins prior to the digestion step and capture of proteolytic peptides after digestion of the sample. The latter can be performed both using antibodies specifically developed to capture target proteolytic peptides, as well as by the less explored use of anti-protein antibodies to capture the proteolytic epitope peptide. Molecularly imprinted polymers (MIPs), also called plastic antibodies are another affinity-based approach emerging as sample preparation technique in LC-MS based protein biomarker analysis. The current review gives a critical and comprehensive overview of proteolytic peptide capture using antibodies and MIPs in LC-MS based protein biomarker determination during the last five years. The main emphasis is on capture of non-modified peptides, while a brief overview of affinity capture of peptides containing post-translational modifications (PTMs) is provided.
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11
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Van Puyvelde B, Van Uytfanghe K, Tytgat O, Van Oudenhove L, Gabriels R, Bouwmeester R, Daled S, Van Den Bossche T, Ramasamy P, Verhelst S, De Clerck L, Corveleyn L, Willems S, Debunne N, Wynendaele E, De Spiegeleer B, Judak P, Roels K, De Wilde L, Van Eenoo P, Reyns T, Cherlet M, Dumont E, Debyser G, t'Kindt R, Sandra K, Gupta S, Drouin N, Harms A, Hankemeier T, Jones DJL, Gupta P, Lane D, Lane CS, El Ouadi S, Vincendet JB, Morrice N, Oehrle S, Tanna N, Silvester S, Hannam S, Sigloch FC, Bhangu-Uhlmann A, Claereboudt J, Anderson NL, Razavi M, Degroeve S, Cuypers L, Stove C, Lagrou K, Martens GA, Deforce D, Martens L, Vissers JPC, Dhaenens M. Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients. JACS AU 2021. [PMID: 34254058 DOI: 10.1101/2020.11.18.20231688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include accurate monitoring of the spread, as this provides one of the few alternatives to total lockdown. However, COVID-19 diagnosis is currently performed almost exclusively by reverse transcription polymerase chain reaction (RT-PCR). Although this is efficient, automatable, and acceptably cheap, reliance on one type of technology comes with serious caveats, as illustrated by recurring reagent and test shortages. We therefore developed an alternative diagnostic test that detects proteolytically digested SARS-CoV-2 proteins using mass spectrometry (MS). We established the Cov-MS consortium, consisting of 15 academic laboratories and several industrial partners to increase applicability, accessibility, sensitivity, and robustness of this kind of SARS-CoV-2 detection. This, in turn, gave rise to the Cov-MS Digital Incubator that allows other laboratories to join the effort, navigate, and share their optimizations and translate the assay into their clinic. As this test relies on viral proteins instead of RNA, it provides an orthogonal and complementary approach to RT-PCR using other reagents that are relatively inexpensive and widely available, as well as orthogonally skilled personnel and different instruments. Data are available via ProteomeXchange with identifier PXD022550.
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Affiliation(s)
- Bart Van Puyvelde
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Katleen Van Uytfanghe
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Olivier Tytgat
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
- Department of Life Science Technologies, Imec, 3000 Leuven, Belgium
| | | | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Robbin Bouwmeester
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Simon Daled
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Tim Van Den Bossche
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Pathmanaban Ramasamy
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
- Interuniversity Institute of Bioinformatics in Brussels, ULB/VUB, 1050 Brussels, Belgium
| | - Sigrid Verhelst
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Laura De Clerck
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Laura Corveleyn
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Sander Willems
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Nathan Debunne
- Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Evelien Wynendaele
- Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Bart De Spiegeleer
- Drug Quality and Registration Group, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Peter Judak
- Doping Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Kris Roels
- Doping Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Laurie De Wilde
- Doping Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Peter Van Eenoo
- Doping Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Tim Reyns
- Department of Clinical Chemistry, Ghent University Hospital, 9000 Ghent, Belgium
| | - Marc Cherlet
- Department of Pharmacology, Toxicology, and Biochemistry, Faculty of Veterinary Medicine, Ghent University 9000 Ghent, Belgium
| | - Emmie Dumont
- Research Institute for Chromatography (RIC), 8500 Kortrijk, Belgium
| | - Griet Debyser
- Research Institute for Chromatography (RIC), 8500 Kortrijk, Belgium
| | - Ruben t'Kindt
- Research Institute for Chromatography (RIC), 8500 Kortrijk, Belgium
| | - Koen Sandra
- Research Institute for Chromatography (RIC), 8500 Kortrijk, Belgium
| | - Surya Gupta
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Nicolas Drouin
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Amy Harms
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Thomas Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Donald J L Jones
- Leicester Cancer Research Centre, RKCSB, University of Leicester, U.K., and John and Lucille van Geest Biomarker Facility, Cardiovascular Research Centre, Glenfield Hospital, Leicester LE1 7RH, United Kingdom
| | - Pankaj Gupta
- The Department of Chemical Pathology and Metabolic Diseases, Level 4, Sandringham Building, Leicester Royal Infirmary, Leicester LE1 7RH, United Kingdom
| | - Dan Lane
- The Department of Chemical Pathology and Metabolic Diseases, Level 4, Sandringham Building, Leicester Royal Infirmary, Leicester LE1 7RH, United Kingdom
| | | | - Said El Ouadi
- AB Sciex, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | | | - Nick Morrice
- AB Sciex, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Stuart Oehrle
- Waters Corporation, Milford, Massachusetts 01757, United States
| | - Nikunj Tanna
- Waters Corporation, Milford, Massachusetts 01757, United States
| | - Steve Silvester
- Alderley Analytical, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Sally Hannam
- Alderley Analytical, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | | | | | | | - N Leigh Anderson
- SISCAPA Assay Technologies, Inc., Washington, D.C. 20009, United States
| | - Morteza Razavi
- SISCAPA Assay Technologies, Inc., Washington, D.C. 20009, United States
| | - Sven Degroeve
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Lize Cuypers
- Clinical Department of Laboratory Medicine, UZ Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Christophe Stove
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, Belgium
| | - Katrien Lagrou
- Clinical Department of Laboratory Medicine, UZ Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Geert A Martens
- AZ Delta Medical Laboratories, AZ Delta General Hospital, 8800 Roeselare, Belgium
| | - Dieter Deforce
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Lennart Martens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | | | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
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12
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Van Puyvelde B, Van Uytfanghe K, Tytgat O, Van Oudenhove L, Gabriels R, Bouwmeester R, Daled S, Van Den Bossche T, Ramasamy P, Verhelst S, De Clerck L, Corveleyn L, Willems S, Debunne N, Wynendaele E, De Spiegeleer B, Judak P, Roels K, De Wilde L, Van Eenoo P, Reyns T, Cherlet M, Dumont E, Debyser G, t’Kindt R, Sandra K, Gupta S, Drouin N, Harms A, Hankemeier T, Jones DJL, Gupta P, Lane D, Lane CS, El Ouadi S, Vincendet JB, Morrice N, Oehrle S, Tanna N, Silvester S, Hannam S, Sigloch FC, Bhangu-Uhlmann A, Claereboudt J, Anderson NL, Razavi M, Degroeve S, Cuypers L, Stove C, Lagrou K, Martens GA, Deforce D, Martens L, Vissers JPC, Dhaenens M. Cov-MS: A Community-Based Template Assay for Mass-Spectrometry-Based Protein Detection in SARS-CoV-2 Patients. JACS AU 2021; 1:750-765. [PMID: 34254058 PMCID: PMC8230961 DOI: 10.1021/jacsau.1c00048] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Indexed: 05/03/2023]
Abstract
Rising population density and global mobility are among the reasons why pathogens such as SARS-CoV-2, the virus that causes COVID-19, spread so rapidly across the globe. The policy response to such pandemics will always have to include accurate monitoring of the spread, as this provides one of the few alternatives to total lockdown. However, COVID-19 diagnosis is currently performed almost exclusively by reverse transcription polymerase chain reaction (RT-PCR). Although this is efficient, automatable, and acceptably cheap, reliance on one type of technology comes with serious caveats, as illustrated by recurring reagent and test shortages. We therefore developed an alternative diagnostic test that detects proteolytically digested SARS-CoV-2 proteins using mass spectrometry (MS). We established the Cov-MS consortium, consisting of 15 academic laboratories and several industrial partners to increase applicability, accessibility, sensitivity, and robustness of this kind of SARS-CoV-2 detection. This, in turn, gave rise to the Cov-MS Digital Incubator that allows other laboratories to join the effort, navigate, and share their optimizations and translate the assay into their clinic. As this test relies on viral proteins instead of RNA, it provides an orthogonal and complementary approach to RT-PCR using other reagents that are relatively inexpensive and widely available, as well as orthogonally skilled personnel and different instruments. Data are available via ProteomeXchange with identifier PXD022550.
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Affiliation(s)
- Bart Van Puyvelde
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Katleen Van Uytfanghe
- Laboratory
of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical
Sciences, Ghent University, 9000 Ghent, Belgium
| | - Olivier Tytgat
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
- Department
of Life Science Technologies, Imec, 3000 Leuven, Belgium
| | | | - Ralf Gabriels
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Robbin Bouwmeester
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Simon Daled
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Tim Van Den Bossche
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Pathmanaban Ramasamy
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
- Interuniversity
Institute of Bioinformatics in Brussels, ULB/VUB, 1050 Brussels, Belgium
| | - Sigrid Verhelst
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Laura De Clerck
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Laura Corveleyn
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Sander Willems
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Nathan Debunne
- Drug Quality and Registration Group, Faculty of Pharmaceutical
Sciences, Ghent University, 9000 Ghent, Belgium
| | - Evelien Wynendaele
- Drug Quality and Registration Group, Faculty of Pharmaceutical
Sciences, Ghent University, 9000 Ghent, Belgium
| | - Bart De Spiegeleer
- Drug Quality and Registration Group, Faculty of Pharmaceutical
Sciences, Ghent University, 9000 Ghent, Belgium
| | - Peter Judak
- Doping
Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Kris Roels
- Doping
Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Laurie De Wilde
- Doping
Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Peter Van Eenoo
- Doping
Control Laboratory, Department of Diagnostic Sciences, Ghent University, 9000 Ghent, Belgium
| | - Tim Reyns
- Department
of Clinical Chemistry, Ghent University
Hospital, 9000 Ghent, Belgium
| | - Marc Cherlet
- Department
of Pharmacology, Toxicology, and Biochemistry, Faculty of Veterinary
Medicine, Ghent University 9000 Ghent, Belgium
| | - Emmie Dumont
- Research Institute for Chromatography
(RIC), 8500 Kortrijk, Belgium
| | - Griet Debyser
- Research Institute for Chromatography
(RIC), 8500 Kortrijk, Belgium
| | - Ruben t’Kindt
- Research Institute for Chromatography
(RIC), 8500 Kortrijk, Belgium
| | - Koen Sandra
- Research Institute for Chromatography
(RIC), 8500 Kortrijk, Belgium
| | - Surya Gupta
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Nicolas Drouin
- Division
of Systems Biomedicine and Pharmacology, Leiden Academic
Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Amy Harms
- Division
of Systems Biomedicine and Pharmacology, Leiden Academic
Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Thomas Hankemeier
- Division
of Systems Biomedicine and Pharmacology, Leiden Academic
Centre for Drug Research, Leiden University, 2311 G Leiden, The Netherlands
| | - Donald J. L. Jones
- Leicester
Cancer Research Centre, RKCSB, University of Leicester, U.K., and
John and Lucille van Geest Biomarker Facility, Cardiovascular Research
Centre, Glenfield Hospital, Leicester LE1 7RH, United Kingdom
| | - Pankaj Gupta
- The
Department of Chemical Pathology and Metabolic Diseases, Level 4,
Sandringham Building, Leicester Royal Infirmary, Leicester LE1 7RH, United Kingdom
| | - Dan Lane
- The
Department of Chemical Pathology and Metabolic Diseases, Level 4,
Sandringham Building, Leicester Royal Infirmary, Leicester LE1 7RH, United Kingdom
| | | | - Said El Ouadi
- AB Sciex, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | | | - Nick Morrice
- AB Sciex, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Stuart Oehrle
- Waters Corporation, Milford, Massachusetts 01757, United States
| | - Nikunj Tanna
- Waters Corporation, Milford, Massachusetts 01757, United States
| | - Steve Silvester
- Alderley Analytical, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | - Sally Hannam
- Alderley Analytical, Alderley Park, Macclesfield SK10 4TG, United Kingdom
| | | | | | | | - N. Leigh Anderson
- SISCAPA Assay Technologies, Inc., Washington, D.C. 20009, United States
| | - Morteza Razavi
- SISCAPA Assay Technologies, Inc., Washington, D.C. 20009, United States
| | - Sven Degroeve
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | - Lize Cuypers
- Clinical
Department of Laboratory Medicine, UZ Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Christophe Stove
- Laboratory
of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical
Sciences, Ghent University, 9000 Ghent, Belgium
| | - Katrien Lagrou
- Clinical
Department of Laboratory Medicine, UZ Leuven, KU Leuven, 3000 Leuven, Belgium
| | - Geert A. Martens
- AZ
Delta Medical Laboratories, AZ Delta General
Hospital, 8800 Roeselare, Belgium
| | - Dieter Deforce
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
| | - Lennart Martens
- VIB-UGent
Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium
- Department
of Biomolecular Medicine, Ghent University, 9000 Ghent Belgium
| | | | - Maarten Dhaenens
- ProGenTomics,
Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
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13
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Ahire DS, Basit A, Karasu M, Prasad B. Ultrasensitive Quantification of Drug-metabolizing Enzymes and Transporters in Small Sample Volume by Microflow LC-MS/MS. J Pharm Sci 2021; 110:2833-2840. [PMID: 33785352 DOI: 10.1016/j.xphs.2021.03.020] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 01/31/2023]
Abstract
Protein abundance data of drug-metabolizing enzymes and transporters (DMETs) are broadly applicable to the characterization of in vitro and in vivo models, in vitro to in vivo extrapolation (IVIVE), and interindividual variability prediction. However, the emerging need of DMET quantification in small sample volumes such as organ-on a chip effluent, organoids, and biopsies requires ultrasensitive protein quantification methods. We present an ultrasensitive method that relies on an optimized sample preparation approach involving acetone precipitation coupled with a microflow-based liquid chromatography-tandem mass spectrometry (µLC-MS/MS) for the DMET quantification using limited sample volume or protein concentration, i.e., liver tissues (1-100 mg), hepatocyte counts (~4000 to 1 million cells), and microsomal protein concentration (0.01-1 mg/ml). The method was applied to quantify DMETs in differential tissue S9 fractions (liver, intestine, kidney, lung, and heart) and cryopreserved human intestinal mucosa (i.e., CHIM). The method successfully quantified >75% of the target DMETs in the trypsin digests of 1 mg tissue homogenate, 15,000 hepatocytes, and 0.06 mg/ml microsomal protein concentration. The precision of DMET quantification measured as the coefficient of variation across different tissue weights, cell counts, or microsomal protein concentration was within 30%. The method confirmed significant extrahepatic abundance of non-cytochrome P450 enzymes such as dihydropyridine dehydrogenase (DPYD), epoxide hydrolases (EPXs), arylacetamide deacetylase (AADAC), paraoxonases (PONs), and glutathione S-transferases (GSTs). The ultrasensitive method developed here is applicable to characterize emerging miniaturized in vitro models and small volume biopsies. In addition, the differential tissue abundance data of the understudied DMETs will be important for physiologically-based pharmacokinetic (PBPK) modeling of drugs.
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Affiliation(s)
- Deepak Suresh Ahire
- Department of Pharmaceutical Sciences, Washington State University, 12 E Spokane Falls Blvd, Spokane, WA 99202, USA
| | - Abdul Basit
- Department of Pharmaceutical Sciences, Washington State University, 12 E Spokane Falls Blvd, Spokane, WA 99202, USA
| | - Matthew Karasu
- Department of Pharmaceutical Sciences, Washington State University, 12 E Spokane Falls Blvd, Spokane, WA 99202, USA
| | - Bhagwat Prasad
- Department of Pharmaceutical Sciences, Washington State University, 12 E Spokane Falls Blvd, Spokane, WA 99202, USA.
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14
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Stauffer A, Ray C, Hall M. A Flexible Multiplatform Bioanalytical Strategy for Measurement of Total Circulating Shed Target Receptors: Application to Soluble B Cell Maturation Antigen Levels in the Presence of a Bispecific Antibody Drug. Assay Drug Dev Technol 2020; 19:17-26. [PMID: 33232610 DOI: 10.1089/adt.2020.1024] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
B cell maturation antigen (BCMA) is a membrane-bound receptor that is overexpressed on multiple myeloma cells and can be targeted with biotherapeutics. Soluble shed forms of membrane-associated receptors in circulation can act as a drug sink, especially when it is present in high molar ratio compared to drug concentration, potentially derailing the intended pharmacological mechanism and impacting pharmacokinetic (PK) measurements and efficacious dose predictions. In this study, we present a bioanalytical strategy for assessing dynamic levels of total soluble BCMA before and during treatment with a bispecific antibody targeting BCMA and CD3. Implementation of a ligand binding assay was not successful due to extensive bispecific antibody interference. Instead, we explored two types of immunoaffinity (IA) liquid chromatography-tandem mass spectrometry (LC-MS/MS) assays, one at the protein level and one at the surrogate peptide level. Ultimately, the protein-level IA-LC-MS/MS method was optimized for use in a cynomolgus monkey PK/pharmacodynamic study. In addition, we demonstrated that the method was easily adapted for use with human samples in preparation for translation to the clinic. This work demonstrates the benefit of flexibility and agility in bioanalytical method development in early drug development. Multiplatform suitability assessments enable rapid, resource-sparing identification and qualification of clinically translatable assays. We recommend early adoption of this strategy to provide enough time for critical reagent development and assay validation for analysis of shed targets.
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Affiliation(s)
- Angela Stauffer
- Biomedicine Design, Pfizer Worldwide Research, Development, and Medical, San Diego, California, USA
| | - Chad Ray
- Zoetis Incorporated, Fort Collins, Colorado, USA
| | - Michael Hall
- Biomedicine Design, Pfizer Worldwide Research, Development, and Medical, San Diego, California, USA
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15
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Na CH, Sathe G, Rosenthal LS, Moghekar AR, Dawson VL, Dawson TM, Pandey A. Development of a novel method for the quantification of tyrosine 39 phosphorylated α- and β-synuclein in human cerebrospinal fluid. Clin Proteomics 2020; 17:13. [PMID: 32390785 PMCID: PMC7197159 DOI: 10.1186/s12014-020-09277-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 04/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder. Biomarkers that can help monitor the progression of PD or response to disease-modifying agents will be invaluable in making appropriate therapeutic decisions. Further, biomarkers that could be used to distinguish PD from other related disorders with PD-like symptoms will be useful for accurate diagnosis and treatment. C-Abl tyrosine kinase is activated in PD resulting in increased phosphorylation of the tyrosine residue at position 39 (Y39) of α-synuclein (α-syn) (pY39 α-syn), which contributes to the death of dopaminergic neurons. Because pY39 α-syn may be pathogenic, monitoring pY39 α-syn could allow us to diagnose presymptomatic PD and help monitor disease progression and response to treatment. We sought to investigate if increased phosphorylation of pY39 α-syn can be detected in the cerebrospinal fluid (CSF) of PD patients by targeted mass spectrometry. METHODS Here, we report a two-step enrichment method in which phosphotyrosine peptides were first enriched with an anti-phosphotyrosine antibody followed by a second round of enrichment by titanium dioxide (TiO2) beads to detect EGVLpYVGSK sequence derived from tyrosine 39 region of α- and β-synuclein (αβ-syn). Accurate quantification was achieved by adding a synthetic heavy version of pY39 αβ-syn peptide before enzymatic digestion. RESULTS Using the developed enrichment methods and optimized parallel reaction monitoring (PRM) assays, we detected pY39 αβ-syn peptide in human CSF and demonstrated that the ratio of pY39 αβ-syn to Y39 αβ-syn was significantly increased in the CSF of patients with PD. CONCLUSIONS We anticipate that this optimized two-step enrichment-based PRM detection method will help monitor c-Abl activation in PD patients and can also be used to quantify other phosphotyrosine peptides of low abundance in biological samples.
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Affiliation(s)
- Chan Hyun Na
- Neurodegeneration Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
| | - Gajanan Sathe
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
- Present Address: Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560 029 India
| | - Liana S. Rosenthal
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Abhay R. Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Valina L. Dawson
- Neurodegeneration Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Ted M. Dawson
- Neurodegeneration Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Akhilesh Pandey
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
- Department of Biological Chemistry, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Manipal Academy of Higher Education (MAHE), Manipal, 576104 Karnataka India
- Present Address: Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
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16
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Precision multiparameter tracking of inflammation on timescales of hours to years using serial dried blood spots. Bioanalysis 2020; 12:937-955. [PMID: 32253915 PMCID: PMC7372997 DOI: 10.4155/bio-2019-0278] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Aim: High-frequency longitudinal tracking of inflammation using dried blood microsamples provides a new window for personalized monitoring of infections, chronic inflammatory disease and clinical trials of anti-inflammatory drugs. Results/methodology: Using 1662 dried blood spot samples collected by 16 subjects over periods of weeks to years, we studied the behavior of 12 acute phase response and related proteins in inflammation events correlated with infection, vaccination, surgery, intense exercise and Crohn's disease. Proteins were measured using SISCAPA mass spectrometry and normalized to constant plasma volume using low-variance proteins, generating high precision within-person biomarker trajectories with well-characterized personal baselines. Discussion/conclusion: The results shed new light on the dynamic regulation of APR responses, offering a new approach to visualization of multidimensional inflammation trajectories.
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17
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Hamza GM, Bergo VB, Mamaev S, Wojchowski DM, Toran P, Worsfold CR, Castaldi MP, Silva JC. Affinity-Bead Assisted Mass Spectrometry (Affi-BAMS): A Multiplexed Microarray Platform for Targeted Proteomics. Int J Mol Sci 2020; 21:E2016. [PMID: 32188029 PMCID: PMC7139916 DOI: 10.3390/ijms21062016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Revised: 03/10/2020] [Accepted: 03/13/2020] [Indexed: 02/06/2023] Open
Abstract
The ability to quantitatively probe diverse panels of proteins and their post-translational modifications (PTMs) across multiple samples would aid a broad spectrum of biological, biochemical and pharmacological studies. We report a novel, microarray analytical technology that combines immuno-affinity capture with Matrix Assisted Laser Desorption Ionization Mass Spectrometry (MALDI MS), which is capable of supporting highly multiplexed, targeted proteomic assays. Termed "Affinity-Bead Assisted Mass Spectrometry" (Affi-BAMS), this LC-free technology enables development of highly specific and customizable assay panels for simultaneous profiling of multiple proteins and PTMs. While affinity beads have been used previously in combination with MS, the Affi-BAMS workflow uses enrichment on a single bead that contains one type of antibody, generally capturing a single analyte (protein or PTM) while having enough binding capacity to enable quantification within approximately 3 orders of magnitude. The multiplexing capability is achieved by combining Affi-BAMS beads with different protein specificities. To enable screening of bead-captured analytes by MS, we further developed a novel method of performing spatially localized elution of targets from individual beads arrayed on a microscope slide. The resulting arrays of micro spots contain highly concentrated analytes localized within 0.5 mm diameter spots that can be directly measured using MALDI MS. While both intact proteins and protein fragments can be monitored by Affi-BAMS, we initially focused on applying this technology for bottom-up proteomics to enable screening of hundreds of samples per day by combining the robust magnetic bead-based workflow with the high throughput nature of MALDI MS acquisition. To demonstrate the variety of applications and robustness of Affi-BAMS, several studies are presented that focus on the response of 4EBP1, RPS6, ERK1/ERK2, mTOR, Histone H3 and C-MET to stimuli including rapamycin, H2O2, EPO, SU11274, Staurosporine and Vorinostat.
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Affiliation(s)
- Ghaith M. Hamza
- Discovery Sciences, BioPharmaceutical R&D, AstraZeneca, Boston, MA 02451, USA; (G.M.H.); (M.P.C.)
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (D.M.W.); (P.T.)
| | - Vladislav B. Bergo
- Adeptrix Corporation, Beverly, MA 01915, USA; (V.B.B.); (S.M.); (C.R.W.)
| | - Sergey Mamaev
- Adeptrix Corporation, Beverly, MA 01915, USA; (V.B.B.); (S.M.); (C.R.W.)
| | - Don M. Wojchowski
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (D.M.W.); (P.T.)
| | - Paul Toran
- Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH 03824, USA; (D.M.W.); (P.T.)
| | | | - M. Paola Castaldi
- Discovery Sciences, BioPharmaceutical R&D, AstraZeneca, Boston, MA 02451, USA; (G.M.H.); (M.P.C.)
| | - Jeffrey C. Silva
- Adeptrix Corporation, Beverly, MA 01915, USA; (V.B.B.); (S.M.); (C.R.W.)
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18
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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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19
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Suárez-Fernández A, González-Antuña A, Rodríguez-González P, Alonso JIG. Determination of Cystatin C in human urine by isotope dilution tandem mass spectrometry. J Pharm Biomed Anal 2020; 177:112889. [PMID: 31568966 DOI: 10.1016/j.jpba.2019.112889] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 09/13/2019] [Accepted: 09/19/2019] [Indexed: 11/29/2022]
Abstract
This work presents the development of a methodology for the accurate and precise quantification of the renal biomarker Cystatin C in human urine by Isotope Dilution Mass Spectrometry (IDMS). The procedure is based on the addition of a known quantity of the proteotypic peptide ALDFAVG*EYNK labelled with 13C2-glycine to the urine sample followed by protein hydrolysis using trypsin. Then, preconcentration and purification of the isotope diluted peptide was carried out by a selective monoclonal antibody bound to magnetic beads and final measurement was done after injection of the sample in a HPLC-MS/MS triple quadrupole instrument. The isotopic distribution of the isotope diluted proteotypic peptide was measured by low resolution selected reaction monitoring. Using this aquisition mode, the bandpass of the first quadrupole was widened (FWHM =13 u) so the whole isotopic clusters for both the natural abundance and the labelled peptides entered the collision cell. The proposed acquisition mode provided similar accuracy and precision than the regular SRM mode (FWHM =0.7 u) but a higher sensitivity was observed. The purification of the sample by antibody based enrichment of the target peptide was shown to remove interfering compounds more efficiently in comparison with a sample purification based on semipreparative liquid chromatography. Using 5 ng of the labelled peptide it was possible to quantify Cystatin C in human urine in patients with normal and impaired renal function. Recoveries from 100 to 104% were obtained in samples containing from 90 to 700 μg L-1 of Cystatin C with relative standard deviations from 0.5 to 6%. The stability of Cystatin C in urine samples was evaluated under different storage conditions showing that only when the urine samples were stored at room temperature during more than 10 days, a significant degradation of Cystatin C was observed.
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Affiliation(s)
- Amanda Suárez-Fernández
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Ana González-Antuña
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
| | - Pablo Rodríguez-González
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain.
| | - J Ignacio García Alonso
- Department of Physical and Analytical Chemistry, Faculty of Chemistry, University of Oviedo, Julián Clavería 8, 33006 Oviedo, Spain
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20
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Gaither C, Popp R, Mohammed Y, Borchers CH. Determination of the concentration range for 267 proteins from 21 lots of commercial human plasma using highly multiplexed multiple reaction monitoring mass spectrometry. Analyst 2020; 145:3634-3644. [DOI: 10.1039/c9an01893j] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Multiple reaction monitoring (MRM) is a key tool for biomarker validation and the translation of potential biomarkers into the clinic.
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Affiliation(s)
| | | | - Yassene Mohammed
- University of Victoria – Genome British Columbia Proteomics Centre
- University of Victoria
- Victoria
- Canada
- Center for Proteomics and Metabolomics
| | - Christoph H. Borchers
- University of Victoria – Genome British Columbia Proteomics Centre
- University of Victoria
- Victoria
- Canada
- Department of Biochemistry and Microbiology
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21
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Prasad B, Achour B, Artursson P, Hop CECA, Lai Y, Smith PC, Barber J, Wisniewski JR, Spellman D, Uchida Y, Zientek M, Unadkat JD, Rostami-Hodjegan A. Toward a Consensus on Applying Quantitative Liquid Chromatography-Tandem Mass Spectrometry Proteomics in Translational Pharmacology Research: A White Paper. Clin Pharmacol Ther 2019; 106:525-543. [PMID: 31175671 PMCID: PMC6692196 DOI: 10.1002/cpt.1537] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2019] [Accepted: 05/22/2019] [Indexed: 12/18/2022]
Abstract
Quantitative translation of information on drug absorption, disposition, receptor engagement, and drug-drug interactions from bench to bedside requires models informed by physiological parameters that link in vitro studies to in vivo outcomes. To predict in vivo outcomes, biochemical data from experimental systems are routinely scaled using protein quantity in these systems and relevant tissues. Although several laboratories have generated useful quantitative proteomic data using state-of-the-art mass spectrometry, no harmonized guidelines exit for sample analysis and data integration to in vivo translation practices. To address this gap, a workshop was held on September 27 and 28, 2018, in Cambridge, MA, with 100 experts attending from academia, the pharmaceutical industry, and regulators. Various aspects of quantitative proteomics and its applications in translational pharmacology were debated. A summary of discussions and best practices identified by this expert panel are presented in this "White Paper" alongside unresolved issues that were outlined for future debates.
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Affiliation(s)
- Bhagwat Prasad
- Department of Pharmaceutics, University of Washington, Seattle, WA
| | - Brahim Achour
- Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, UK
| | - Per Artursson
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | | | | | - Philip C Smith
- Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jill Barber
- Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, UK
| | - Jacek R Wisniewski
- Biochemical Proteomics Group, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Daniel Spellman
- Pharmacokinetics, Pharmacodynamics & Drug Metabolism, Merck & Co., Inc., West Point, PA
| | - Yasuo Uchida
- Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai, Japan
| | | | | | - Amin Rostami-Hodjegan
- Centre for Applied Pharmacokinetic Research, University of Manchester, Manchester, UK
- Certara UK Ltd. (Simcyp Division), 1 Concourse Way, Sheffield, UK
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22
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Kontostathi G, Makridakis M, Zoidakis J, Vlahou A. Applications of multiple reaction monitoring targeted proteomics assays in human plasma. Expert Rev Mol Diagn 2019; 19:499-515. [PMID: 31057016 DOI: 10.1080/14737159.2019.1615448] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Introduction: Multiple (or selected) reaction monitoring-mass spectrometry (MRM/SRM) is a targeted proteomic method that can be used for relative and absolute quantification. Multiple reports exist supporting the potential of the approach in proteomic biomarker validation. Areas covered: To get an overview of the applications of MRM in protein quantification in plasma, a search in MedLine/PubMed was performed using the keywords: 'MRM/SRM plasma proteomic/proteomics/proteome'. The retrieved studies were further filtered to focus on disease biomarkers and the main results are summarized. Expert opinion: MRM is increasingly employed for the quantification of both well-established but also newly discovered putative biomarkers and occasionally their post-translationally modified forms in plasma. Fractionation is regularly required for the detection of low abundance proteins. Standardized procedures to facilitate assay establishment and marker quantification have been proposed and, in few cases, implemented. Nevertheless, in most cases, absolute quantification is not performed. To advance, multiple technical issues including the regular use of standard labeled peptides and appropriate quality controls to monitor assay performance should be considered. Additionally, clinical aspects involving careful study design to address biomarker clinical use should also be considered.
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Affiliation(s)
- Georgia Kontostathi
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Manousos Makridakis
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Jerome Zoidakis
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
| | - Antonia Vlahou
- a Biotechnology Division , Biomedical Research Foundation, Academy of Athens (BRFAA) , Athens , Greece
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23
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Lee J, Kim H, Sohn A, Yeo I, Kim Y. Cost-Effective Automated Preparation of Serum Samples for Reproducible Quantitative Clinical Proteomics. J Proteome Res 2019; 18:2337-2345. [PMID: 30985128 DOI: 10.1021/acs.jproteome.9b00023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Reproducible sample preparation remains a significant challenge in large-scale clinical research using selected reaction monitoring-mass spectrometry (SRM-MS), which enables a highly sensitive multiplexed assay. Although automated liquid-handling platforms have tremendous potential for addressing this issue, the high cost of their consumables is a drawback that renders routine operation expensive. Here we evaluated the performance of a liquid-handling platform in preparing serum samples compared with a standard experiment while reducing the outlay for consumables, such as tips, wasted reagents, and reagent stock plates. A total of 26 multiplex assays were quantified by SRM-MS using four sets of 24 pooled human serum aliquots; the four sets used a fixed number (1, 4, 8, or 24) of tips to dispense digestion reagents. This study demonstrated that the use of 4 or 8 tips is comparable to 24 tips (standard experiment), as evidenced by their coefficients of variation: 13.5% (for 4 and 8 tips) versus 12.0% (24 tips). Thus we can save 37% of the total experimental cost compared with the standard experiment, maintaining nearly equivalent reproducibility. The routine operation of cost-effective liquid-handling platforms can enable researchers to process large-scale samples with high throughput, adding credibility to their findings by minimizing human error.
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Affiliation(s)
| | - Hyunsoo Kim
- Institute of Medical and Biological Engineering, MRC , Seoul National University , Seoul , Korea
| | | | - Injoon Yeo
- Interdisciplinary Program of Bioengineering , Seoul National University College of Engineering , Seoul , Korea
| | - Youngsoo Kim
- Institute of Medical and Biological Engineering, MRC , Seoul National University , Seoul , Korea.,Interdisciplinary Program of Bioengineering , Seoul National University College of Engineering , Seoul , Korea
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24
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Razavi M, Farrokhi V, Yip R, Anderson NL, Pearson TW, Neubert H. Measuring the Turnover Rate of Clinically Important Plasma Proteins using an Automated SISCAPA Workflow. Clin Chem 2019; 65:492-494. [DOI: 10.1373/clinchem.2018.294892] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
| | - Vahid Farrokhi
- Biomedicine Design, Worldwide Research & Development, Pfizer Inc. Andover, MA
| | - Richard Yip
- SISCAPA Assay Technologies, Inc. Washington, DC
| | | | | | - Hendrik Neubert
- Biomedicine Design, Worldwide Research & Development, Pfizer Inc. Andover, MA
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25
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Levernæs MCS, Farhat B, Oulie I, Abdullah SS, Paus E, Reubsaet L, Halvorsen TG. Immunocapture sample clean-up in determination of low abundant protein biomarkers – a feasibility study of peptide capture by anti-protein antibodies. RSC Adv 2019; 9:34902-34911. [PMID: 35702551 PMCID: PMC9097496 DOI: 10.1039/c9ra05071j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/21/2019] [Indexed: 01/04/2023] Open
Abstract
Immunocapture in mass spectrometry based targeted protein analysis using a bottom-up workflow is nowadays mainly performed by target protein extraction using anti-protein antibodies followed by tryptic digestion. Already available monoclonal antibodies (mAbs) which were developed against intact target proteins (anti-protein antibodies) can capture proteotypic epitope containing peptides after tryptic digestion of the sample. In the present paper considerations when developing a method for targeted protein quantitation through capture of epitope containing peptides are discussed and a method applying peptide capture by anti-protein antibodies is compared with conventional immunocapture MS. The model protein used for this purpose was progastrin releasing peptide (ProGRP), a validated low abundant biomarker for Small Cell Lung Cancer with reference values in serum in the pg mL−1 range. A set of mAbs which bind linear epitopes of ProGRP are available, and after a theoretical consideration, three mAbs (E146, E149 and M18) were evaluated for extraction of proteotypic epitope peptides from a complex sample. M18 was the best performing mAb for peptide capture by anti-protein antibodies, matching the LOD (54 pg mL−1) and LOQ (181 pg mL−1) of the existing conventional immunocapture LC-MS/MS method for determination of ProGRP. Peptide and protein capture using the same mAb were also compared with respect to sample clean-up, and the peptide capture workflow yielded cleaner extracts and therewith less complex chromatograms. Analysis of five patient samples demonstrated that peptide capture by anti-protein antibodies can be used for the determination of various levels of endogenously present ProGRP. Targeted protein biomarker determination by immunocapture LC-MS/MS: comparison of peptide and protein capture using anti-protein antibodies.![]()
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Affiliation(s)
| | - Bassem Farhat
- Department Pharmacy
- University of Oslo
- 0316 Oslo
- Norway
| | - Inger Oulie
- Department Pharmacy
- University of Oslo
- 0316 Oslo
- Norway
| | | | - Elisabeth Paus
- Department of Medical Biochemistry
- Norwegian Radium Hospital
- Oslo University Hospital
- Norway
| | - Léon Reubsaet
- Department Pharmacy
- University of Oslo
- 0316 Oslo
- Norway
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26
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Vlahou A. Implementation of Clinical Proteomics: A Step Closer to Personalized Medicine? Proteomics Clin Appl 2018; 13:e1800088. [DOI: 10.1002/prca.201800088] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 11/23/2018] [Indexed: 01/19/2023]
Affiliation(s)
- Antonia Vlahou
- Biomedical Research FoundationAcademy of Athens Soranou Efessiou 4 11527 Athens Greece
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27
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Osbak KK, Van Raemdonck GA, Dom M, Cameron CE, Meehan CJ, Deforce D, Ostade XV, Kenyon CR, Dhaenens M. Candidate Treponema pallidum biomarkers uncovered in urine from individuals with syphilis using mass spectrometry. Future Microbiol 2018; 13:1497-1510. [PMID: 30311792 DOI: 10.2217/fmb-2018-0182] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
AIM A diagnostic test that could detect Treponema pallidum antigens in urine would facilitate the prompt diagnosis of syphilis. MATERIALS & METHODS Urine from 54 individuals with various clinical stages of syphilis and 6 controls were pooled according to disease stage and interrogated with complementary mass spectrometry techniques to uncover potential syphilis biomarkers. RESULTS & CONCLUSION In total, 26 unique peptides were uncovered corresponding to four unique T. pallidum proteins that have low genetic sequence similarity to other prokaryotes and human proteins. This is the first account of direct T. pallidum protein detection in human clinical samples using mass spectrometry. The implications of these findings for future diagnostic test development is discussed. Data are available via ProteomeXchange with identifier PXD009707.
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Affiliation(s)
- Kara K Osbak
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium
| | - Geert A Van Raemdonck
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Laboratory for Protein Science, Proteomics & Epigenetic Signalling & Centre for Proteomics, University of Antwerp, Wilrijk, Belgium
| | - Martin Dom
- Laboratory for Protein Science, Proteomics & Epigenetic Signalling & Centre for Proteomics, University of Antwerp, Wilrijk, Belgium
| | - Caroline E Cameron
- Department of Biochemistry & Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Conor J Meehan
- Department of Biomedical Sciences, Institute for Tropical Medicine, Antwerp, Belgium
| | - Dieter Deforce
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
| | - Xaveer Van Ostade
- Laboratory for Protein Science, Proteomics & Epigenetic Signalling & Centre for Proteomics, University of Antwerp, Wilrijk, Belgium
| | - Chris R Kenyon
- HIV/STI Unit, Institute of Tropical Medicine, Antwerp, Belgium.,Division of Infectious Diseases & HIV Medicine, University of Cape Town, Cape Town, South Africa
| | - Maarten Dhaenens
- Laboratory for Pharmaceutical Biotechnology, Ghent University, Ghent, Belgium
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28
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Popp R, Li H, Borchers CH. Immuno-MALDI (iMALDI) mass spectrometry for the analysis of proteins in signaling pathways. Expert Rev Proteomics 2018; 15:701-708. [DOI: 10.1080/14789450.2018.1516147] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Affiliation(s)
- Robert Popp
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Huiyan Li
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - Christoph H. Borchers
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec, Canada
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29
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Yin X, Baig F, Haudebourg E, Blankley RT, Gandhi T, Müller S, Reiter L, Hinterwirth H, Pechlaner R, Tsimikas S, Santer P, Willeit J, Kiechl S, Witztum JL, Sullivan A, Mayr M. Plasma Proteomics for Epidemiology: Increasing Throughput With Standard-Flow Rates. ACTA ACUST UNITED AC 2018; 10:CIRCGENETICS.117.001808. [PMID: 29237681 DOI: 10.1161/circgenetics.117.001808] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2017] [Accepted: 10/03/2017] [Indexed: 12/26/2022]
Abstract
BACKGROUND Mass spectrometry is selective and sensitive, permitting routine quantification of multiple plasma proteins. However, commonly used nanoflow liquid chromatography (LC) approaches hamper sample throughput, reproducibility, and robustness. For this reason, most publications using plasma proteomics to date are small in study size. METHODS AND RESULTS Here, we tested a standard-flow LC mass spectrometry (MS) method using multiple reaction monitoring for the application to large epidemiological cohorts. We have reduced the LC-MS run time to almost a third of the nanoflow LC-MS approach. On the basis of a comparison of the quantification of 100 plasma proteins in >1500 LC-MS runs, the SD range of the retention time during continuous operation was substantially lower with the standard-flow LC-MS (<0.05 minutes) compared with the nanoflow LC-MS method (0.26-0.44 minutes). In addition, the standard-flow LC method also offered less variation in protein measurements. However, 5× more sample volume was required to achieve similar sensitivity. Two different commercial multiple reaction monitoring kits and an antibody-based multiplexing kit were used to compare the apolipoprotein measurements in a subset of samples. In general, good agreement was observed between the 2 multiple reaction monitoring kits, but some of the multiple reaction monitoring-based measurements differed from antibody-based assays. CONCLUSIONS The multiplexing capability of LC-MS combined with a standard-flow method increases throughput and reduces the costs of large-scale protein measurements in epidemiological cohorts, but protein rather than peptide standards will be required for defined absolute proteoform quantification.
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Affiliation(s)
- Xiaoke Yin
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Ferheen Baig
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Eloi Haudebourg
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Richard T Blankley
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Tejas Gandhi
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Sebastian Müller
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Lukas Reiter
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Helmut Hinterwirth
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Raimund Pechlaner
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Sotirios Tsimikas
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Peter Santer
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Johann Willeit
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Stefan Kiechl
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Joseph L Witztum
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Anthony Sullivan
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.)
| | - Manuel Mayr
- From the King's British Heart Foundation Centre, King's College London, United Kingdom (X.Y., F.B., E.H., H.H., M.M.); Agilent Technologies Ltd, Cheadle, United Kingdom (R.T.B., A.S.); Biognosys AG, Schlieren, Switzerland (T.G., S.M., L.R.); Department of Neurology, Medical University of Innsbruck, Austria (R.P., J.W., S.K.); School of Medicine, University of California San Diego (S.T., J.L.W.); and Department of Laboratory Medicine, Bruneck Hospital, Italy (P.S.).
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30
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Development of an automated, interference-free, 2D-LC–MS/MS assay for quantification of a therapeutic mAb in human sera. Bioanalysis 2018; 10:1023-1037. [DOI: 10.4155/bio-2017-0252] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Aim: Hybrid LC–MS/MS assays are increasingly used to quantitate proteins in biological matrices. These assays involve analyte enrichment at the protein level. Although suitability has been demonstrated, they are limited by the lack of appropriate affinity reagents and may suffer from interferences caused by binding proteins or antibodies. Results: An online stable isotope standards and capture by anti-peptide antibodies assay was developed, which involves tryptic digestion of a therapeutic monoclonal antibody in human serum to destroy interfering proteins followed by enrichment using high affinity peptide antibodies. The assay was validated and compared with a standard ligand-binding assay currently used for quantification. Conclusion: The data show that the stable isotope standards and capture by anti-peptide antibodies-2D-LC–MS/MS assay can be used as an alternative method for measurement of monoclonal antibodies in clinical samples.
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31
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Topbas C, Swick A, Razavi M, Anderson NL, Pearson TW, Bystrom C. Measurement of Lipoprotein-Associated Phospholipase A2 by Use of 3 Different Methods: Exploration of Discordance between ELISA and Activity Assays. Clin Chem 2018; 64:697-704. [DOI: 10.1373/clinchem.2017.279752] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 12/18/2017] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
Lipoprotein-associated phospholipase A2 (Lp-PLA2), an enzyme associated with inflammation, is used as a biomarker for cardiovascular disease risk. Both the concentration and activity of Lp-PLA2 have been shown to be clinically relevant. However, there is a discordance between the serum concentration of Lp-PLA2 measured by the standard ELISA-based immunoassays and the activity of this enzyme, leading to substantial discordance in risk categorization depending on assay format.
METHODS
We developed 2 LC-MS/MS–based assays to quantify serum Lp-PLA2 activity (multiple reaction monitoring detection of product) and concentration [stable isotope standards and capture by antipeptide antibody (SISCAPA) immunoaffinity], and we investigated their correlation to commercially offered colorimetric activity and immunometric concentrations assays. Associations between Lp-PLA2 and lipoproteins and the effect of selected detergents in liberating Lp-PLA2 were evaluated by use of immunoprecipitation and Western blot analyses.
RESULTS
Serum Lp-PLA2 concentrations measured by quantitative SISCAPA-mass spectrometry were substantially higher than concentrations typically measured by immunoassay and showed an improved agreement with Lp-PLA2 activity. With detergents, liberation of Lp-PLA2 from lipoprotein complexes dramatically increased the amount of protein detected by immunoassay and improved the agreement with activity measurements.
CONCLUSIONS
Quantitative analysis of Lp-PLA2 concentration and activity by LC-MS/MS assays provided key insight into resolving the well-documented discordance between Lp-PLA2 concentration (determined by immunoassay) and activity. Quantitative detection of Lp-PLA2 by immunoassay appears to be strongly inhibited by interaction of Lp-PLA2 with lipoprotein. Together, the results illustrate the advantages of quantitative LC-MS/MS for measurement of Lp-PLA2 concentration (by SISCAPA) and activity (by direct product detection).
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32
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Dittrich J, Adam M, Maas H, Hecht M, Reinicke M, Ruhaak LR, Cobbaert C, Engel C, Wirkner K, Löffler M, Thiery J, Ceglarek U. Targeted On-line SPE-LC-MS/MS Assay for the Quantitation of 12 Apolipoproteins from Human Blood. Proteomics 2018; 18. [PMID: 29280342 DOI: 10.1002/pmic.201700279] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/01/2017] [Indexed: 12/22/2022]
Abstract
Laborious sample pretreatment of biological samples represents the most limiting factor for the translation of targeted proteomics assays from research to clinical routine. An optimized method for the simultaneous quantitation of 12 major apolipoproteins (apos) combining on-line SPE and fast LC-MS/MS analysis in 6.5 min total run time was developed, reducing the manual sample pretreatment time of 3 μL serum or plasma by 60%. Within-run and between-day imprecisions below 10 and 15% (n = 10) and high recovery rates (94-131%) were obtained applying the high-throughput setup. High-quality porcine trypsin was used, which outperformed cost-effective bovine trypsin regarding digestion efficiency. Comparisons with immunoassays and another LC-MS/MS assay demonstrated good correlation (Pearson's R: 0.81-0.98). Further, requirements on sample quality concerning sampling, processing, and long-term storage up to 1 year were investigated revealing significant influences of the applied sampling material and coagulant on quantitation results. Apo profiles of 1339 subjects of the LIFE-Adult-Study were associated with lifestyle and physiological parameters as well as establish parameters of lipid metabolism (e.g., triglycerides, cholesterol). Besides gender effects, most significant impact was seen regarding lipid-lowering medication. In conclusion, this novel highly standardized, high-throughput targeted proteomics assay utilizes a fast, simultaneous analysis of 12 apos from least sample amounts.
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Affiliation(s)
- Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany.,LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Melanie Adam
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Hilke Maas
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Max Hecht
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Madlen Reinicke
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Christa Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Christoph Engel
- LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany.,Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
| | - Kerstin Wirkner
- LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Markus Löffler
- LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany.,Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
| | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany.,LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany.,LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
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33
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HASHII N, UTOH M, OHTSU Y, KATO N, GODA R, GOTO R, SHIMIZU H, TAKAMURA F, HOSHINO M, MABUCHI M, YAMAGUCHI T, ISHII-WATABE A, KATORI N. Bioanalytical Quantification of Therapeutic Antibodies by Liquid Chromatography/mass Spectrometry. CHROMATOGRAPHY 2018. [DOI: 10.15583/jpchrom.2017.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
| | | | | | - Nozomu KATO
- Translational Research Department, Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma Corp
| | | | | | | | | | | | - Masanari MABUCHI
- DMPK Research Laboratories, Sohyaku Innovative Research Division, Mitsubishi Tanabe Pharma Corp
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34
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Next-Generation Proteomics and Its Application to Clinical Breast Cancer Research. THE AMERICAN JOURNAL OF PATHOLOGY 2017; 187:2175-2184. [DOI: 10.1016/j.ajpath.2017.07.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2017] [Revised: 07/05/2017] [Accepted: 07/06/2017] [Indexed: 12/17/2022]
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35
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Geyer PE, Holdt LM, Teupser D, Mann M. Revisiting biomarker discovery by plasma proteomics. Mol Syst Biol 2017; 13:942. [PMID: 28951502 PMCID: PMC5615924 DOI: 10.15252/msb.20156297] [Citation(s) in RCA: 514] [Impact Index Per Article: 73.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/04/2017] [Accepted: 08/15/2017] [Indexed: 01/13/2023] Open
Abstract
Clinical analysis of blood is the most widespread diagnostic procedure in medicine, and blood biomarkers are used to categorize patients and to support treatment decisions. However, existing biomarkers are far from comprehensive and often lack specificity and new ones are being developed at a very slow rate. As described in this review, mass spectrometry (MS)-based proteomics has become a powerful technology in biological research and it is now poised to allow the characterization of the plasma proteome in great depth. Previous "triangular strategies" aimed at discovering single biomarker candidates in small cohorts, followed by classical immunoassays in much larger validation cohorts. We propose a "rectangular" plasma proteome profiling strategy, in which the proteome patterns of large cohorts are correlated with their phenotypes in health and disease. Translating such concepts into clinical practice will require restructuring several aspects of diagnostic decision-making, and we discuss some first steps in this direction.
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Affiliation(s)
- Philipp E Geyer
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
| | - Lesca M Holdt
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Daniel Teupser
- Institute of Laboratory Medicine, University Hospital, LMU Munich, Munich, Germany
| | - Matthias Mann
- Department of Proteomics and Signal Transduction, Max Planck Institute of Biochemistry, Martinsried, Germany
- Faculty of Health Sciences, NNF Center for Protein Research, University of Copenhagen, Copenhagen, Denmark
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36
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Hsiao YC, Chi LM, Chien KY, Chiang WF, Chen SF, Chuang YN, Lin SY, Wu CC, Chang YT, Chu LJ, Chen YT, Chia SL, Chien CY, Chang KP, Chang YS, Yu JS. Development of a Multiplexed Assay for Oral Cancer Candidate Biomarkers Using Peptide Immunoaffinity Enrichment and Targeted Mass Spectrometry. Mol Cell Proteomics 2017; 16:1829-1849. [PMID: 28821604 DOI: 10.1074/mcp.ra117.000147] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Indexed: 01/15/2023] Open
Abstract
Oral cancer is one of the most common cancers worldwide, and there are currently no biomarkers approved for aiding its management. Although many potential oral cancer biomarkers have been discovered, very few have been verified in body fluid specimens in parallel to evaluate their clinical utility. The lack of appropriate multiplexed assays for chosen targets represents one of the bottlenecks to achieving this goal. In the present study, we develop a peptide immunoaffinity enrichment-coupled multiple reaction monitoring-mass spectrometry (SISCAPA-MRM) assay for verifying multiple reported oral cancer biomarkers in saliva. We successfully produced 363 clones of mouse anti-peptide monoclonal antibodies (mAbs) against 36 of 49 selected targets, and characterized useful mAbs against 24 targets in terms of their binding affinity for peptide antigens and immuno-capture ability. Comparative analyses revealed that an equilibrium dissociation constant (KD ) cut-off value < 2.82 × 10-9 m could identify most clones with an immuno-capture recovery rate >5%. Using these mAbs, we assembled a 24-plex SISCAPA-MRM assay and optimized assay conditions in a 25-μg saliva matrix background. This multiplexed assay showed reasonable precision (median coefficient of variation, 7.16 to 32.09%), with lower limits of quantitation (LLOQ) of <10, 10-50, and >50 ng/ml for 14, 7 and 3 targets, respectively. When applied to a model saliva sample pooled from oral cancer patients, this assay could detect 19 targets at higher salivary levels than their LLOQs. Finally, we demonstrated the utility of this assay for quantification of multiple targets in individual saliva samples (20 healthy donors and 21 oral cancer patients), showing that levels of six targets were significantly altered in cancer compared with the control group. We propose that this assay could be used in future studies to compare the clinical utility of multiple oral cancer biomarker candidates in a large cohort of saliva samples.
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Affiliation(s)
- Yung-Chin Hsiao
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,§Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Lang-Ming Chi
- ¶Clinical Proteomics Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kun-Yi Chien
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,¶Clinical Proteomics Core Laboratory, Chang Gung Memorial Hospital, Taoyuan, Taiwan.,‖Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Fan Chiang
- **Department of Oral & Maxillofacial Surgery, Chi-Mei Medical Center, Liouying, Taiwan.,‡‡School of Dentistry, National Yang Ming University, Taipei, Taiwan
| | - Szu-Fan Chen
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Yao-Ning Chuang
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Shih-Yu Lin
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Chun Wu
- ‖Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Ya-Ting Chang
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Lichieh Julie Chu
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,§Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yi-Ting Chen
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,‖Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,§§Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,¶¶Department of Nephrology, Chang Gung Memorial Hospital, Linkou Medical Center, Taoyuan, Taiwan
| | - Shu-Li Chia
- ‖‖Health Promotion Administration, Ministry of Health and Welfare, Taiwan
| | - Chih-Yen Chien
- Department of Otolaryngology, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung, Taiwan
| | - Kai-Ping Chang
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Departments of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Yu-Sun Chang
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan.,Departments of Otolaryngology-Head & Neck Surgery, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Jau-Song Yu
- From the ‡Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan; .,§Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.,‖Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan.,Department of Cell and Molecular Biology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
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37
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Li H, Popp R, Frohlich B, Chen MX, Borchers CH. Peptide and Protein Quantification Using Automated Immuno-MALDI (iMALDI). J Vis Exp 2017. [PMID: 28872133 DOI: 10.3791/55933] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Mass spectrometry (MS) is one of the most commonly used technologies for quantifying proteins in complex samples, with excellent assay specificity as a result of the direct detection of the mass-to-charge ratio of each target molecule. However, MS-based proteomics, like most other analytical techniques, has a bias towards measuring high-abundance analytes, so it is challenging to achieve detection limits of low ng/mL or pg/mL in complex samples, and this is the concentration range for many disease-relevant proteins in biofluids such as human plasma. To assist in the detection of low-abundance analytes, immuno-enrichment has been integrated into the assay to concentrate and purify the analyte before MS measurement, significantly improving assay sensitivity. In this work, the immuno- Matrix-Assisted Laser Desorption/Ionization (iMALDI) technology is presented for the quantification of proteins and peptides in biofluids, based on immuno-enrichment on beads, followed by MALDI-MS measurement without prior elution. The anti-peptide antibodies are functionalized on magnetic beads, and incubated with samples. After washing, the beads are directly transferred onto a MALDI target plate, and the signals are measured by a MALDI-Time of Flight (MALDI-TOF) instrument after the matrix solution has been applied to the beads. The sample preparation procedure is simplified compared to other immuno-MS assays, and the MALDI measurement is fast. The whole sample preparation is automated with a liquid handling system, with improved assay reproducibility and higher throughput. In this article, the iMALDI assay is used for determining the peptide angiotensin I (Ang I) concentration in plasma, which is used clinically as readout of plasma renin activity for the screening of primary aldosteronism (PA).
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Affiliation(s)
- Huiyan Li
- University of Victoria-Genome BC Proteomics Centre
| | - Robert Popp
- University of Victoria-Genome BC Proteomics Centre
| | | | | | - Christoph H Borchers
- University of Victoria-Genome BC Proteomics Centre; Dept of Biochemistry and Microbiology, University of Victoria; Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University; Gerald Bronfman Department of Oncology, Jewish General Hospital;
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38
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Thomas A, Schänzer W, Thevis M. Immunoaffinity techniques coupled to mass spectrometry for the analysis of human peptide hormones: advances and applications. Expert Rev Proteomics 2017; 14:799-807. [PMID: 28758805 DOI: 10.1080/14789450.2017.1362338] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
INTRODUCTION The accurate and comprehensive determination of peptide hormones from biological fluids has represented a considerable challenge to analytical chemists for decades. Besides long-established bioanalytical ligand binding assays (or ELISA, RIA, etc.), more and more mass spectrometry-based methods have been developed recently for purposes commonly referred to as targeted proteomics. Eventually the combination of both, analyte extraction by immunoaffinity and subsequent detection by mass spectrometry, has shown to synergistically enhance the test methods' performance characteristics. Areas covered: The review provides an overview about the actual state of existing methods and applications concerning the analysis of endogenous peptide hormones. Here, special focus is on recent developments considering the extraction procedures with immobilized antibodies, the subsequent separation of target analytes, and their detection by mass spectrometry. Expert commentary: Key aspects of procedures aiming at the detection and/or quantification of peptidic analytes in biological matrices have experienced considerable improvements in the last decade, particularly in terms of the assays' sensitivity, the option of multiplexing target compounds, automatization, and high throughput operation. Despite these advances and progress as expected to be seen in the near future, immunoaffinity purification coupled to mass spectrometry is not yet a standard procedure in routine analysis compared to ELISA/RIA.
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Affiliation(s)
- Andreas Thomas
- a Institute of Biochemistry/Center for Preventive Doping Research , German Sport University Cologne , Cologne , Germany
| | - Wilhelm Schänzer
- a Institute of Biochemistry/Center for Preventive Doping Research , German Sport University Cologne , Cologne , Germany
| | - Mario Thevis
- a Institute of Biochemistry/Center for Preventive Doping Research , German Sport University Cologne , Cologne , Germany.,b European Monitoring Center for Emerging Doping Agents (EuMoCEDA) , Cologne/Bonn , Germany
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39
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Wang H, Drake SK, Yong C, Gucek M, Lyes MA, Rosenberg AZ, Soderblom E, Arthur Moseley M, Dekker JP, Suffredini AF. A Genoproteomic Approach to Detect Peptide Markers of Bacterial Respiratory Pathogens. Clin Chem 2017; 63:1398-1408. [PMID: 28588123 PMCID: PMC10863334 DOI: 10.1373/clinchem.2016.269647] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 05/02/2017] [Indexed: 12/16/2022]
Abstract
BACKGROUND Rapid identification of respiratory pathogens may facilitate targeted antimicrobial therapy. Direct identification of bacteria in bronchoalveolar lavage (BAL) by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry is confounded by interfering substances. We describe a method to identify unique peptide markers of 5 gram-negative bacteria by liquid chromatography-tandem mass spectrometry (LC-MS/MS) for direct pathogen identification in BAL. METHODS In silico translation and digestion were performed on 14-25 whole genomes representing strains of Acinetobacter baumannii, Moraxella catarrhalis, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, and Klebsiella pneumoniae. Peptides constituting theoretical core peptidomes in each were identified. Rapid tryptic digestion was performed; peptides were analyzed by LC-MS/MS and compared with the theoretical core peptidomes. High-confidence core peptides (false discovery rate <1%) were identified and analyzed with the lowest common ancestor search to yield potential species-specific peptide markers. The species specificity of each peptide was verified with protein BLAST. Further, 1 or 2 pathogens were serially diluted into pooled inflamed BAL, and a targeted LC-MS/MS assay was used to detect 25 peptides simultaneously. RESULTS Five unique peptides with the highest abundance for each pathogen distinguished these pathogens with varied detection sensitivities. Peptide markers for A. baumannii and P. aeruginosa, when spiked simultaneously into inflamed BAL, were detected with as few as 3.6 (0.2) × 103 and 2.2 (0.6) × 103 colony-forming units, respectively, by targeted LC-MS/MS. CONCLUSIONS This proof-of-concept study shows the feasibility of identifying unique peptides in BAL for 5 gram-negative bacterial pathogens, and it may provide a novel approach for rapid direct identification of bacterial pathogens in BAL.
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Affiliation(s)
- Honghui Wang
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Steven K Drake
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Chen Yong
- Proteomic Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Marjan Gucek
- Proteomic Core Facility, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Matthew A Lyes
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Avi Z Rosenberg
- Kidney Disease Section, National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD
| | - Erik Soderblom
- Proteomics and Metabolomics Shared Resource, Duke University School of Medicine, Durham, NC
| | - M Arthur Moseley
- Proteomics and Metabolomics Shared Resource, Duke University School of Medicine, Durham, NC
| | - John P Dekker
- Microbiology Service, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, MD
| | - Anthony F Suffredini
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, MD;
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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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Li H, Popp R, Chen M, MacNamara EM, Juncker D, Borchers CH. Bead-Extractor Assisted Ready-to-Use Reagent System (BEARS) for Immunoprecipitation Coupled to MALDI-MS. Anal Chem 2017; 89:3834-3839. [DOI: 10.1021/acs.analchem.6b04169] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Huiyan Li
- University of Victoria - Genome BC Proteomics Centre, #3101-4464 Markham Street, Vancouver
Island Technology Park, Victoria, British Columbia V8Z 7X8, Canada
- Biomedical
Engineering Department, McGill University, Duff Medical Building, McGill University,
3775, rue University, Room 316, Montreal, Quebec H3A 2B4, Canada
- McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue, Room 6206, Montreal, Quebec H3A 1A4, Canada
| | - Robert Popp
- University of Victoria - Genome BC Proteomics Centre, #3101-4464 Markham Street, Vancouver
Island Technology Park, Victoria, British Columbia V8Z 7X8, Canada
| | - Michael Chen
- Jewish General Hospital, 3755
Côte-Ste-Catherine Road, Montreal, Quebec H3T 1E2, Canada
| | | | - David Juncker
- Biomedical
Engineering Department, McGill University, Duff Medical Building, McGill University,
3775, rue University, Room 316, Montreal, Quebec H3A 2B4, Canada
- McGill University and Genome Quebec Innovation Centre, 740 Dr. Penfield Avenue, Room 6206, Montreal, Quebec H3A 1A4, Canada
| | - Christoph H. Borchers
- University of Victoria - Genome BC Proteomics Centre, #3101-4464 Markham Street, Vancouver
Island Technology Park, Victoria, British Columbia V8Z 7X8, Canada
- Department
of Biochemistry and Microbiology, University of Victoria, Petch Building
Room 207, 3800 Finnerty Road, Victoria, British Columbia V8P 5C2, Canada
- Gerald Bronfman
Department of Oncology, Jewish General Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada
- Proteomics
Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General
Hospital, McGill University, Montreal, Quebec, H3T 1E2, Canada
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Kistowski M, Dębski J, Karczmarski J, Paziewska A, Olędzki J, Mikula M, Ostrowski J, Dadlez M. A Strong Neutrophil Elastase Proteolytic Fingerprint Marks the Carcinoma Tumor Proteome. Mol Cell Proteomics 2016; 16:213-227. [PMID: 27927741 DOI: 10.1074/mcp.m116.058818] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Revised: 11/12/2016] [Indexed: 12/18/2022] Open
Abstract
Proteolytic cascades are deeply involved in critical stages of cancer progression. During the course of peptide-wise analysis of shotgun proteomic data sets representative of colon adenocarcinoma (AC) and ulcerative colitis (UC), we detected a cancer-specific proteolytic fingerprint composed of a set of numerous protein fragments cleaved C-terminally to V, I, A, T, or C residues, significantly overrepresented in AC. A peptide set linked by a common VIATC cleavage consensus was the only prominent cancer-specific proteolytic fingerprint detected. This sequence consensus indicated neutrophil elastase as a source of the fingerprint. We also found that a large fraction of affected proteins are RNA processing proteins associated with the nuclear fraction and mostly cleaved within their functionally important RNA-binding domains. Thus, we detected a new class of cancer-specific peptides that are possible markers of tumor-infiltrating neutrophil activity, which often correlates with the clinical outcome. Data are available via ProteomeXchange with identifiers: PXD005274 (Data set 1) and PXD004249 (Data set 2). Our results indicate the value of peptide-wise analysis of large global proteomic analysis data sets as opposed to protein-wise analysis, in which outlier differential peptides are usually neglected.
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Affiliation(s)
- Michał Kistowski
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw
| | - Janusz Dębski
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw
| | - Jakub Karczmarski
- §Department of Genetics, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wilhelma Konrada Roentgena 5, 02-781 Warsaw, Poland
| | - Agnieszka Paziewska
- §Department of Genetics, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wilhelma Konrada Roentgena 5, 02-781 Warsaw, Poland
| | - Jacek Olędzki
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw
| | - Michał Mikula
- §Department of Genetics, Maria Skłodowska-Curie Memorial Cancer Center and Institute of Oncology, Wilhelma Konrada Roentgena 5, 02-781 Warsaw, Poland
| | - Jerzy Ostrowski
- ¶Department of Gastroenterology Hepatology and Clinical Oncology, Medical Center for Postgraduate Education, Warsaw, Poland
| | - Michał Dadlez
- From the ‡Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5A, 02-106 Warsaw;
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Squeezing more value from the analytes we have: personal baselines for multiple analytes in serial DBS. Bioanalysis 2016; 8:1539-1542. [DOI: 10.4155/bio-2016-0088] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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Multiplexed longitudinal measurement of protein biomarkers in DBS using an automated SISCAPA workflow. Bioanalysis 2016; 8:1597-1609. [PMID: 27420772 DOI: 10.4155/bio-2016-0059] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND The use of DBS for quantitative protein biomarker measurement has been hindered by issues associated with blood hematocrit variations and lack of detection sensitivity, particularly when multiple biomarkers are measured. MATERIALS & METHODS An automated, multiplexed SISCAPA analysis was used to normalize blood volume variations in DBS and quantify proteins of varying abundance in longitudinal specimens. CONCLUSION The results showed that after normalizing the spot-to-spot hematocrit variations, peptide surrogates of protein biomarkers could be accurately quantitated in DBS. This allowed the establishment of baselines for a variety of biomarkers in multiple individuals and enabled detection of changes over time, thus offering an effective solution for longitudinal personal monitoring of biomarkers relevant in health and disease.
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Percy AJ, Byrns S, Pennington SR, Holmes DT, Anderson NL, Agreste TM, Duffy MA. Clinical translation of MS-based, quantitative plasma proteomics: status, challenges, requirements, and potential. Expert Rev Proteomics 2016; 13:673-84. [DOI: 10.1080/14789450.2016.1205950] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Andrew J. Percy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
| | - Simon Byrns
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Stephen R. Pennington
- Department of Pathology, School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Daniel T. Holmes
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - N. Leigh Anderson
- Department of Clinical Biomarkers, SISCAPA Assay Technologies, Inc., Washington, DC, USA
| | - Tasha M. Agreste
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
| | - Maureen A. Duffy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
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