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Chamrád I, Simerský R, Lenobel R, Novák O. Exploring affinity chromatography in proteomics: A comprehensive review. Anal Chim Acta 2024; 1306:342513. [PMID: 38692783 DOI: 10.1016/j.aca.2024.342513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 03/19/2024] [Accepted: 03/20/2024] [Indexed: 05/03/2024]
Abstract
Over the past decades, the proteomics field has undergone rapid growth. Progress in mass spectrometry and bioinformatics, together with separation methods, has brought many innovative approaches to the study of the molecular biology of the cell. The potential of affinity chromatography was recognized immediately after its first application in proteomics, and since that time, it has become one of the cornerstones of many proteomic protocols. Indeed, this chromatographic technique exploiting the specific binding between two molecules has been employed for numerous purposes, from selective removal of interfering (over)abundant proteins or enrichment of scarce biomarkers in complex biological samples to mapping the post-translational modifications and protein interactions with other proteins, nucleic acids or biologically active small molecules. This review presents a comprehensive survey of this versatile analytical tool in current proteomics. To navigate the reader, the haphazard space of affinity separations is classified according to the experiment's aims and the separated molecule's nature. Different types of available ligands and experimental strategies are discussed in further detail for each of the mentioned procedures.
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Affiliation(s)
- Ivo Chamrád
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic.
| | - Radim Simerský
- Department of Chemical Biology, Faculty of Science, Palacký University, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - René Lenobel
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
| | - Ondřej Novák
- Laboratory of Growth Regulators, Faculty of Science, Palacký University and Institute of Experimental Botany of the Czech Academy of Sciences, Šlechtitelů 241/27, CZ-77900, Olomouc, Holice, Czech Republic
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Song JG, Baral KC, Kim GL, Park JW, Seo SH, Kim DH, Jung DH, Ifekpolugo NL, Han HK. Quantitative analysis of therapeutic proteins in biological fluids: recent advancement in analytical techniques. Drug Deliv 2023; 30:2183816. [PMID: 36880122 PMCID: PMC10003146 DOI: 10.1080/10717544.2023.2183816] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2023] Open
Abstract
Pharmaceutical application of therapeutic proteins has been continuously expanded for the treatment of various diseases. Efficient and reliable bioanalytical methods are essential to expedite the identification and successful clinical development of therapeutic proteins. In particular, selective quantitative assays in a high-throughput format are critical for the pharmacokinetic and pharmacodynamic evaluation of protein drugs and to meet the regulatory requirements for new drug approval. However, the inherent complexity of proteins and many interfering substances presented in biological matrices have a great impact on the specificity, sensitivity, accuracy, and robustness of analytical assays, thereby hindering the quantification of proteins. To overcome these issues, various protein assays and sample preparation methods are currently available in a medium- or high-throughput format. While there is no standard or universal approach suitable for all circumstances, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) assay often becomes a method of choice for the identification and quantitative analysis of therapeutic proteins in complex biological samples, owing to its high sensitivity, specificity, and throughput. Accordingly, its application as an essential analytical tool is continuously expanded in pharmaceutical R&D processes. Proper sample preparation is also important since clean samples can minimize the interference from co-existing substances and improve the specificity and sensitivity of LC-MS/MS assays. A combination of different methods can be utilized to improve bioanalytical performance and ensure more accurate quantification. This review provides an overview of various protein assays and sample preparation methods, with particular emphasis on quantitative protein analysis by LC-MS/MS.
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Affiliation(s)
- Jae Geun Song
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Kshitis Chandra Baral
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Gyu-Lin Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Ji-Won Park
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Soo-Hwa Seo
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Da-Hyun Kim
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Dong Hoon Jung
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Nonye Linda Ifekpolugo
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
| | - Hyo-Kyung Han
- BK21 FOUR Team and Integrated Research Institute for Drug Development, College of Pharmacy, Dongguk University-Seoul, Goyang, Korea
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Chen YT, Liao WR, Wang HT, Chen HW, Chen SF. Targeted protein quantitation in human body fluids by mass spectrometry. Mass Spectrom Rev 2023; 42:2379-2403. [PMID: 35702881 DOI: 10.1002/mas.21788] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/11/2022] [Accepted: 04/08/2022] [Indexed: 06/15/2023]
Abstract
Human body fluids (biofluids) contain various proteins, some of which reflect individuals' physiological conditions or predict diseases. Therefore, the analysis of biofluids can provide substantial information on novel biomarkers for clinical diagnosis and prognosis. In the past decades, mass spectrometry (MS)-based technologies have been developed as proteomic strategies not only for the identification of protein biomarkers but also for biomarker verification/validation in body fluids for clinical applications. The main advantage of targeted MS-based methodologies is the accurate and specific simultaneous quantitation of multiple biomarkers with high sensitivity. Here, we review MS-based methodologies that are currently used for the targeted quantitation of protein components in human body fluids, especially in plasma, urine, cerebrospinal fluid, and saliva. In addition, the currently used MS-based methodologies are summarized with a specific focus on applicable clinical sample types, MS configurations, and acquisition modes.
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Affiliation(s)
- Yi-Ting Chen
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Nephrology, Kidney Research Center, Linkou Medical Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wan-Rou Liao
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
| | - Hsueh-Ting Wang
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
| | - Hsiao-Wei Chen
- Molecular and Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Sung-Fang Chen
- Department of Chemistry, National Taiwan Normal University, Taipei, Taiwan
- Instrumentation Center, National Taiwan Normal University, Taipei, Taiwan
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Gautam SS, Singh SP. Immunopurification Reagents and Their Application in Biologics and Biomarker Quantitation Using LC-MS/MS in Drug Discovery. J Chromatogr Sci 2023; 61:799-805. [PMID: 36469494 DOI: 10.1093/chromsci/bmac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Indexed: 10/01/2023]
Abstract
The LC-MS/MS technology is one of the most utilized bio-analytical tools owing to its advantage of selectivity, sensitivity and multitasking. The advent of novel biological therapies and increasing demand for protein biomarker identification and quantitation have put the LC-MS/MS technology at the forefront. The questions which are been posed to the LC-MS/MS scientist are complex. The complexity of the question increases further with the matrices in which these questions need to be answered. To bring down the complexity of the analysis, LC-MS/MS technology is utilizing the immunopurification (IP) technique as the new sample preparation technique. The IP reagents are the most common reagents which are used to decrease the matrices' complexity and allow the LC-MS/MS system to reach greater sensitivity. The utilization of these reagents is increasing every day, but the proper utilization of these reagents is still unknown to the common analyst in drug discovery. The present review throws light on the utilization aspect of these reagents, as we have classified these reagents on basis of their utilization, which will allow the readers to gain an understanding of these reagents. This review will also talk about the merits and the demerits of each approach and the current understanding of utilizing these reagents.
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Affiliation(s)
- Shashyendra Singh Gautam
- Toxicokinetics Laboratory/Analytical Chemistry Laboratory, Regulatory Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 200102, India
- Biocon-Bristol-Myers Squibb Research Centre, Syngene International Ltd, Bangalore 560100, India
| | - Sheelendra Pratap Singh
- Toxicokinetics Laboratory/Analytical Chemistry Laboratory, Regulatory Toxicology Group, CSIR-Indian Institute of Toxicology Research (CSIR-IITR), Lucknow 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 200102, India
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Farkona S, Pastrello C, Konvalinka A. Proteomics: Its Promise and Pitfalls in Shaping Precision Medicine in Solid Organ Transplantation. Transplantation 2023; 107:2126-2142. [PMID: 36808112 DOI: 10.1097/tp.0000000000004539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/22/2023]
Abstract
Solid organ transplantation is an established treatment of choice for end-stage organ failure. However, all transplant patients are at risk of developing complications, including allograft rejection and death. Histological analysis of graft biopsy is still the gold standard for evaluation of allograft injury, but it is an invasive procedure and prone to sampling errors. The past decade has seen an increased number of efforts to develop minimally invasive procedures for monitoring allograft injury. Despite the recent progress, limitations such as the complexity of proteomics-based technology, the lack of standardization, and the heterogeneity of populations that have been included in different studies have hindered proteomic tools from reaching clinical transplantation. This review focuses on the role of proteomics-based platforms in biomarker discovery and validation in solid organ transplantation. We also emphasize the value of biomarkers that provide potential mechanistic insights into the pathophysiology of allograft injury, dysfunction, or rejection. Additionally, we forecast that the growth of publicly available data sets, combined with computational methods that effectively integrate them, will facilitate a generation of more informed hypotheses for potential subsequent evaluation in preclinical and clinical studies. Finally, we illustrate the value of combining data sets through the integration of 2 independent data sets that pinpointed hub proteins in antibody-mediated rejection.
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Affiliation(s)
- Sofia Farkona
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
| | - Chiara Pastrello
- Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute University Health Network, Toronto, ON, Canada
- Data Science Discovery Centre for Chronic Diseases, Krembil Research Institute, Toronto Western Hospital, University Health Network, Toronto, ON, Canada
| | - Ana Konvalinka
- Toronto General Hospital Research Institute, University Health Network, Toronto, ON, Canada
- Soham and Shaila Ajmera Family Transplant Centre, University Health Network, Toronto, ON, Canada
- Department of Medicine, Division of Nephrology, University Health Network, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Institute of Medical Science, University of Toronto, Toronto, ON, Canada
- Canadian Donation and Transplantation Research Program, Edmonton, AB, Canada
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Zailani NNB, Ho PCL. Dried Blood Spots-A Platform for Therapeutic Drug Monitoring (TDM) and Drug/Disease Response Monitoring (DRM). Eur J Drug Metab Pharmacokinet 2023; 48:467-494. [PMID: 37495930 PMCID: PMC10480258 DOI: 10.1007/s13318-023-00846-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2023] [Indexed: 07/28/2023]
Abstract
This review provides an overview on the current applications of dried blood spots (DBS) as matrices for therapeutic drug (TDM) and drug or disease response monitoring (DRM). Compared with conventional methods using plasma/serum, DBS offers several advantages, including minimally invasiveness, a small blood volume requirement, reduced biohazardous risk, and improved sample stability. Numerous assays utilising DBS for TDM have been reported in the literature over the past decade, covering a wide range of therapeutic drugs. Several factors can affect the accuracy and reliability of the DBS sampling method, including haematocrit (HCT), blood volume, sampling paper and chromatographic effects. It is crucial to evaluate the correlation between DBS concentrations and conventional plasma/serum concentrations, as the latter has traditionally been used for clinical decision. The feasibility of using DBS sampling method as an option for home-based TDM is also discussed. Furthermore, DBS has also been used as a matrix for monitoring the drug or disease responses (DRM) through various approaches such as genotyping, viral load measurement, assessment of inflammatory factors, and more recently, metabolic profiling. Although this research is still in the development stage, advancements in technology are expected to lead to the identification of surrogate biomarkers for drug treatment in DBS and a better understanding of the correlation between DBS drug levels and drug responses. This will make DBS a valuable matrix for TDM and DRM, facilitating the achievement of pharmacokinetic and pharmacodynamic correlations and enabling personalised therapy.
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Affiliation(s)
- Nur Nabihah Binte Zailani
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore
| | - Paul Chi-Lui Ho
- Department of Pharmacy, National University of Singapore, 18 Science Drive 4, Singapore, 117543, Singapore.
- School of Pharmacy, Monash University Malaysia, Level 5, Building 2, 47500, Bandar Sunway, Selangor Darul Ehsan, Malaysia.
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Rao YF, Wang J, Cheng DN, Xu Y, Ren X, Yang W, Liu G, Xu W, Yan XH, Song Y, Zheng YB, An P, Zhong DL, He ZP, Ren JJ, Zhao Y. The Controversy of Pepsinogen A/Pepsin A in Detecting Extra-Gastroesophageal Reflux. J Voice 2023; 37:748-756. [PMID: 34090740 DOI: 10.1016/j.jvoice.2021.04.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Revised: 03/31/2021] [Accepted: 04/20/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND Pepsinogen A (PGA)/pepsin A is often used as a diagnostic marker of extra-gastroesophageal reflux. We aimed to explore whether its positivity in upper aerodigestive tract (UADT) was specific enough to diagnose reflux. METHODS PGA/pepsin A protein levels were examined in 10 types of tissues and 10 types of body fluid by immunological staining, western blot or Elisa, using three different commercially available brands simultaneously. Liquid chromatography-tandem mass spectrometry parallel reaction monitoring (LC-MS/MS PRM) served as a gold reference for the detection of PGA/pepsin A proteins. PGA gene expression was analyzed by reverse transcriptase sequencing methods for tissue samples. Specifically, 24 hour pH monitoring technique was conducted for patients who donated saliva samples. RESULTS Eight out of ten types of human tissue samples (stomach, esophagus, lung, kidney, colon, parotid gland, nasal turbinate and nasal polyps) were confirmed positive for PGA/pepsin A gene and protein by genetic and PRM technique, respectively. Two out of ten types of body fluid samples (gastric fluid, urine) were confirmed positive for PGA/pepsin A protein by PRM technique. The consistence rates of PGA/pepsin A positivity among three commercial antibody brands and Elisa kit were poor, and Elisa results of salivary did not match with 24-hour pH monitoring. CONCLUSIONS Multiple tissues and body fluid could be detected baseline expression levels of PGA/pepsin A gene and protein. However, those commercially available PGA/pepsin A antibodies achieved poor sensitivity and specificity, therefore, relying on the detection of PGA/pepsin A in UADT by single antibodies to diagnose extra-gastroesophageal reflux without a specific positive cut-off value is unreliable.
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Affiliation(s)
- Yu-Fang Rao
- Department of Oto-Rhino-Laryngology, and West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Jing Wang
- Department of Oto-Rhino-Laryngology, and West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Dan-Ni Cheng
- Department of Oto-Rhino-Laryngology, and West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Yang Xu
- Department of Oto-Rhino-Laryngology, and West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Xue Ren
- Institute of statistics and management, Shanghai University of Finance and Economics, Shanghai, China
| | - Wen Yang
- Department of Oto-Rhino-Laryngology, and West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Geoffrey Liu
- Princess Margaret Cancer Centre and University Health Network, University of Toronto, Toronto, ON, Canada.; Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada
| | - Wei Xu
- Dalla Lana School of Public Health, University of Toronto, Toronto, ON, Canada; Department of Biostatistics, Princess Margaret Cancer Centre, Toronto, ON, Canada
| | - Xiao-Hong Yan
- Department of Oto-Rhino-Laryngology, and West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Yao Song
- Institute of statistics and management, Shanghai University of Finance and Economics, Shanghai, China
| | - Yong-Bo Zheng
- Department of Oto-Rhino-Laryngology, and West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Ping An
- Department of Oto-Rhino-Laryngology, and West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Da-Lin Zhong
- Department of Oto-Rhino-Laryngology, and West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China
| | - Zhao-Ping He
- Department of Biomedical Research, Nemours/Alfred I.duPont Hospital for Children, Wilmington, Delaware, USA
| | - Jian-Jun Ren
- Department of Oto-Rhino-Laryngology, and West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China.; Princess Margaret Cancer Centre and University Health Network, University of Toronto, Toronto, ON, Canada..
| | - Yu Zhao
- Department of Oto-Rhino-Laryngology, and West China Biomedical Big Data Center, West China Hospital of Sichuan University, Chengdu, Sichuan Province, China..
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Abstract
Mass spectrometry (MS)-based proteomics have been increasingly implemented in various disciplines of laboratory medicine to identify and quantify biomolecules in a variety of biological specimens. MS-based proteomics is continuously expanding and widely applied in biomarker discovery for early detection, prognosis and markers for treatment response prediction and monitoring. Furthermore, making these advanced tests more accessible and affordable will have the greatest healthcare benefit.This review article highlights the new paradigms MS-based clinical proteomics has created in microbiology laboratories, cancer research and diagnosis of metabolic disorders. The technique is preferred over conventional methods in disease detection and therapy monitoring for its combined advantages in multiplexing capacity, remarkable analytical specificity and sensitivity and low turnaround time.Despite the achievements in the development and adoption of a number of MS-based clinical proteomics practices, more are expected to undergo transition from bench to bedside in the near future. The review provides insights from early trials and recent progresses (mainly covering literature from the NCBI database) in the application of proteomics in clinical laboratories.
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Vialaret J, Vignon M, Badiou S, Baptista G, Fichter L, Dupuy AM, Maceski AM, Fayolle M, Brousse M, Cristol JP, Jeandel C, Hirtz C, Lehmann S. New Perspectives of Multiplex Mass Spectrometry Blood Protein Quantification on Microsamples in Biological Monitoring of Elderly Patients. Int J Mol Sci 2023; 24:ijms24086989. [PMID: 37108152 PMCID: PMC10139225 DOI: 10.3390/ijms24086989] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/04/2023] [Accepted: 04/05/2023] [Indexed: 04/29/2023] Open
Abstract
Blood microsampling combined with large panels of clinically relevant tests are of major interest for the development of home sampling and predictive medicine. The aim of the study was to demonstrate the practicality and medical utility of microsamples quantification using mass spectrometry (MS) in a clinical setting by comparing two types of microsamples for multiplex MS protein detection. In a clinical trial based on elderly population, we compared 2 µL of plasma to dried blood spot (DBS) with a clinical quantitative multiplex MS approach. The analysis of the microsamples allowed the quantification of 62 proteins with satisfactory analytical performances. A total of 48 proteins were significantly correlated between microsampling plasma and DBS (p < 0.0001). The quantification of 62 blood proteins allowed us to stratify patients according to their pathophysiological status. Apolipoproteins D and E were the best biomarker link to IADL (instrumental activities of daily living) score in microsampling plasma as well as in DBS. It is, thus, possible to detect multiple blood proteins from micro-samples in compliance with clinical requirements and this allows, for example, to monitor the nutritional or inflammatory status of patients. The implementation of this type of analysis opens new perspectives in the field of diagnosis, monitoring and risk assessment for personalized medicine approaches.
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Affiliation(s)
- Jérôme Vialaret
- IRMB-PPC, INM, Montpellier University Hospital, INSERM, CNRS, University of Montpellier, 34295 Montpellier, France
| | - Margaux Vignon
- IRMB-PPC, INM, Montpellier University Hospital, INSERM, CNRS, University of Montpellier, 34295 Montpellier, France
| | - Stéphanie Badiou
- Department of Biochemistry and Hormonology, Montpellier University Hospital, University of Montpellier, 191 Avenue du Doyen Giraud, 34295 Montpellier, France
| | - Gregory Baptista
- Centre de Gérontologie Clinique Antonin-Balmès, Montpellier University Hospital, University of Montpellier, 39 Avenue Charles Flahault, 34090 Montpellier, France
| | - Laura Fichter
- IRMB-PPC, INM, Montpellier University Hospital, INSERM, CNRS, University of Montpellier, 34295 Montpellier, France
| | - Anne-Marie Dupuy
- Department of Biochemistry and Hormonology, Montpellier University Hospital, University of Montpellier, 191 Avenue du Doyen Giraud, 34295 Montpellier, France
| | - Aleksandra Maleska Maceski
- IRMB-PPC, INM, Montpellier University Hospital, INSERM, CNRS, University of Montpellier, 34295 Montpellier, France
| | - Martin Fayolle
- IRMB-PPC, INM, Montpellier University Hospital, INSERM, CNRS, University of Montpellier, 34295 Montpellier, France
- Department of Biochemistry and Hormonology, Montpellier University Hospital, University of Montpellier, 191 Avenue du Doyen Giraud, 34295 Montpellier, France
| | - Mehdi Brousse
- IRMB-PPC, INM, Montpellier University Hospital, INSERM, CNRS, University of Montpellier, 34295 Montpellier, France
- Department of Biochemistry and Hormonology, Montpellier University Hospital, University of Montpellier, 191 Avenue du Doyen Giraud, 34295 Montpellier, France
| | - Jean-Paul Cristol
- Department of Biochemistry and Hormonology, Montpellier University Hospital, University of Montpellier, 191 Avenue du Doyen Giraud, 34295 Montpellier, France
| | - Claude Jeandel
- Centre de Gérontologie Clinique Antonin-Balmès, Montpellier University Hospital, University of Montpellier, 39 Avenue Charles Flahault, 34090 Montpellier, France
| | - Christophe Hirtz
- IRMB-PPC, INM, Montpellier University Hospital, INSERM, CNRS, University of Montpellier, 34295 Montpellier, France
| | - Sylvain Lehmann
- IRMB-PPC, INM, Montpellier University Hospital, INSERM, CNRS, University of Montpellier, 34295 Montpellier, France
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Kelley EJ, Henson SN, Rahee F, Boyle AS, Engelbrektson AL, Nelson GA, Mead HL, Anderson NL, Razavi M, Yip R, Ladner JT, Scriba TJ, Altin JA. Virome-wide detection of natural infection events and the associated antibody dynamics using longitudinal highly-multiplexed serology. Nat Commun 2023; 14:1783. [PMID: 36997517 PMCID: PMC10062260 DOI: 10.1038/s41467-023-37378-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 03/07/2023] [Indexed: 04/03/2023] Open
Abstract
Current methods for detecting infections either require a sample collected from an actively infected site, are limited in the number of agents they can query, and/or yield no information on the immune response. Here we present an approach that uses temporally coordinated changes in highly-multiplexed antibody measurements from longitudinal blood samples to monitor infection events at sub-species resolution across the human virome. In a longitudinally-sampled cohort of South African adolescents representing >100 person-years, we identify >650 events across 48 virus species and observe strong epidemic effects, including high-incidence waves of Aichivirus A and the D68 subtype of Enterovirus D earlier than their widespread circulation was appreciated. In separate cohorts of adults who were sampled at higher frequency using self-collected dried blood spots, we show that such events temporally correlate with symptoms and transient inflammatory biomarker elevations, and observe the responding antibodies to persist for periods ranging from ≤1 week to >5 years. Our approach generates a rich view of viral/host dynamics, supporting novel studies in immunology and epidemiology.
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Affiliation(s)
- Erin J Kelley
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | - Sierra N Henson
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | - Fatima Rahee
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | - Annalee S Boyle
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | - Anna L Engelbrektson
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | - Georgia A Nelson
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | - Heather L Mead
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA
| | | | | | - Richard Yip
- SISCAPA Assay Technologies, Inc., Washington, DC, USA
| | - Jason T Ladner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Thomas J Scriba
- South African Tuberculosis Vaccine Initiative and Institute of Infectious Disease and Molecular Medicine, Division of Immunology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - John A Altin
- The Translational Genomics Research Institute (TGen), Flagstaff and Phoenix, AZ, USA.
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12
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Lin TT, Zhang T, Kitata RB, Liu T, Smith RD, Qian WJ, Shi T. Mass spectrometry-based targeted proteomics for analysis of protein mutations. Mass Spectrom Rev 2023; 42:796-821. [PMID: 34719806 PMCID: PMC9054944 DOI: 10.1002/mas.21741] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2021] [Revised: 09/28/2021] [Accepted: 10/07/2021] [Indexed: 05/03/2023]
Abstract
Cancers are caused by accumulated DNA mutations. This recognition of the central role of mutations in cancer and recent advances in next-generation sequencing, has initiated the massive screening of clinical samples and the identification of 1000s of cancer-associated gene mutations. However, proteomic analysis of the expressed mutation products lags far behind genomic (transcriptomic) analysis. With comprehensive global proteomics analysis, only a small percentage of single nucleotide variants detected by DNA and RNA sequencing have been observed as single amino acid variants due to current technical limitations. Proteomic analysis of mutations is important with the potential to advance cancer biomarker development and the discovery of new therapeutic targets for more effective disease treatment. Targeted proteomics using selected reaction monitoring (also known as multiple reaction monitoring) and parallel reaction monitoring, has emerged as a powerful tool with significant advantages over global proteomics for analysis of protein mutations in terms of detection sensitivity, quantitation accuracy and overall practicality (e.g., reliable identification and the scale of quantification). Herein we review recent advances in the targeted proteomics technology for enhancing detection sensitivity and multiplexing capability and highlight its broad biomedical applications for analysis of protein mutations in human bodily fluids, tissues, and cell lines. Furthermore, we review recent applications of top-down proteomics for analysis of protein mutations. Unlike the commonly used bottom-up proteomics which requires digestion of proteins into peptides, top-down proteomics directly analyzes intact proteins for more precise characterization of mutation isoforms. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale targeted detection and quantification of important protein mutations are discussed.
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Affiliation(s)
- Tai-Tu Lin
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tong Zhang
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Reta B. Kitata
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tao Liu
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Richard D. Smith
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Wei-Jun Qian
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
| | - Tujin Shi
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99354, USA
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13
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Sato S, Gillette M, de Santiago PR, Kuhn E, Burgess M, Doucette K, Feng Y, Mendez-Dorantes C, Ippoliti PJ, Hobday S, Mitchell MA, Doberstein K, Gysler SM, Hirsch MS, Schwartz L, Birrer MJ, Skates SJ, Burns KH, Carr SA, Drapkin R. LINE-1 ORF1p as a candidate biomarker in high grade serous ovarian carcinoma. Sci Rep 2023; 13:1537. [PMID: 36707610 PMCID: PMC9883229 DOI: 10.1038/s41598-023-28840-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Accepted: 01/25/2023] [Indexed: 01/29/2023] Open
Abstract
Long interspersed element 1 (LINE-1) open reading frame 1 protein (ORF1p) expression is a common feature of many cancer types, including high-grade serous ovarian carcinoma (HGSOC). Here, we report that ORF1p is not only expressed but also released by ovarian cancer and primary tumor cells. Immuno-multiple reaction monitoring-mass spectrometry assays showed that released ORF1p is confidently detectable in conditioned media, ascites, and patients' plasma, implicating ORF1p as a potential biomarker. Interestingly, ORF1p expression is detectable in fallopian tube (FT) epithelial precursors of HGSOC but not in benign FT, suggesting that ORF1p expression in an early event in HGSOC development. Finally, treatment of FT cells with DNA methyltransferase inhibitors led to robust expression and release of ORF1p, validating the regulatory role of DNA methylation in LINE-1 repression in non-tumorigenic tissue.
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Affiliation(s)
- Sho Sato
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Michael Gillette
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA, 02114, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Pamela R de Santiago
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Eric Kuhn
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Michael Burgess
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Kristen Doucette
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yi Feng
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | | | - Paul J Ippoliti
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Sara Hobday
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Marilyn A Mitchell
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Kai Doberstein
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Stefan M Gysler
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA
| | - Michelle S Hirsch
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, 02115, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Lauren Schwartz
- Department of Pathology and Laboratory Medicine, Hospital of the University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Michael J Birrer
- Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, 35233, USA
| | - Steven J Skates
- Harvard Medical School, Boston, MA, 02115, USA.,Biostatistics and Computational Biology, Massachusetts General Hospital, Boston, MA, USA
| | - Kathleen H Burns
- Harvard Medical School, Boston, MA, 02115, USA.,Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Steven A Carr
- The Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Harvard Medical School, Boston, MA, 02115, USA
| | - Ronny Drapkin
- Penn Ovarian Cancer Research Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA. .,Basser Center for BRCA, Abramson Cancer Center, University of Pennsylvania, Perelman School of Medicine, Philadelphia, PA, 19104, USA.
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14
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Van Puyvelde B, Van Uytfanghe K, Van Oudenhove L, Gabriels R, Van Royen T, Matthys A, Razavi M, Yip R, Pearson T, Drouin N, Claereboudt J, Foley D, Wardle R, Wyndham K, Hankemeier T, Jones D, Saelens X, Martens G, Stove CP, Deforce D, Martens L, Vissers JPC, Anderson NL, Dhaenens M. Cov 2MS: An Automated and Quantitative Matrix-Independent Assay for Mass Spectrometric Measurement of SARS-CoV-2 Nucleocapsid Protein. Anal Chem 2022; 94:17379-17387. [PMID: 36490367 PMCID: PMC9773173 DOI: 10.1021/acs.analchem.2c01610] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The pandemic readiness toolbox needs to be extended, targeting different biomolecules, using orthogonal experimental set-ups. Here, we build on our Cov-MS effort using LC-MS, adding SISCAPA technology to enrich proteotypic peptides of the SARS-CoV-2 nucleocapsid (N) protein from trypsin-digested patient samples. The Cov2MS assay is compatible with most matrices including nasopharyngeal swabs, saliva, and plasma and has increased sensitivity into the attomole range, a 1000-fold improvement compared to direct detection in a matrix. A strong positive correlation was observed with qPCR detection beyond a quantification cycle of 30-31, the level where no live virus can be cultured. The automatable sample preparation and reduced LC dependency allow analysis of up to 500 samples per day per instrument. Importantly, peptide enrichment allows detection of the N protein in pooled samples without sensitivity loss. Easily multiplexed, we detect variants and propose targets for Influenza A and B detection. Thus, the Cov2MS assay can be adapted to test for many different pathogens in pooled samples, providing longitudinal epidemiological monitoring of large numbers of pathogens within a population as an early warning system.
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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
| | | | - Ralf Gabriels
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biomolecular Medicine, Ghent University, 9000 Ghent, Belgium
| | - Tessa Van Royen
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent 9000 Belgium
| | - Arne Matthys
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent 9000 Belgium
| | - Morteza Razavi
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Richard Yip
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Terry Pearson
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
| | - Nicolas Drouin
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | | | - Dominic Foley
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - Robert Wardle
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - Kevin Wyndham
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - Thomas Hankemeier
- Division of Systems Biomedicine and Pharmacology, Leiden Academic Centre for Drug Research, Leiden University, 2333 AL Leiden, The Netherlands
| | - Donald Jones
- Leicester Cancer Research Centre, RKCSB, Cardiovascular Research Centre, Glenfield Hospital, University of Leicester, Leicester LE1 7RH, United Kingdom.,John and Lucille van Geest Biomarker Facility, Leicester LE3 9QP, United Kingdom.,The Department of Chemical Pathology and Metabolic Diseases, Leicester Royal Infirmary, Level 4, Sandringham Building, Leicester LE1 7RH, United Kingdom
| | - Xavier Saelens
- VIB-UGent Center for Medical Biotechnology, VIB, 9000 Ghent, Belgium.,Department of Biochemistry and Microbiology, Ghent University, Ghent 9000 Belgium
| | - Geert Martens
- AZ Delta Medical Laboratories, AZ Delta General Hospital, 8800 Roeselare, Belgium
| | - Christophe P Stove
- Laboratory of Toxicology, Department of Bioanalysis, Faculty of Pharmaceutical Sciences, Ghent University, 9000 Ghent, 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
| | - Johannes P C Vissers
- Waters Corporation, Wilmslow SK9 4AX, United Kingdom.,Waters Corporation, Milford, Massachusetts 01757, United States
| | - N Leigh Anderson
- SISCAPA Assay Technologies, Inc., Box 53309, Washington, DC 20009, United States
| | - Maarten Dhaenens
- ProGenTomics, Laboratory of Pharmaceutical Biotechnology, Ghent University, 9000 Ghent, Belgium
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15
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Halvorsen TG, Reubsaet L. The utility of molecularly imprinted polymers for mass spectrometric protein and proteomics analysis. Proteomics 2022; 22:e2100395. [PMID: 36217925 DOI: 10.1002/pmic.202100395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 09/30/2022] [Accepted: 10/04/2022] [Indexed: 11/08/2022]
Abstract
Selective and efficient sample clean-up is important in mass spectrometric protein- and proteomics analyses from biological matrices. Molecularly imprinted polymers (MIPs), polymers prepared to have tailor-made cavities for capture of target analytes may by such represent an interesting alternative for selective clean-up. The present review aims to give an overview of the utility of MIPs for protein capture from biological matrices prior to mass spectrometry (MS) analysis. The application of MIPs in depletion of abundant proteins, in protein and proteotypic peptide capture as well as in capture of post-translational modifications (PTMs) is described and discussed. In addition, an overview of available MIP formats and their advantages and challenges is given, together with an overview of the mass spectrometric techniques used in protein analysis after MIP capture. Overall, the present literature demonstrates that for many applications MIPs for sample clean-up in mass spectrometric protein and proteomics analysis from biological matrices is still not fully matured. MIPs for proteotypic peptide capture is the most mature approach and a method for routine use may be available within the next few years.
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Affiliation(s)
| | - Léon Reubsaet
- Department of Pharmacy, University of Oslo, Oslo, Norway
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16
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He B, Huang Z, Huang C, Nice EC. Clinical applications of plasma proteomics and peptidomics: Towards precision medicine. Proteomics Clin Appl 2022; 16:e2100097. [PMID: 35490333 DOI: 10.1002/prca.202100097] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023]
Abstract
In the context of precision medicine, disease treatment requires individualized strategies based on the underlying molecular characteristics to overcome therapeutic challenges posed by heterogeneity. For this purpose, it is essential to develop new biomarkers to diagnose, stratify, or possibly prevent diseases. Plasma is an available source of biomarkers that greatly reflects the physiological and pathological conditions of the body. An increasing number of studies are focusing on proteins and peptides, including many involving the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), and proteomics and peptidomics techniques are emerging as critical tools for developing novel precision medicine preventative measures. Excitingly, the emerging plasma proteomics and peptidomics toolbox exhibits a huge potential for studying pathogenesis of diseases (e.g., COVID-19 and cancer), identifying valuable biomarkers and improving clinical management. However, the enormous complexity and wide dynamic range of plasma proteins makes plasma proteome profiling challenging. Herein, we summarize the recent advances in plasma proteomics and peptidomics with a focus on their emerging roles in COVID-19 and cancer research, aiming to emphasize the significance of plasma proteomics and peptidomics in clinical applications and precision medicine.
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Affiliation(s)
- Bo He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China.,Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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17
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Austin TR, McHugh CP, Brody JA, Bis JC, Sitlani CM, Bartz TM, Biggs ML, Bansal N, Buzkova P, Carr SA, deFilippi CR, Elkind MSV, Fink HA, Floyd JS, Fohner AE, Gerszten RE, Heckbert SR, Katz DH, Kizer JR, Lemaitre RN, Longstreth WT, McKnight B, Mei H, Mukamal KJ, Newman AB, Ngo D, Odden MC, Vasan RS, Shojaie A, Simon N, Smith GD, Davies NM, Siscovick DS, Sotoodehnia N, Tracy RP, Wiggins KL, Zheng J, Psaty BM. Proteomics and Population Biology in the Cardiovascular Health Study (CHS): design of a study with mentored access and active data sharing. Eur J Epidemiol 2022; 37:755-765. [PMID: 35790642 PMCID: PMC9255954 DOI: 10.1007/s10654-022-00888-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 06/03/2022] [Indexed: 11/08/2022]
Abstract
BACKGROUND In the last decade, genomic studies have identified and replicated thousands of genetic associations with measures of health and disease and contributed to the understanding of the etiology of a variety of health conditions. Proteins are key biomarkers in clinical medicine and often drug-therapy targets. Like genomics, proteomics can advance our understanding of biology. METHODS AND RESULTS In the setting of the Cardiovascular Health Study (CHS), a cohort study of older adults, an aptamer-based method that has high sensitivity for low-abundance proteins was used to assay 4979 proteins in frozen, stored plasma from 3188 participants (61% women, mean age 74 years). CHS provides active support, including central analysis, for seven phenotype-specific working groups (WGs). Each CHS WG is led by one or two senior investigators and includes 10 to 20 early or mid-career scientists. In this setting of mentored access, the proteomic data and analytic methods are widely shared with the WGs and investigators so that they may evaluate associations between baseline levels of circulating proteins and the incidence of a variety of health outcomes in prospective cohort analyses. We describe the design of CHS, the CHS Proteomics Study, characteristics of participants, quality control measures, and structural characteristics of the data provided to CHS WGs. We additionally highlight plans for validation and replication of novel proteomic associations. CONCLUSION The CHS Proteomics Study offers an opportunity for collaborative data sharing to improve our understanding of the etiology of a variety of health conditions in older adults.
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Affiliation(s)
- Thomas R Austin
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA. .,Department of Epidemiology, University of Washington, Seattle, WA, USA.
| | | | - Jennifer A Brody
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Colleen M Sitlani
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Traci M Bartz
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA.,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Mary L Biggs
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Nisha Bansal
- Division of Nephrology, University of Washington, Seattle, WA, USA
| | - Petra Buzkova
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | | | | | | | - Howard A Fink
- Geriatric Research Education & Clinical Center, Minneapolis VA Healthcare System, Minneapolis, MN, USA
| | - James S Floyd
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Department of Epidemiology, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Alison E Fohner
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Department of Epidemiology, University of Washington, Seattle, WA, USA.,Institute of Public Health Genetics, University of Washington, Seattle, WA, USA
| | - Robert E Gerszten
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Daniel H Katz
- Division of Cardiovascular Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Jorge R Kizer
- Cardiology Section, San Francisco VA Health Care System, San Francisco, CA, USA.,Department of Biostatistics, University of California San Francisco, San Francisco, CA, USA.,Department of Epidemology, University of California San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Rozenn N Lemaitre
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - W T Longstreth
- Department of Epidemiology, University of Washington, Seattle, WA, USA.,Department of Neurology, University of Washington, Seattle, WA, USA
| | - Barbara McKnight
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hao Mei
- Department of Data Science, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Anne B Newman
- Department of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA, USA
| | - Debby Ngo
- Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Michelle C Odden
- Department of Epidemiology and Population Health, Stanford University, Stanford, CA, USA
| | - Ramachandran S Vasan
- Department of Epidemiology, School of Public Health, Boston University, Boston, MA, USA.,Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Ali Shojaie
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Noah Simon
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Neil M Davies
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK.,K.G. Jebsen Center for Genetic Epidemiology, Department of Public Health and Nursing, NTNU, Norwegian University of Science and Technology, Norwegian, Norway.,Bristol Medical School, Population Health Sciences, University of Bristol, Bristol, UK
| | | | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Division of Cardiology, University of Washington, Seattle, WA, USA
| | - Russell P Tracy
- Departments of Pathology & Laboratory Medicine, and Biochemistry, Larner College of Medicine, University of Vermont, Burlington, VT, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA
| | - Jie Zheng
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol, UK
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA.,Department of Epidemiology, University of Washington, Seattle, WA, USA.,Department of Medicine, University of Washington, Seattle, WA, USA.,Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
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18
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Hsiao JT, Chen KH, Sheu F. Determination of the soybean allergen Gly m 6 and its stability in food processing using liquid chromatography-tandem mass spectrometry coupled with stable-isotope dimethyl labelling. Food Addit Contam Part A Chem Anal Control Expo Risk Assess 2022; 39:1033-1046. [PMID: 35363120 DOI: 10.1080/19440049.2022.2056639] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 03/04/2022] [Accepted: 03/11/2022] [Indexed: 10/18/2022]
Abstract
A cost-effective method using liquid chromatography-tandem mass spectrometry (LC-MS/MS) coupled with stable-isotope dimethyl labelling was used for the determination of Gly m 6. The validation results revealed that the recoveries and precisions obtained from five spiked levels were in the ranges of 88.8-113.0% and 8.3-22.0%, respectively. The content and stability of the major soybean allergen Gly m 6 in various food processing procedures were evaluated by the quantification results of its surrogate signature peptide. The Gly m 6 content in soybean decreased by 42% after natto fermentation, and by 31% and 35% in pasteurised soymilk and sterilised soymilk, respectively, relative to the raw soymilk. Only 19% of Gly m 6 in raw soymilk was retained in the soymilk film. This study extended the feasibility of dimethyl labelling to soy-based food samples and examined the proteolysis of Gly m 6 in natto fermentation and its thermal instability.
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Affiliation(s)
- Jhih-Ting Hsiao
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Kuan-Hong Chen
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
| | - Fuu Sheu
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei, Taiwan
- Centre for Biotechnology, National Taiwan University, Taipei, Taiwan
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19
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Maus A, Renuse S, Kemp J, Moehnke K, Mangalaparthi KK, Chavan S, Madugundu AK, Vanderboom PM, Dasari S, Kipp BR, Singh RJ, Grebe SK, Pandey A. Comparison of anti-peptide and anti-protein antibody-based purification techniques for detection of SARS-CoV-2 by targeted LC-MS/MS. Advances in Sample Preparation 2022. [PMCID: PMC9108341 DOI: 10.1016/j.sampre.2022.100018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
The COVID-19 pandemic has necessitated exploration of alternative testing methods for detection of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) to ensure clinical laboratories can continue to provide critical testing results. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) is established in many clinical laboratories due its high specificity and sensitivity, making it a logical alternative methodology. However, matching the sensitivity of quantitative reverse transcription-polymerase chain reaction (qRT-PCR) remains challenging, which forced utilization of antibody-based enrichment prior to targeted LC-MS/MS analysis. When utilizing antibody purification techniques, investigators must decide whether to enrich the target protein or peptides, but there are few studies comparing the two approaches to assist in this decision-making process. In this work, we present a comparison of intact protein and peptide antibody-based purification for LC-MS/MS based detection of SARS-CoV-2. We have found that protein purification yields more intense LC-MS/MS signals, but is also less specific, yielding higher noise and more background when compared to peptide purification techniques. Therefore, when using traditional data analysis techniques, the enrichment technique that provides superior sensitivity varies for individual peptides and no definitive overall conclusion can be made. These observations are corroborated when using a novel machine learning approach to determine positive/negative test results, which yielded superior sensitivity when using protein purification, but better specificity and area under the ROC curve when performing peptide purification.
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20
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Vasilieva AD, Yurina LV, Azarova DY, Ivanov VS, Strelnikova PA, Bugrova AE, Indeykina MI, Kononikhin AS, Nikolaev EN, Rosenfeld MA. Development of a Diagnostic Approach Based on the Detection of Post-Translation Modifications of Fibrinogen Associated with Oxidative Stress by the Method of High Efficiency Liquid Chromatography. Russ J Phys Chem B 2022. [DOI: 10.1134/s1990793122010316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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21
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Khanal N, Chen Z, Alelyunas YW, Szapacs ME, Wrona MD, Sikorski TW. Systematic optimization of targeted and multiplexed MS-based screening workflows for protein biomarkers. Bioanalysis 2022; 14:341-356. [PMID: 35255714 DOI: 10.4155/bio-2021-0245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background: The capability of targeted MS-based methods to simultaneously measure multiple analytes with high selectivity and sensitivity greatly facilitates the discovery and quantitation of novel biomarkers. However, the complexity of biological samples is a major bottleneck that requires extensive sample preparation. Results: This paper reports a generic workflow to optimize surrogate peptide-based protein biomarker screening for seven human proteins in a multiplexed manner without the need for any specific affinity reagents. Each step of the sample processing and LC-MS methods is systematically assessed and optimized for better analytical performance. Conclusion: The established method is used for the screening of multiple myeloma patient samples to determine which proteins could be robustly measured and serve as potential biomarkers of the disease.
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Affiliation(s)
- Neelam Khanal
- Bioanalysis, Immunogenicity & Biomarkers, In-vitro/In-vivo Translation, Research, GlaxoSmithKline, 1250 South Collegeville Rd., Collegeville, PA 19426, USA
- Scientific Operations, Waters Corporation, 34 Maple Street, Milford, MA 01757, USA
| | - Zhuo Chen
- Bioanalysis, Immunogenicity & Biomarkers, In-vitro/In-vivo Translation, Research, GlaxoSmithKline, 1250 South Collegeville Rd., Collegeville, PA 19426, USA
| | - Yun W Alelyunas
- Scientific Operations, Waters Corporation, 34 Maple Street, Milford, MA 01757, USA
| | - Matthew E Szapacs
- Bioanalysis, Immunogenicity & Biomarkers, In-vitro/In-vivo Translation, Research, GlaxoSmithKline, 1250 South Collegeville Rd., Collegeville, PA 19426, USA
| | - Mark D Wrona
- Scientific Operations, Waters Corporation, 34 Maple Street, Milford, MA 01757, USA
| | - Timothy W Sikorski
- Bioanalysis, Immunogenicity & Biomarkers, In-vitro/In-vivo Translation, Research, GlaxoSmithKline, 1250 South Collegeville Rd., Collegeville, PA 19426, USA
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22
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Davidovics R, Saw YL, Brown CO, Prinz M, McKiernan HE, Danielson PB, Legg KM. High-throughput seminal fluid identification by automated immunoaffinity mass spectrometry. J Forensic Sci 2022; 67:1184-1190. [PMID: 35023573 DOI: 10.1111/1556-4029.14975] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 12/19/2021] [Accepted: 12/22/2021] [Indexed: 11/27/2022]
Abstract
The identification of semen during a criminal investigation may be a critical component in the prosecution of a sexual assault. Commonly employed enzymatic and affinity-based methods for detection lack specificity, are time-consuming, and only provide a presumptive indication that semen is present where microscopic visualization is unable to meet the throughput demands. Contrary to traditional approaches, protein mass spectrometry provides true confirmatory results, but multiday sample preparation and nanoflow sample separation requirements have limited the practical applicability of these approaches. Aiming at streamlining sexual assault screening by mass spectrometry, the work here coupled a 60-minute rapid tryptic digestion, semenogelin-II peptide affinity purification on an Agilent AssayMap Bravo automation platform, and a 3-minute targeted LC-MS/MS method on an Agilent 6495 triple quadrupole mass spectrometer operating in multiple reaction monitoring mode for detecting semenogelin-II peptides in sexual assault samples. The developed assay was assessed using casework-type samples and was successful in detecting trace levels (0.0001 μl) of semen recovered from both cotton and vaginal swabs, as well as semen recovered from vaginal swabs during menses or adulterated with personal lubricants. This work represents a promising technique for high-throughput seminal fluid identification in sexual assault-type samples by mass spectrometry.
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Affiliation(s)
- Rachel Davidovics
- NMS Labs, Horsham, Pennsylvania, USA.,College of Life Sciences, Thomas Jefferson University, Philadelphia, Pennsylvania, USA
| | - Yih Ling Saw
- Department of Chemistry and Physics, Arcadia University, Glenside, Pennsylvania, USA
| | - Catherine O Brown
- Department of Biological Sciences, The University of Denver, Denver, Colordo, USA
| | - Mechthild Prinz
- John Jay College of Criminal Justice, New York, New York, USA
| | - Heather E McKiernan
- Department of Chemistry and Physics, Arcadia University, Glenside, Pennsylvania, USA
| | - Phillip B Danielson
- Department of Biological Sciences, The University of Denver, Denver, Colordo, USA
| | - Kevin M Legg
- College of Life Sciences, Thomas Jefferson University, Philadelphia, Pennsylvania, USA.,The Center for Forensic Science Research & Education, Willow Grove, Pennsylvania, USA
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23
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Farrokhi V, Walsh J, Palandra J, Brodfuehrer J, Caiazzo T, Owens J, Binks M, Neelakantan S, Yong F, Dua P, Le Guiner C, Neubert H. Dystrophin and mini-dystrophin quantification by mass spectrometry in skeletal muscle for gene therapy development in Duchenne muscular dystrophy. Gene Ther 2022; 29:608-15. [PMID: 34737451 DOI: 10.1038/s41434-021-00300-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 10/05/2021] [Accepted: 10/13/2021] [Indexed: 01/09/2023]
Abstract
Duchenne muscular dystrophy (DMD) is a lethal, degenerative muscle disorder caused by mutations in the DMD gene, leading to severe reduction or absence of the protein dystrophin. Gene therapy strategies that aim to increase expression of a functional dystrophin protein (mini-dystrophin) are under investigation. The ability to accurately quantify dystrophin/mini-dystrophin is essential in assessing the level of gene transduction. We demonstrated the validation and application of a novel peptide immunoaffinity liquid chromatography-tandem mass spectrometry (IA-LC-MS/MS) assay. Data showed that dystrophin expression in Becker muscular dystrophy and DMD tissues, normalized against the mean of non-dystrophic control tissues (n = 20), was 4-84.5% (mean 32%, n = 20) and 0.4-24.1% (mean 5%, n = 20), respectively. In a DMD rat model, biceps femoris tissue from dystrophin-deficient rats treated with AAV9.hCK.Hopti-Dys3978.spA, an adeno-associated virus vector containing a mini-dystrophin transgene, showed a dose-dependent increase in mini-dystrophin expression at 6 months post-dose, exceeding wildtype dystrophin levels at high doses. Validation data showed that inter- and intra-assay precision were ≤20% (≤25% at the lower limit of quantification [LLOQ]) and inter- and intra-run relative error was within ±20% (±25% at LLOQ). IA-LC-MS/MS accurately quantifies dystrophin/mini-dystrophin in human and preclinical species with sufficient sensitivity for immediate application in preclinical/clinical trials.
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24
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Abstract
BACKGROUND The successful identification of breast cancer (BRCA) prognostic biomarkers is essential for the strategic interference of BRCA patients. Recently, various methods have been proposed for exploring a small prognostic gene set that can distinguish the high-risk group from the low-risk group. METHODS Regularized Cox proportional hazards (RCPH) models were proposed to discover prognostic biomarkers of BRCA from gene expression data. Firstly, the maximum connected network with 1142 genes by mapping 956 differentially expressed genes (DEGs) and 677 previously BRCA-related genes into the gene regulatory network (GRN) was constructed. Then, the 72 union genes of the four feature gene sets identified by Lasso-RCPH, Enet-RCPH, [Formula: see text]-RCPH and SCAD-RCPH models were recognized as the robust prognostic biomarkers. These biomarkers were validated by literature checks, BRCA-specific GRN and functional enrichment analysis. Finally, an index of prognostic risk score (PRS) for BRCA was established based on univariate and multivariate Cox regression analysis. Survival analysis was performed to investigate the PRS on 1080 BRCA patients from the internal validation. Particularly, the nomogram was constructed to express the relationship between PRS and other clinical information on the discovery dataset. The PRS was also verified on 1848 BRCA patients of ten external validation datasets or collected cohorts. RESULTS The nomogram highlighted that the importance of PRS in guiding significance for the prognosis of BRCA patients. In addition, the PRS of 301 normal samples and 306 tumor samples from five independent datasets showed that it is significantly higher in tumors than in normal tissues ([Formula: see text]). The protein expression profiles of the three genes, i.e., ADRB1, SAV1 and TSPAN14, involved in the PRS model demonstrated that the latter two genes are more strongly stained in tumor specimens. More importantly, external validation illustrated that the high-risk group has worse survival than the low-risk group ([Formula: see text]) in both internal and external validations. CONCLUSIONS The proposed pipelines of detecting and validating prognostic biomarker genes for BRCA are effective and efficient. Moreover, the proposed PRS is very promising as an important indicator for judging the prognosis of BRCA patients.
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Affiliation(s)
- Lingyu Li
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, 250061, China
| | - Zhi-Ping Liu
- Department of Biomedical Engineering, School of Control Science and Engineering, Shandong University, Jinan, 250061, China.
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25
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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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26
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van Duijl TT, Ruhaak LR, Smit NPM, Pieterse MM, Romijn FPHTM, Dolezal N, Drijfhout JW, de Fijter JW, Cobbaert CM. Development and Provisional Validation of a Multiplex LC-MRM-MS Test for Timely Kidney Injury Detection in Urine. J Proteome Res 2021; 20:5304-5314. [PMID: 34735145 PMCID: PMC8650098 DOI: 10.1021/acs.jproteome.1c00532] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
![]()
Kidney injury is
a complication frequently encountered in hospitalized
patients. Early detection of kidney injury prior to loss of renal
function is an unmet clinical need that should be targeted by a protein-based
biomarker panel. In this study, we aim to quantitate urinary kidney
injury biomarkers at the picomolar to nanomolar level by liquid chromatography
coupled to tandem mass spectrometry in multiple reaction monitoring
mode (LC-MRM-MS). Proteins were immunocaptured from urinary samples,
denatured, reduced, alkylated, and digested into peptides before LC-MRM-MS
analysis. Stable-isotope-labeled peptides functioned as internal standards,
and biomarker concentrations were attained by an external calibration
strategy. The method was evaluated for selectivity, carryover, matrix
effects, linearity, and imprecision. The LC-MRM-MS method enabled
the quantitation of KIM-1, NGAL, TIMP2, IGFBP7, CXCL9, nephrin, and
SLC22A2 and the detection of TGF-β1, cubilin, and uromodulin.
Two to three peptides were included per protein, and three transitions
were monitored per peptide for analytical selectivity. The analytical
carryover was <1%, and minimal urine matrix effects were observed
by combining immunocapture and targeted LC-MRM-MS analysis. The average
total CV of all quantifier peptides was 26%. The linear measurement
range was determined per measurand and found to be 0.05–30
nmol/L. The targeted MS-based method enables the multiplex quantitation
of low-abundance urinary kidney injury biomarkers for future clinical
evaluation.
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Affiliation(s)
- Tirsa T van Duijl
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Nico P M Smit
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Mervin M Pieterse
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Natasja Dolezal
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Jan Wouter Drijfhout
- Department of Immunology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Johan W de Fijter
- Department of Nephrology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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27
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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28
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Hober A, Tran-Minh KH, Foley D, McDonald T, Vissers JPC, Pattison R, Ferries S, Hermansson S, Betner I, Uhlén M, Razavi M, Yip R, Pope ME, Pearson TW, Andersson LN, Bartlett A, Calton L, Alm JJ, Engstrand L, Edfors F. Rapid and sensitive detection of SARS-CoV-2 infection using quantitative peptide enrichment LC-MS analysis. eLife 2021; 10:e70843. [PMID: 34747696 PMCID: PMC8626084 DOI: 10.7554/elife.70843] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 11/04/2021] [Indexed: 12/11/2022] Open
Abstract
Reliable, robust, large-scale molecular testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is essential for monitoring the ongoing coronavirus disease 2019 (COVID-19) pandemic. We have developed a scalable analytical approach to detect viral proteins based on peptide immuno-affinity enrichment combined with liquid chromatography-mass spectrometry (LC-MS). This is a multiplexed strategy, based on targeted proteomics analysis and read-out by LC-MS, capable of precisely quantifying and confirming the presence of SARS-CoV-2 in phosphate-buffered saline (PBS) swab media from combined throat/nasopharynx/saliva samples. The results reveal that the levels of SARS-CoV-2 measured by LC-MS correlate well with their correspondingreal-time polymerase chain reaction (RT-PCR) read-out (r = 0.79). The analytical workflow shows similar turnaround times as regular RT-PCR instrumentation with a quantitative read-out of viral proteins corresponding to cycle thresholds (Ct) equivalents ranging from 21 to 34. Using RT-PCR as a reference, we demonstrate that the LC-MS-based method has 100% negative percent agreement (estimated specificity) and 95% positive percent agreement (estimated sensitivity) when analyzing clinical samples collected from asymptomatic individuals with a Ct within the limit of detection of the mass spectrometer (Ct ≤ 30). These results suggest that a scalable analytical method based on LC-MS has a place in future pandemic preparedness centers to complement current virus detection technologies.
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Affiliation(s)
| | - Khue Hua Tran-Minh
- Science for Life LaboratorySolnaSweden
- The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and HealthStockholmSweden
| | | | | | | | | | | | | | | | - Mathias Uhlén
- Science for Life LaboratorySolnaSweden
- The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and HealthStockholmSweden
| | | | - Richard Yip
- SISCAPA Assay Technologies, IncVictoriaCanada
| | | | | | | | | | | | - Jessica J Alm
- Karolinska Institutet, Department of Microbiology, Tumor and Cell Biology & National Pandemic Center, Karolinska InstitutetSolnaSweden
| | - Lars Engstrand
- Microbiology, Tumour and Cell Biology, Karolinska InstitutetStockholmSweden
| | - Fredrik Edfors
- Science for Life LaboratorySolnaSweden
- The Royal Institute of Technology, Division of Systems Biology, Department of Protein Science, School of Chemistry, Biotechnology and HealthStockholmSweden
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29
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Anselm V, Sommersdorf C, Carrasco-Triguero M, Katavolos P, Planatscher H, Steinhilber A, Joos T, Poetz O. Matrix and Sampling Effects on Quantification of Protein Biomarkers of Drug-Induced Liver Injury. J Proteome Res 2021; 20:4985-4994. [PMID: 34554759 DOI: 10.1021/acs.jproteome.1c00478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Macrophage colony stimulating factor 1 receptor (MCSF1R), osteopontin (OPN), high-mobility group protein B1 (HMGB1), glutamate dehydrogenase (GLDH), keratin 18 (K18), and caspase-cleaved keratin 18 (ccK18) are considered promising mechanistic biomarkers for the diagnosis of drug-induced liver injury. Here, we aim to elucidate the impact of the sample matrix and handling on the quantification of these emerging protein biomarkers. We investigated effects such as time from collection to centrifugation during serum (± gel) or EDTA plasma preparation on two assay platforms: immunoaffinity liquid chromatography mass spectrometric assays and sandwich immunoassays. Furthermore, we measured GLDH activity with an enzymatic activity assay. Matrix effects were observed particularly for HMGB1 and MCSF1R. HMGB1 levels were higher in serum than in plasma, whereas higher concentrations of MCSF1R were observed in plasma than in serum. A comparison of sample collection to centrifugation time ranging from 15 to 60 min demonstrated increasing levels of HMGB1 in serum, while MCSF1R, OPN, GLDH, and ccK18 concentrations remained stable. Additionally, there was a poor correlation in HMGB1 and ccK18 levels between serum and plasma. Considering the observed matrix effects, we recommend plasma as a matrix of choice and cross-study comparison studies to be limited to those using the same matrix.
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Affiliation(s)
| | | | | | - Paula Katavolos
- Genentech, San Francisco, California 94080, United States.,Bristol-Myers Squibb, New Brunswick, New Jersey 08901, United States (at Genentech during the conduct of this study)
| | | | | | - Thomas Joos
- SIGNATOPE GmbH, Reutlingen 72770, Germany.,NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
| | - Oliver Poetz
- SIGNATOPE GmbH, Reutlingen 72770, Germany.,NMI Natural and Medical Sciences Institute at the University of Tuebingen, Reutlingen 72770, Germany
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30
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Fernández AS, Rodríguez-González P, Álvarez L, García M, Iglesias HG, García Alonso JI. Multiple heart-cutting two dimensional liquid chromatography and isotope dilution tandem mass spectrometry for the absolute quantification of proteins in human serum. Anal Chim Acta 2021; 1184:339022. [PMID: 34625263 DOI: 10.1016/j.aca.2021.339022] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 07/28/2021] [Accepted: 08/30/2021] [Indexed: 10/20/2022]
Abstract
We evaluate here the combination of two-dimensional liquid chromatography (2D-LC) in the multiple heart cutting mode and isotope dilution tandem mass spectrometry for the direct analysis of tryptic digests of serum samples. As a proof of concept, we attempt the quantification of proteotypic peptides of Apolipoprotein AIV (APOA4), Complement C3 (C3) and Vitronectin (VTN) which have been previously identified as potential candidate biomarkers of glaucoma. Using this 2D-LC strategy, analyte enrichment steps are avoided and the sample preparation involved after enzymatic digestion amounted to a simple centrifugation, evaporation of the supernatant and reconstitution in the 1D mobile phase. A mobile phase not compatible with the ESI source (10 mM KH2PO4 at pH 2.7) was used in the first dimension as it provided a satisfactory chromatographic resolution of the peptides and a high buffering capacity avoiding changes in retention times when analyzing complex matrices like human serum. We also demonstrate that using coeluting labelled analogues of the target peptides, protein concentrations were not affected by slight retention time shifts affecting the amount of target peptides transferred to the second dimension. Satisfactory results were obtained when analyzing fortified serum samples (recoveries from 98 to 113%). Precisions in the range of 1-9% RSD were obtained when replicating the analysis of a pooled serum sample. The comparative analysis of serum samples from n = 94 control subjects and n = 91 patients diagnosed with primary open-angle glaucoma did not show significant differences in the APOA4, VTN and C3 concentrations in contrast with previous studies using immunoassays.
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Affiliation(s)
- Amanda Suárez Fernández
- Department of Physical and Analytical Chemistry, University of Oviedo, Calle Julián Clavería 8, 33006, Oviedo, Spain
| | - Pablo Rodríguez-González
- Department of Physical and Analytical Chemistry, University of Oviedo, Calle Julián Clavería 8, 33006, Oviedo, Spain.
| | - Lydia Álvarez
- Instituto Universitario Fernández-Vega (Fundación de Investigación Oftalmológica, Universidad de Oviedo), 33012, Oviedo, Spain
| | - Montserrat García
- Instituto Universitario Fernández-Vega (Fundación de Investigación Oftalmológica, Universidad de Oviedo), 33012, Oviedo, Spain; Instituto Oftalmológico Fernández-Vega, Avda. Dres. Fernández-Vega, 34, 33012, Oviedo, Spain
| | - Héctor González Iglesias
- Instituto Universitario Fernández-Vega (Fundación de Investigación Oftalmológica, Universidad de Oviedo), 33012, Oviedo, Spain; Instituto Oftalmológico Fernández-Vega, Avda. Dres. Fernández-Vega, 34, 33012, Oviedo, Spain
| | - J Ignacio García Alonso
- Department of Physical and Analytical Chemistry, University of Oviedo, Calle Julián Clavería 8, 33006, Oviedo, Spain
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31
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Abstract
The mass spectrometry-based analysis of protein post-translational modifications requires large amounts of sample, complicating the analysis of samples with limited amounts of proteins such as clinical biopsies. Here, we present a tip-based N-terminal analysis method, tipNrich. The entire procedure is processed in a single pipette tip to minimize sample loss, which is so highly optimized to analyze small amounts of proteins, even femtomole-scale of a single protein. With tipNrich, we investigated various single proteins purified from different organisms using a low-resolution mass spectrometer and identified several N-terminal peptides with different Nt-modifications such as ragged N-termini. Furthermore, we applied matrix-assisted laser desorption ionization time-of-flight mass spectrometry to our method for shortening the analysis time. Moreover, we showed that our method could be utilized in disease diagnosis as exemplified by the characterization of wild-type transthyretin amyloidosis patients compared to the healthy individuals based on N-terminome profiling. In summary, tipNrich will satisfy the need of identifying N-terminal peptides even with highly scarce amounts of proteins and of having faster processing time to check the quality of protein products or to characterize N-terminal proteoform-related diseases.
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Affiliation(s)
- Seonjeong Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
| | - Shinyeong Ju
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea
| | - Seok Jin Kim
- Department of Health Sciences and Technology, Samsung Advanced Institute for Health Sciences and Technology, Sungkyunkwan University, Seoul 02792, Korea.,Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 02792, Korea
| | - Jin-Oh Choi
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 02792, Korea
| | - Kihyun Kim
- Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 02792, Korea
| | - Darae Kim
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 02792, Korea
| | - Eun-Seok Jeon
- Division of Cardiology, Department of Medicine, Heart Vascular Stroke Institute, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul 02792, Korea
| | - Cheolju Lee
- Center for Theragnosis, Korea Institute of Science and Technology, Seoul 02792, Republic of Korea.,Division of Bio-Medical Science and Technology, KIST School, Korea University of Science and Technology, Seoul 02792, Republic of Korea
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Mangalaparthi KK, Chavan S, Madugundu AK, Renuse S, Vanderboom PM, Maus AD, Kemp J, Kipp BR, Grebe SK, Singh RJ, Pandey A. A SISCAPA-based approach for detection of SARS-CoV-2 viral antigens from clinical samples. Clin Proteomics 2021; 18:25. [PMID: 34686148 PMCID: PMC8532087 DOI: 10.1186/s12014-021-09331-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/01/2021] [Indexed: 12/24/2022] Open
Abstract
SARS-CoV-2, a novel human coronavirus, has created a global disease burden infecting > 100 million humans in just over a year. RT-PCR is currently the predominant method of diagnosing this viral infection although a variety of tests to detect viral antigens have also been developed. In this study, we adopted a SISCAPA-based enrichment approach using anti-peptide antibodies generated against peptides from the nucleocapsid protein of SARS-CoV-2. We developed a targeted workflow in which nasopharyngeal swab samples were digested followed by enrichment of viral peptides using the anti-peptide antibodies and targeted parallel reaction monitoring (PRM) analysis using a high-resolution mass spectrometer. This workflow was applied to 41 RT-PCR-confirmed clinical SARS-CoV-2 positive nasopharyngeal swab samples and 30 negative samples. The workflow employed was highly specific as none of the target peptides were detected in negative samples. Further, the detected peptides showed a positive correlation with the viral loads as measured by RT-PCR Ct values. The SISCAPA-based platform described in the current study can serve as an alternative method for SARS-CoV-2 viral detection and can also be applied for detecting other microbial pathogens directly from clinical samples.
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Affiliation(s)
- Kiran K Mangalaparthi
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Sandip Chavan
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Anil K Madugundu
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA.,Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India.,Institute of Bioinformatics, International Technology Park, Bangalore, 560066, Karnataka, India.,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Hosur Road, Bangalore, 560029, Karnataka, India
| | - Santosh Renuse
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA.,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA
| | - Patrick M Vanderboom
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Anthony D Maus
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Jennifer Kemp
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Benjamin R Kipp
- Department of Laboratory Medicine and Pathology, Division of Laboratory Genetics and Genomics, Mayo Clinic, Rochester, MN, 55905, USA
| | - Stefan K Grebe
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA.,Department of Medicine, Division of Endocrinology, Mayo Clinic, Rochester, MN, 55902, USA
| | - Ravinder J Singh
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA
| | - Akhilesh Pandey
- Department of Laboratory Medicine and Pathology, Division of Clinical Biochemistry and Immunology, Mayo Clinic, Rochester, MN, 55905, USA. .,Center for Molecular Medicine, National Institute of Mental Health and Neurosciences, Hosur Road, Bangalore, 560029, Karnataka, India. .,Center for Individualized Medicine, Mayo Clinic, Rochester, MN, 55905, USA.
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33
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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. Advanced acquisition methods improve focus of mass spectrometers on target peptides. This review discusses existing methods based on two strategies. Retention time adjustment-based methods enable intelligent scheduling of peptide RTs. In spike-in triggered acquisition methods targeted scans are initiated by spike-ins.
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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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Halvorsen TG, McKitterick N, Kish M, Reubsaet L. 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] [What about the content of this article? (0)] [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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Whiteaker JR, Sharma K, Hoffman MA, Kuhn E, Zhao L, Cocco AR, Schoenherr RM, Kennedy JJ, Voytovich U, Lin C, Fang B, Bowers K, Whiteley G, Colantonio S, Bocik W, Roberts R, Hiltke T, Boja E, Rodriguez H, McCormick F, Holderfield M, Carr SA, Koomen JM, Paulovich AG. Targeted mass spectrometry-based assays enable multiplex quantification of receptor tyrosine kinase, MAP Kinase, and AKT signaling. Cell Rep Methods 2021; 1:100015. [PMID: 34671754 PMCID: PMC8525888 DOI: 10.1016/j.crmeth.2021.100015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 02/16/2021] [Accepted: 05/07/2021] [Indexed: 02/07/2023]
Abstract
SUMMARY A primary goal of the US National Cancer Institute's Ras initiative at the Frederick National Laboratory for Cancer Research is to develop methods to quantify RAS signaling to facilitate development of novel cancer therapeutics. We use targeted proteomics technologies to develop a community resource consisting of 256 validated multiple reaction monitoring (MRM)-based, multiplexed assays for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. As proof of concept, we quantify the response of melanoma (A375 and SK-MEL-2) and colorectal cancer (HCT-116 and HT-29) cell lines to BRAF inhibition by PLX-4720. These assays replace over 60 Western blots with quantitative mass spectrometry-based assays of high molecular specificity and quantitative precision, showing the value of these methods for pharmacodynamic measurements and mechanism of action studies. Methods, fit-for-purpose validation, and results are publicly available as a resource for the community at assays.cancer.gov. MOTIVATION A lack of quantitative, multiplexable assays for phosphosignaling limits comprehensive investigation of aberrant signaling in cancer and evaluation of novel treatments. To alleviate this limitation, we sought to develop assays using targeted mass spectrometry for quantifying protein expression and phosphorylation through the receptor tyrosine kinase, MAPK, and AKT signaling networks. The resulting assays provide a resource for replacing over 60 Western blots in examining cancer signaling and tumor biology with high molecular specificity and quantitative rigor.
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Affiliation(s)
- Jeffrey R. Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kanika Sharma
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
| | - Melissa A. Hoffman
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Eric Kuhn
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Lei Zhao
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Alexandra R. Cocco
- Gillings School of Global Public Health, Kenan-Flagler Business School, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Regine M. Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Jacob J. Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ulianna Voytovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Chenwei Lin
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Bin Fang
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Kiah Bowers
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Gordon Whiteley
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Simona Colantonio
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - William Bocik
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Rhonda Roberts
- Antibody Characterization Laboratory, Leidos Biochemical Research Inc, Frederick National Laboratory for Cancer Research ATRF, Frederick, MD 21701, USA
| | - Tara Hiltke
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Emily Boja
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Henry Rodriguez
- Office of Cancer Clinical Proteomics Research, National Cancer Institute, Bethesda, MD 20892, USA
| | - Frank McCormick
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA 94158, USA
| | - Matthew Holderfield
- NCI RAS Initiative, Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, MD 21701, USA
- Department of Biology, Revolution Medicines, Inc., Redwood City, CA 94063, USA
| | - Steven A. Carr
- Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - John M. Koomen
- Proteomics and Metabolomics Core, Department of Molecular Oncology, and Department of Tumor Biology, Moffitt Cancer Center & Research Institute, Tampa, FL 33612, USA
| | - Amanda G. Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Kvivik I, Jonsson G, Omdal R, Brede C. Sample Preparation Strategies for Antibody-Free Quantitative Analysis of High Mobility Group Box 1 Protein. Pharmaceuticals (Basel) 2021; 14:ph14060537. [PMID: 34205112 PMCID: PMC8230321 DOI: 10.3390/ph14060537] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 05/31/2021] [Accepted: 05/31/2021] [Indexed: 11/16/2022] Open
Abstract
Sickness behavior and fatigue are induced by cerebral mechanisms involving inflammatory cytokines. High mobility group box 1 (HMGB1) is an alarmin, and a potential key player in this process. Reliable quantification methods for total HMGB1 and its redox variants must be established in order to clearly understand how it functions. Current methods pose significant challenges due to interference from other plasma proteins and autoantibodies. We aimed to develop an antibody-free sample preparation method followed by liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) to measure HMGB1 in human plasma. Different methods were applied for the removal of interfering proteins and the enrichment of HMGB1 from spiked human plasma samples. A comparison of methods showed an overall low extraction recovery (<40%), probably due to the stickiness of HMGB1. Reversed-phase liquid chromatography separation of intact proteins in diluted plasma yielded the most promising results. The method produced an even higher degree of HMGB1 purification than that observed with immunoaffinity extraction. Detection sensitivity needs to be further improved for the measurement of HMGB1 in patient samples. Nevertheless, it has been demonstrated that a versatile and fully antibody-free sample preparation method is possible, which could be of great use in further investigations.
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Affiliation(s)
- Ingeborg Kvivik
- Research Department, Stavanger University Hospital, 4011 Stavanger, Norway;
| | - Grete Jonsson
- Department of Medical Biochemistry, Stavanger University Hospital, 4011 Stavanger, Norway;
| | - Roald Omdal
- Department of Clinical Science, Faculty of Medicine, University of Bergen, 5020 Bergen, Norway;
- Clinical Immunology Unit, Department of Internal Medicine, Stavanger University Hospital, 4011 Stavanger, Norway
| | - Cato Brede
- Department of Medical Biochemistry, Stavanger University Hospital, 4011 Stavanger, Norway;
- Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, 4021 Stavanger, Norway
- Correspondence:
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Collins CJ, Yi F, Dayuha R, Duong P, Horslen S, Camarata M, Coskun AK, Houwen RHJ, Pop TL, Zoller H, Yoo HW, Jung SW, Weiss KH, Schilsky ML, Ferenci P, Hahn SH. Direct Measurement of ATP7B Peptides Is Highly Effective in the Diagnosis of Wilson Disease. Gastroenterology 2021; 160:2367-2382.e1. [PMID: 33640437 PMCID: PMC8243898 DOI: 10.1053/j.gastro.2021.02.052] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/09/2021] [Accepted: 02/21/2021] [Indexed: 02/08/2023]
Abstract
BACKGROUND & AIMS Both existing clinical criteria and genetic testing have significant limitations for the diagnosis of Wilson disease (WD), often creating ambiguities in patient identification and leading to delayed diagnosis and ineffective management. ATP7B protein concentration, indicated by direct measurement of surrogate peptides from patient dried blood spot samples, could provide primary evidence of WD. ATP7B concentrations were measured in patient samples from diverse backgrounds, diagnostic potential is determined, and results are compared with biochemical and genetic results from individual patients. METHODS Two hundred and sixty-four samples from biorepositories at 3 international and 2 domestic academic centers and 150 normal controls were obtained after Institutional Review Board approval. Genetically or clinically confirmed WD patients with a Leipzig score >3 and obligate heterozygote (carriers) from affected family members were included. ATP7B peptide measurements were made by immunoaffinity enrichment mass spectrometry. RESULTS Two ATP7B peptides were used to measure ATP7B protein concentration. Receiver operating characteristics curve analysis generates an area under the curve of 0.98. ATP7B peptide analysis of the sequence ATP7B 887 was found to have a sensitivity of 91.2%, specificity of 98.1%, positive predictive value of 98.0%, and a negative predictive value of 91.5%. In patients with normal ceruloplasmin concentrations (>20 mg/dL), 14 of 16 (87.5%) were ATP7B-deficient. In patients without clear genetic results, 94% were ATP7B-deficient. CONCLUSIONS Quantification of ATP7B peptide effectively identified WD patients in 92.1% of presented cases and reduced ambiguities resulting from ceruloplasmin and genetic analysis. Clarity is brought to patients with ambiguous genetic results, significantly aiding in noninvasive diagnosis. A proposed diagnostic score and algorithm incorporating ATP7B peptide concentrations can be rapidly diagnostic and supplemental to current Leipzig scoring systems.
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Affiliation(s)
| | - Fan Yi
- Seattle Children's Research Institute, Seattle, Washington
| | | | - Phi Duong
- Seattle Children's Research Institute, Seattle, Washington
| | - Simon Horslen
- University of Washington School of Medicine, Seattle, Washington
| | | | - Ayse K Coskun
- Yale University School of Medicine, New Haven, Connecticut
| | - Roderick H J Houwen
- Wilhelmina Children's Hospital, University Medical Center, Utrecht, The Netherlands
| | - Tudor L Pop
- Second Pediatric Clinic, University of Medicine and Pharmacy, Iuliu Hatieganu, Cluj-Napoca, Romania
| | - Heinz Zoller
- Medical University of Innsbruck, Innsbruck, Austria
| | | | - Sung Won Jung
- Gachon University School of Medicine, Incheon, Korea
| | - Karl H Weiss
- Heidelberg University Hospital, Heidelberg, Germany
| | | | | | - Si Houn Hahn
- Seattle Children's Research Institute, Seattle, Washington; University of Washington School of Medicine, Seattle, Washington.
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Parker GJ, McKiernan HE, Legg KM, Goecker ZC. Forensic proteomics. Forensic Sci Int Genet 2021; 54:102529. [PMID: 34139528 DOI: 10.1016/j.fsigen.2021.102529] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/06/2021] [Accepted: 05/07/2021] [Indexed: 12/19/2022]
Abstract
Protein is a major component of all biological evidence, often the matrix that embeds other biomolecules such as polynucleotides, lipids, carbohydrates, and small molecules. The proteins in a sample reflect the transcriptional and translational program of the originating cell types. Because of this, proteins can be used to identify body fluids and tissues, as well as convey genetic information in the form of single amino acid polymorphisms, the result of non-synonymous SNPs. This review explores the application and potential of forensic proteomics. The historical role that protein analysis played in the development of forensic science is examined. This review details how innovations in proteomic mass spectrometry have addressed many of the historical limitations of forensic protein science, and how the application of forensic proteomics differs from proteomics in the life sciences. Two more developed applications of forensic proteomics are examined in detail: body fluid and tissue identification, and proteomic genotyping. The review then highlights developing areas of proteomics that have the potential to impact forensic science in the near future: fingermark analysis, species identification, peptide toxicology, proteomic sex estimation, and estimation of post-mortem intervals. Finally, the review highlights some of the newer innovations in proteomics that may drive further development of the field. In addition to potential impact, this review also attempts to evaluate the stage of each application in the development, validation and implementation process. This review is targeted at investigators who are interested in learning about proteomics in a forensic context and expanding the amount of information they can extract from biological evidence.
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Shi J, Chen X, Diao J, Jiang L, Li L, Li S, Liang W, Jin X, Wang Y, Wong C, Zhang XT, Tse FLS. Bioanalysis in the Age of New Drug Modalities. AAPS J 2021; 23:64. [PMID: 33942188 PMCID: PMC8093172 DOI: 10.1208/s12248-021-00594-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 04/09/2021] [Indexed: 12/14/2022]
Abstract
In the absence of regulatory guidelines for the bioanalysis of new drug modalities, many of which contain multiple functional domains, bioanalytical strategies have been carefully designed to characterize the intact drug and each functional domain in terms of quantity, functionality, biotransformation, and immunogenicity. The present review focuses on the bioanalytical challenges and considerations for RNA-based drugs, bispecific antibodies and multi-domain protein therapeutics, prodrugs, gene and cell therapies, and fusion proteins. Methods ranging from the conventional ligand binding assays and liquid chromatography-mass spectrometry assays to quantitative polymerase chain reaction or flow cytometry often used for oligonucleotides and cell and gene therapies are discussed. Best practices for method selection and validation are proposed as well as a future perspective to address the bioanalytical needs of complex modalities.
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Affiliation(s)
- Jing Shi
- Bioanalytical Services Department, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao, Shanghai, 200131, China.
| | - Xuesong Chen
- Bioanalytical Services Department, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao, Shanghai, 200131, China
| | - Jianbo Diao
- Bioanalytical Services Department, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao, Shanghai, 200131, China
| | - Liying Jiang
- Bioanalytical Services Department, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao, Shanghai, 200131, China
| | - Lan Li
- Bioanalytical Services Department, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao, Shanghai, 200131, China
| | - Stephen Li
- Bioanalytical Services Department, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao, Shanghai, 200131, China
| | - Wenzhong Liang
- Bioanalytical Services Department, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao, Shanghai, 200131, China
| | - Xiaoying Jin
- Bioanalytical Services Department, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao, Shanghai, 200131, China
| | - Yonghui Wang
- Bioanalytical Services Department, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao, Shanghai, 200131, China
| | - Colton Wong
- Bioanalytical Services Department, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao, Shanghai, 200131, China
| | - Xiaolong Tom Zhang
- Bioanalytical Services Department, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao, Shanghai, 200131, China
| | - Francis L S Tse
- Bioanalytical Services Department, WuXi AppTec, 288 Fute Zhong Road, Waigaoqiao, Shanghai, 200131, China
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Dejakaisaya H, Harutyunyan A, Kwan P, Jones NC. Altered metabolic pathways in a transgenic mouse model suggest mechanistic role of amyloid precursor protein overexpression in Alzheimer's disease. Metabolomics 2021; 17:42. [PMID: 33876332 DOI: 10.1007/s11306-021-01793-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 04/11/2021] [Indexed: 01/31/2023]
Abstract
INTRODUCTION The mechanistic role of amyloid precursor protein (APP) in Alzheimer's disease (AD) remains unclear. OBJECTIVES Here, we aimed to identify alterations in cerebral metabolites and metabolic pathways in cortex, hippocampus and serum samples from Tg2576 mice, a widely used mouse model of AD. METHODS Metabolomic profilings using liquid chromatography-mass spectrometry were performed and analysed with MetaboAnalyst and weighted correlation network analysis (WGCNA). RESULTS Expressions of 11 metabolites in cortex, including hydroxyphenyllactate-linked to oxidative stress-and phosphatidylserine-lipid metabolism-were significantly different between Tg2576 and WT mice (false discovery rate < 0.05). Four metabolic pathways from cortex, including glycerophospholipid metabolism and pyrimidine metabolism, and one pathway (sulphur metabolism) from hippocampus, were significantly enriched in Tg2576 mice. Network analysis identified five pathways, including alanine, aspartate and glutamate metabolism, and mitochondria electron transport chain, that were significantly correlated with AD genotype. CONCLUSIONS Changes in metabolite concentrations and metabolic pathways are present in the early stage of APP pathology, and may be important for AD development and progression.
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Affiliation(s)
- Hattapark Dejakaisaya
- Department of Neuroscience, Central Clinical School, Monash University, The Alfred Hospital, Melbourne, VIC, 3004, Australia
| | - Anna Harutyunyan
- Department of Medicine (Royal Melbourne Hospital), University of Melbourne, Parkville, VIC, 3052, Australia
| | - Patrick Kwan
- Department of Neuroscience, Central Clinical School, Monash University, The Alfred Hospital, Melbourne, VIC, 3004, Australia.
- Department of Medicine (Royal Melbourne Hospital), University of Melbourne, Parkville, VIC, 3052, Australia.
| | - Nigel C Jones
- Department of Neuroscience, Central Clinical School, Monash University, The Alfred Hospital, Melbourne, VIC, 3004, Australia.
- Department of Medicine (Royal Melbourne Hospital), University of Melbourne, Parkville, VIC, 3052, Australia.
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Anselm V, Steinhilber A, Sommersdorf C, Poetz O. Immunoaffinity-Based Liquid Chromatography Mass Spectrometric Assay to Accurately Quantify the Protein Concentration of HMGB1 in EDTA Plasma. Methods Mol Biol 2021; 2261:277-289. [PMID: 33420996 DOI: 10.1007/978-1-0716-1186-9_17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/02/2023]
Abstract
Targeted protein quantification can be challenging in body fluids such as plasma with regard to sensitivity and selectivity. In this chapter, we present a protocol for the quantification of high mobility group box 1 protein (HMGB1) in plasma using an immunoaffinity liquid chromatography mass spectrometric assay (IA-LC-MSMS). The protocol provides detailed assay instructions involving sample proteolysis, peptide-targeted immunoprecipitation, and LC-MSMS-based read out.
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42
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Metzemaekers M, Abouelasrar Salama S, Vandooren J, Mortier A, Janssens R, Vandendriessche S, Ganseman E, Martens E, Gouwy M, Neerinckx B, Verschueren P, De Somer L, Wouters C, Struyf S, Opdenakker G, Van Damme J, Proost P. From ELISA to Immunosorbent Tandem Mass Spectrometry Proteoform Analysis: The Example of CXCL8/Interleukin-8. Front Immunol 2021; 12:644725. [PMID: 33777041 PMCID: PMC7991300 DOI: 10.3389/fimmu.2021.644725] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Accepted: 02/12/2021] [Indexed: 11/15/2022] Open
Abstract
With ELISAs one detects the ensemble of immunoreactive molecules in biological samples. For biomolecules undergoing proteolysis for activation, potentiation or inhibition, other techniques are necessary to study biology. Here we develop methodology that combines immunosorbent sample preparation and nano-scale liquid chromatography—tandem mass spectrometry (nano-LC-MS/MS) for proteoform analysis (ISTAMPA) and apply this to the aglycosyl chemokine CXCL8. CXCL8, the most powerful human chemokine with neutrophil chemotactic and –activating properties, occurs in different NH2-terminal proteoforms due to its susceptibility to site-specific proteolytic modification. Specific proteoforms display up to 30-fold enhanced activity. The immunosorbent ion trap top-down mass spectrometry-based approach for proteoform analysis allows for simultaneous detection and quantification of full-length CXCL8(1-77), elongated CXCL8(-2-77) and all naturally occurring truncated CXCL8 forms in biological samples. For the first time we demonstrate site-specific proteolytic activation of CXCL8 in synovial fluids from patients with chronic joint inflammation and address the importance of sample collection and processing.
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Affiliation(s)
- Mieke Metzemaekers
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sara Abouelasrar Salama
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jennifer Vandooren
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Anneleen Mortier
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Rik Janssens
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sofie Vandendriessche
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Eva Ganseman
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Erik Martens
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Mieke Gouwy
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Barbara Neerinckx
- Department of Development and Regeneration, Skeletal Biology and Engineering Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Patrick Verschueren
- Department of Development and Regeneration, Skeletal Biology and Engineering Research Center, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Lien De Somer
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Carine Wouters
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Sofie Struyf
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Ghislain Opdenakker
- Laboratory of Immunobiology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Jo Van Damme
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Paul Proost
- Laboratory of Molecular Immunology, Department of Microbiology, Immunology and Transplantation, Rega Institute, Katholieke Universiteit Leuven, Leuven, Belgium
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Mukherjee S, Perez KA, Lago LC, Klatt S, McLean CA, Birchall IE, Barnham KJ, Masters CL, Roberts BR. Quantification of N-terminal amyloid-β isoforms reveals isomers are the most abundant form of the amyloid-β peptide in sporadic Alzheimer's disease. Brain Commun 2021; 3:fcab028. [PMID: 33928245 PMCID: PMC8062259 DOI: 10.1093/braincomms/fcab028] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 01/09/2021] [Accepted: 01/15/2021] [Indexed: 12/30/2022] Open
Abstract
Plaques that characterize Alzheimer’s disease accumulate over 20 years as a result of decreased clearance of amyloid-β peptides. Such long-lived peptides are subjected to multiple post-translational modifications, in particular isomerization. Using liquid chromatography ion mobility separations mass spectrometry, we characterized the most common isomerized amyloid-β peptides present in the temporal cortex of sporadic Alzheimer’s disease brains. Quantitative assessment of amyloid-β N-terminus revealed that > 80% of aspartates (Asp-1 and Asp-7) in the N-terminus was isomerized, making isomerization the most dominant post-translational modification of amyloid-β in Alzheimer’s disease brain. Total amyloid-β1–15 was ∼85% isomerized at Asp-1 and/or Asp-7 residues, with only 15% unmodified amyloid-β1–15 left in Alzheimer’s disease. While amyloid-β4–15 the next most abundant N-terminus found in Alzheimer’s disease brain, was only ∼50% isomerized at Asp-7 in Alzheimer’s disease. Further investigations into different biochemically defined amyloid-β-pools indicated a distinct pattern of accumulation of extensively isomerized amyloid-β in the insoluble fibrillar plaque and membrane-associated pools, while the extent of isomerization was lower in peripheral membrane/vesicular and soluble pools. This pattern correlated with the accumulation of aggregation-prone amyloid-β42 in Alzheimer’s disease brains. Isomerization significantly alters the structure of the amyloid-β peptide, which not only has implications for its degradation, but also for oligomer assembly, and the binding of therapeutic antibodies that directly target the N-terminus, where these modifications are located.
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Affiliation(s)
- Soumya Mukherjee
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Keyla A Perez
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Larissa C Lago
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Stephan Klatt
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Catriona A McLean
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC 3010, Australia.,Department of Anatomical Pathology, Alfred Hospital, Prahran, VIC 3004, Australia
| | - Ian E Birchall
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Kevin J Barnham
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Colin L Masters
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Blaine R Roberts
- Florey Institute of Neuroscience and Mental Health, University of Melbourne, Melbourne, VIC 3010, Australia.,Department of Biochemistry, Emory University School of Medicine, Atlanta, GA 30322, USA.,Department of Neurology, Emory University School of Medicine, Atlanta, GA 30322, USA
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45
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Smit NPM, Ruhaak LR, Romijn FPHTM, Pieterse MM, van der Burgt YEM, Cobbaert CM. The Time Has Come for Quantitative Protein Mass Spectrometry Tests That Target Unmet Clinical Needs. J Am Soc Mass Spectrom 2021; 32:636-647. [PMID: 33522792 PMCID: PMC7944566 DOI: 10.1021/jasms.0c00379] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/22/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
Protein mass spectrometry (MS) is an enabling technology that is ideally suited for precision diagnostics. In contrast to immunoassays with indirect readouts, MS quantifications are multiplexed and include identification of proteoforms in a direct manner. Although widely used for routine measurements of drugs and metabolites, the number of clinical MS-based protein applications is limited. In this paper, we share our experience and aim to take away the concerns that have kept laboratory medicine from implementing quantitative protein MS. To ensure added value of new medical tests and guarantee accurate test results, five key elements of test evaluation have been established by a working group within the European Federation for Clinical Chemistry and Laboratory Medicine. Moreover, it is emphasized to identify clinical gaps in the contemporary clinical pathways before test development is started. We demonstrate that quantitative protein MS tests that provide an additional layer of clinical information have robust performance and meet long-term desirable analytical performance specifications as exemplified by our own experience. Yet, the adoption of quantitative protein MS tests into medical laboratories is seriously hampered due to its complexity, lack of robotization and high initial investment costs. Successful and widespread implementation in medical laboratories requires uptake and automation of this next generation protein technology by the In-Vitro Diagnostics industry. Also, training curricula of lab workers and lab specialists should include education on enabling technologies for transitioning to precision medicine by quantitative protein MS tests.
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Affiliation(s)
- Nico P. M. Smit
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - L. Renee Ruhaak
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Fred P. H. T. M. Romijn
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Mervin M. Pieterse
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Yuri E. M. van der Burgt
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Christa M. Cobbaert
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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46
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Burdman I, Burckhardt BB. Human prorenin determination by hybrid immunocapture liquid chromatography/mass spectrometry: A mixed-solvent-triggered digestion utilizing D-optimal design. Rapid Commun Mass Spectrom 2020; 34:e8932. [PMID: 32845569 DOI: 10.1002/rcm.8932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/03/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Human prorenin, representing the precursor of mature renin, has been discussed as a potential biomarker, e.g. in diagnosing primary hyperaldosteronism or diabetes-induced nephropathy. Currently, only immunoassays are available for prorenin quantification. As the similarity of prorenin to active renin impedes its accurate determination by immunoassay, mass spectrometry appears as an accurate alternative for differentiation of that protein. METHODS Immunoaffinity purification plus a mixed-solvent-triggered digestion was combined with liquid chromatography/mass spectrometry (LC/MS) to enable a fast, sensitive, and less laboratory-intensive approach to the quantification of prorenin. Statistical experimental planning, which is known as Design of Experiments (DOE), was used to identify the optimal conditions for the generation of the signature peptides within a manageable number of experiments. The efficiency of the mixed-solvent-triggered digestion by trypsin was investigated using four different organic solvents: acetonitrile, acetone, tetrahydrofuran and methanol. RESULTS By utilizing a D-optimal design, we found that the optimal mixed-solvent type for the generation of both signature peptides was acetonitrile at a concentration of 84% and an incubation temperature of 16°C. Using the mixed-solvent-triggered digestion, the procedure time allowed a fast analysis of active renin and prorenin with a short digestion time of 98 min. This optimized mixed-solvent-triggered digestion procedure was applied to detect renin and prorenin successfully in human plasma by the newly developed hybrid approach. CONCLUSIONS The identification of unique surrogates for human prorenin enabled the mass spectrometric differentiation between the two similar proteins. The novel hybrid approach successfully proved its ability to purify, detect and distinguish between prorenin and active renin in human plasma.
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Affiliation(s)
- Ilja Burdman
- Institute of Clinical Pharmacy and Pharmacotherapy, Heinrich Heine University, Universitaetsstr. 1, Dusseldorf, Germany
| | - Bjoern B Burckhardt
- Institute of Clinical Pharmacy and Pharmacotherapy, Heinrich Heine University, Universitaetsstr. 1, Dusseldorf, Germany
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Abstract
Developments in immunoassays and mass spectrometry have independently influenced diagnostic technology. However, both techniques possess unique strengths and limitations, which define their ability to meet evolving requirements for faster, more affordable and more accurate clinical tests. In response, hybrid techniques, which combine the accessibility and ease-of-use of immunoassays with the sensitivity, high throughput and multiplexing capabilities of mass spectrometry are continually being explored. Developments in antibody conjugation methodology have expanded the role of these biomolecules to applications outside of conventional colorimetric assays and histology. Furthermore, the range of different mass spectrometry ionisation and analysis technologies has enabled its successful adaptation as a detection method for numerous clinically relevant immunological assays. Several recent examples of combined mass spectrometry-immunoassay techniques demonstrate the potential of these methods as improved diagnostic tests for several important human diseases. The present challenges are to continue technological advancements in mass spectrometry instrumentation and develop improved bioconjugation methods, which can overcome their existing limitations and demonstrate the clinical significance of these hybrid approaches.
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48
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Abstract
Kidney research is entering an era of 'big data' and molecular omics data can provide comprehensive insights into the molecular footprints of cells. In contrast to transcriptomics, proteomics and metabolomics generate data that relate more directly to the pathological symptoms and clinical parameters observed in patients. Owing to its complexity, the proteome still holds many secrets, but has great potential for the identification of drug targets. Proteomics can provide information about protein synthesis, modification and degradation, as well as insight into the physical interactions between proteins, and between proteins and other biomolecules. Thus far, proteomics in nephrology has largely focused on the discovery and validation of biomarkers, but the systematic analysis of the nephroproteome can offer substantial additional insights, including the discovery of mechanisms that trigger and propagate kidney disease. Moreover, proteome acquisition might provide a diagnostic tool that complements the assessment of a kidney biopsy sample by a pathologist. Such applications are becoming increasingly feasible with the development of high-throughput and high-coverage technologies, such as versatile mass spectrometry-based techniques and protein arrays, and encourage further proteomics research in nephrology.
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Affiliation(s)
- Markus M Rinschen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark. .,III. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany. .,Department II of Internal Medicine and Center for Molecular Medicine Cologne, University of Cologne, Cologne, Germany. .,Department of Chemistry, Scripps Center for Metabolomics and Mass Spectrometry, Scripps Research, La Jolla, CA, USA.
| | - Julio Saez-Rodriguez
- Institute for Computational Biomedicine, Faculty of Medicine, Heidelberg University, and Heidelberg University Hospital, Bioquant, Heidelberg, Germany.,Joint Research Center for Computational Biomedicine, RWTH Aachen University Hospital, Aachen, Germany.,Molecular Medicine Partnership Unit, European Molecular Biology Laboratory and Heidelberg University, Heidelberg, Germany
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Caporuscio C, Holmes D, Olah TV, Shipkova P. Immunoaffinity enrichment LC-MS/MS quantitation of CDH17 in tissues. Bioanalysis 2020; 12:1439-47. [PMID: 33006478 DOI: 10.4155/bio-2020-0162] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: There is little information in the literature regarding assays for measuring CDH17 in tissues. Numerous studies indicate overexpression of CDH17 in a variety of diseases including hepatocellular carcinoma, colorectal and gastric cancer. Here we present an immunoaffinity enrichment LC-MS/MS approach for analysis of CDH17 in human tissues, plasma and serum as well as preclinical models. Results: CDH17 levels were measured in colon and ileum tissues from healthy donors and inflamed tissues from patients with Ulcerative Colitus or Crohn's disease. Applicability of the immunocapture LC-MS/MS approach is demonstrated for colon tissues from non-diseased mouse and cynomolgus monkey. Conclusion: The analytical approaches discussed here are suitable for quantitation of CDH17 in various tissues to enable both preclinical and clinical assessment.
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50
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de Jong KA, van Breugel SJ, Hillebrand MJ, Rosing H, Huitema AD, Beijnen JH. Bottom-up sample preparation for the LC-MS/MS quantification of anti-cancer monoclonal antibodies in bio matrices. Bioanalysis 2020; 12:1405-25. [PMID: 32975434 DOI: 10.4155/bio-2020-0204] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Therapeutic monoclonal antibodies (mAbs) are rapidly taking over the treatment of many malignancies, and an astonishing number of mAbs is in development. This causes a high demand for quantification of mAbs in biomatrices both for measuring therapeutic mAb concentrations and to support pharmacokinetics and pharmacodynamics studies. Conventionally, ligand-binding assays are used for these purposes, but LC-MS is gaining popularity. Although intact (top-down) and subunit (middle-down) mAb quantification is reported, signature peptide (bottom-up) quantification is currently most advantageous. This review provides an overview of the reported bottom-up mAb quantification methods in biomatrices as well as general recommendations regarding signature peptide and internal standard selection, reagent use and optimization of digestion in bottom-up quantification methods.
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