1
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Qian Q, Tang Y, Miao P. Quantification of Multiplex miRNAs by Mass Spectrometry with Duplex-Specific Nuclease-Mediated Amplification. Anal Chem 2023; 95:11578-11582. [PMID: 37498281 DOI: 10.1021/acs.analchem.3c02541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
Early quantification of multiplex biomarkers such as microRNAs (miRNAs) is critical during disease pathologic development and therapy. To tackle challenges of low abundance and multiplexing, we herein report a mass-encoded biosensing approach with duplex-specific nuclease (DSN) mediated signal amplification. Magnetic Fe3O4 cores are coated with small gold nanoparticles (AuNPs), which are applied to achieve facile DNA immobilization subsequent separation. This biosensor integrates multiple mass reporters corresponding to different targets (five miRNAs as examples). Due to the excellent resolution of mass spectrometry, these targets can be successfully distinguished in a single spectrum. Wide detection ranges from 10 fM to 1 nM are achieved, and the limits of detection are estimated to be 10 fM. High selectivity is promised due to the enzyme activity of DSN, and practical application in human serum samples performs satisfactorily. The number of targets to be tested can be further expanded by designing different specific mass tags in theory. Therefore, the proposed method can be utilized as an important and valuable tool to quantify multiplex miRNAs for disease screening as well as biomedical investigations.
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Affiliation(s)
- Qing Qian
- University of Science and Technology of China, Hefei 230026, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Yuguo Tang
- University of Science and Technology of China, Hefei 230026, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
| | - Peng Miao
- University of Science and Technology of China, Hefei 230026, China
- Suzhou Institute of Biomedical Engineering and Technology, Chinese Academy of Sciences, Suzhou 215163, China
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2
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Gianazza E, Zoanni B, Mallia A, Brioschi M, Colombo GI, Banfi C. Proteomic studies on apoB-containing lipoprotein in cardiovascular research: A comprehensive review. MASS SPECTROMETRY REVIEWS 2023; 42:1397-1423. [PMID: 34747518 DOI: 10.1002/mas.21747] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 08/05/2021] [Accepted: 08/16/2021] [Indexed: 06/07/2023]
Abstract
The complexity of cardiovascular diseases (CVDs), which remains the leading cause of death worldwide, makes the current clinical pathway for cardiovascular risk assessment unsatisfactory, as there remains a substantial unexplained residual risk. Simultaneous assessment of a large number of plasma proteins may be a promising tool to further refine risk assessment, and lipoprotein-associated proteins have the potential to fill this gap. Technical advances now allow for high-throughput proteomic analysis in a reproducible and cost-effective manner. Proteomics has great potential to identify and quantify hundreds of candidate marker proteins in a sample and allows the translation from isolated lipoproteins to whole plasma, thus providing an individual multiplexed proteomic fingerprint. This narrative review describes the pathophysiological roles of atherogenic apoB-containing lipoproteins and the recent advances in their mass spectrometry-based proteomic characterization and quantitation for better refinement of CVD risk assessment.
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Affiliation(s)
| | | | - Alice Mallia
- Centro Cardiologico Monzino, IRCCS, Milano, Italy
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3
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Mingroni MA, Chaplin Momaney V, Barlow AN, Jaen Maisonet I, Knapp MJ. Measurement of kinetic isotope effects on peptide hydroxylation using MALDI-MS. Methods Enzymol 2022; 679:363-380. [PMID: 36682871 DOI: 10.1016/bs.mie.2022.08.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Primary kinetic isotope effects (KIEs) provide unique insight into enzymatic reactions, as they can reveal rate-limiting steps and detailed chemical mechanisms. HIF hydroxylases, part of a family of 2-oxoglutarate (2OG) oxygenases are central to the regulation of many crucial biological processes through O2-sensing, but present a challenge to monitor due to the large size of the protein substrate and the similarity between native and hydroxylated substrate. MALDI-TOF MS is a convenient tool to measure peptide masses, which can also be used to measure the discontinuous kinetics of peptide hydroxylation for Factor Inhibiting HIF (FIH). Using this technique, rate data can be observed from the mole-fraction of CTAD and CTAD-OH in small volumes, allowing noncompetitive H/D KIEs to be measured. Slow dCTAD substrate leads to extensive uncoupling of O2 consumption from peptide hydroxylation, leading to enzyme autohydroxylation, which is observed using UV-vis spectroscopy. Simultaneously measuring both the normal product, CTAD-OH, and the uncoupled product, autohydroxylated enzyme, the KIE on the microscopic step of hydrogen atom transfer (HAT) can be estimated. MALDI-MS analysis is a strong method for monitoring reactions that hydroxylate peptides, and can be generalized to other similar reactions, and simultaneous kinetic detection of branched products can provide valuable insight on microscopic KIEs at intermediate mechanistic steps.
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Affiliation(s)
- Michael A Mingroni
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
| | | | - Alexandra N Barlow
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States
| | | | - Michael J Knapp
- Department of Chemistry, University of Massachusetts, Amherst, MA, United States.
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4
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Dilmetz BA, Hoffmann P, Condina MR. Quantitative Approach Using Matrix-Assisted Laser Desorption/Ionization Time-of-Flight (MALDI-ToF) Mass Spectrometry. Methods Mol Biol 2021; 2228:159-166. [PMID: 33950490 DOI: 10.1007/978-1-0716-1024-4_12] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Quantitation using mass spectrometry (MS) is a routine approach for multiple analytes, including small molecules and peptides. Electrospray-based MS platforms are typically employed, as they provide highly reproducible outputs for batch processing of multiple samples. Quantitation using matrix-assisted laser desorption/ionization (MALDI) time-of-flight (ToF) mass spectrometry, while less commonly adopted, offers the ability to monitor analytes at significantly higher throughput and lower cost compared with ESI MS. Achieving accurate quantitation using this approach requires the development of appropriate sample preparation, spiking of appropriate internal standards, and acquisition to minimize spot-to-spot variability. Here we describe the preparation of samples for accurate quantitation using MALDI-ToF MS. The methodology presented shows the ability to quantitate perfluorooctanesulfonic acid (PFOS) from contaminated water.
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Affiliation(s)
- Brooke A Dilmetz
- Future Industries Institute, University of South Australia, Adelaide, Australia
| | - Peter Hoffmann
- Future Industries Institute, University of South Australia, Adelaide, Australia
| | - Mark R Condina
- Future Industries Institute, University of South Australia, Adelaide, Australia.
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5
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An immuno-MALDI mass spectrometry assay for the oral cancer biomarker, matrix metalloproteinase-1, in dried saliva spot samples. Anal Chim Acta 2020; 1100:118-130. [DOI: 10.1016/j.aca.2019.12.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Revised: 11/19/2019] [Accepted: 12/01/2019] [Indexed: 01/17/2023]
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6
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Silbereisen A, Alassiri S, Bao K, Grossmann J, Nanni P, Fernandez C, Tervahartiala T, Nascimento GG, Belibasakis GN, Heikkinen A, Lopez R, Sorsa T, Bostanci N. Label‐Free Quantitative Proteomics versus Antibody‐Based Assays to Measure Neutrophil‐Derived Enzymes in Saliva. Proteomics Clin Appl 2020; 14:e1900050. [DOI: 10.1002/prca.201900050] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2019] [Revised: 11/20/2019] [Indexed: 12/25/2022]
Affiliation(s)
- Angelika Silbereisen
- Section of Periodontology and Dental Prevention Division of Oral Diseases Department of Dental Medicine Karolinska Institutet Alfred Nobels allé 8 14152 Huddinge Stockholm Sweden
| | - Saeed Alassiri
- Department of Oral and Maxillofacial Diseases University of Helsinki Helsinki University Central Hospital P.O. Box 41 (Mannerheimintie 172) 00014 Helsinki Finland
| | - Kai Bao
- Section of Periodontology and Dental Prevention Division of Oral Diseases Department of Dental Medicine Karolinska Institutet Alfred Nobels allé 8 14152 Huddinge Stockholm Sweden
| | - Jonas Grossmann
- Functional Genomics Center Zurich ETH Zurich and University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Paolo Nanni
- Functional Genomics Center Zurich ETH Zurich and University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Claudia Fernandez
- Functional Genomics Center Zurich ETH Zurich and University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Taina Tervahartiala
- Department of Oral and Maxillofacial Diseases University of Helsinki Helsinki University Central Hospital P.O. Box 41 (Mannerheimintie 172) 00014 Helsinki Finland
| | - Gustavo G. Nascimento
- Section of Periodontology Department of Dentistry and Oral Health Aarhus University Vennelyst Boulevard 9 8000 Aarhus C Denmark
| | - Georgios N. Belibasakis
- Section of Periodontology and Dental Prevention Division of Oral Diseases Department of Dental Medicine Karolinska Institutet Alfred Nobels allé 8 14152 Huddinge Stockholm Sweden
| | - Anna‐Maria Heikkinen
- Department of Oral and Maxillofacial Diseases University of Helsinki Helsinki University Central Hospital P.O. Box 41 (Mannerheimintie 172) 00014 Helsinki Finland
| | - Rodrigo Lopez
- Section of Periodontology Department of Dentistry and Oral Health Aarhus University Vennelyst Boulevard 9 8000 Aarhus C Denmark
| | - Timo Sorsa
- Section of Periodontology and Dental Prevention Division of Oral Diseases Department of Dental Medicine Karolinska Institutet Alfred Nobels allé 8 14152 Huddinge Stockholm Sweden
- Department of Oral and Maxillofacial Diseases University of Helsinki Helsinki University Central Hospital P.O. Box 41 (Mannerheimintie 172) 00014 Helsinki Finland
| | - Nagihan Bostanci
- Section of Periodontology and Dental Prevention Division of Oral Diseases Department of Dental Medicine Karolinska Institutet Alfred Nobels allé 8 14152 Huddinge Stockholm Sweden
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7
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Pugia MJ, Pradhan M, Qi R, Eastes DL, Vorsilak A, Mills BJ, Baird Z, Wijeratne A, McAhren SM, Mosley A, Shekhar A, Robertson DH. Utilization of electronic health records for the assessment of adiponectin receptor autoantibodies during the progression of cardio-metabolic comorbidities. ARCHIVES OF AUTOIMMUNE DISEASES 2020; 1:17-27. [PMID: 33511378 PMCID: PMC7839988 DOI: 10.46439/autoimmune.1.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
BACKGROUND Diabetes is a complex, multi-symptomatic disease whose complications drives increases in healthcare costs as the diabetes prevalence grows rapidly world-wide. Real-world electronic health records (EHRs) coupled with patient biospecimens, biological understanding, and technologies can characterize emerging diagnostic autoimmune markers resulting from proteomic discoveries. METHODS Circulating autoantibodies for C-terminal fragments of adiponectin receptor 1 (IgG-CTF) were measured by immunoassay to establish the reference range using midpoint samples from 1862 participants in a 20-year observational study of type 2 diabetes and cardiovascular arterial disease (CVAD) conducted by the Fairbanks Institute. The White Blood Cell elastase activity in these patients was assessed using immunoassays for Bikunin and Uristatin. Participants were assigned to four cohorts (healthy, T2D, CV, CV+T2D) based on analysis of their EHRs and the diagnostic biomarkers values and patient status were assessed ten-years post-sample. RESULTS The IgG-CTF reference range was determined to be 75-821 ng/mL and IgG-CTF out-of-range values did not predict cohort or comorbidity as determined from the EHRs at 10 years after sample collection nor did IgG-CTF demonstrate a significant risk for comorbidity or death. Many patients at sample collection time had other conditions (hypertension, hyperlipidemia, or other risk factors) of which only hypertension, Uristatin and Bikunin values correlated with increased risk of developing additional comorbidities (odds ratio 2.58-13.11, P<0.05). CONCLUSIONS This study confirms that retrospective analysis of biorepositories coupled with EHRs can establish reference ranges for novel autoimmune diagnostic markers and provide insights into prediction of specific health outcomes and correlations to other markers.
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Affiliation(s)
- Michael J. Pugia
- Bioanalytical Research Core, Indiana Biosciences Research Institute, Indianapolis IN, USA
| | - Meeta Pradhan
- Applied Data Sciences Center, Indiana Biosciences Research Institute, Indianapolis IN, USA
| | - Rong Qi
- Applied Data Sciences Center, Indiana Biosciences Research Institute, Indianapolis IN, USA
| | - Doreen L. Eastes
- Bioanalytical Research Core, Indiana Biosciences Research Institute, Indianapolis IN, USA
| | - Anna Vorsilak
- Bioanalytical Research Core, Indiana Biosciences Research Institute, Indianapolis IN, USA
| | - Bradley J. Mills
- Applied Data Sciences Center, Indiana Biosciences Research Institute, Indianapolis IN, USA
| | - Zane Baird
- Bioanalytical Research Core, Indiana Biosciences Research Institute, Indianapolis IN, USA
| | | | - Scott M. McAhren
- Eli Lilly and Company, Lilly Corporate Center, Indianapolis IN, USA
| | - Amber Mosley
- Indiana University School of Medicine, Indianapolis IN, USA
| | | | - Daniel H. Robertson
- Applied Data Sciences Center, Indiana Biosciences Research Institute, Indianapolis IN, USA
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8
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Levernæs MCS, Farhat B, Oulie I, Abdullah SS, Paus E, Reubsaet L, Halvorsen TG. Immunocapture sample clean-up in determination of low abundant protein biomarkers – a feasibility study of peptide capture by anti-protein antibodies. RSC Adv 2019; 9:34902-34911. [PMID: 35702551 PMCID: PMC9097496 DOI: 10.1039/c9ra05071j] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 10/21/2019] [Indexed: 01/04/2023] Open
Abstract
Immunocapture in mass spectrometry based targeted protein analysis using a bottom-up workflow is nowadays mainly performed by target protein extraction using anti-protein antibodies followed by tryptic digestion. Already available monoclonal antibodies (mAbs) which were developed against intact target proteins (anti-protein antibodies) can capture proteotypic epitope containing peptides after tryptic digestion of the sample. In the present paper considerations when developing a method for targeted protein quantitation through capture of epitope containing peptides are discussed and a method applying peptide capture by anti-protein antibodies is compared with conventional immunocapture MS. The model protein used for this purpose was progastrin releasing peptide (ProGRP), a validated low abundant biomarker for Small Cell Lung Cancer with reference values in serum in the pg mL−1 range. A set of mAbs which bind linear epitopes of ProGRP are available, and after a theoretical consideration, three mAbs (E146, E149 and M18) were evaluated for extraction of proteotypic epitope peptides from a complex sample. M18 was the best performing mAb for peptide capture by anti-protein antibodies, matching the LOD (54 pg mL−1) and LOQ (181 pg mL−1) of the existing conventional immunocapture LC-MS/MS method for determination of ProGRP. Peptide and protein capture using the same mAb were also compared with respect to sample clean-up, and the peptide capture workflow yielded cleaner extracts and therewith less complex chromatograms. Analysis of five patient samples demonstrated that peptide capture by anti-protein antibodies can be used for the determination of various levels of endogenously present ProGRP. Targeted protein biomarker determination by immunocapture LC-MS/MS: comparison of peptide and protein capture using anti-protein antibodies.![]()
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Affiliation(s)
| | - Bassem Farhat
- Department Pharmacy
- University of Oslo
- 0316 Oslo
- Norway
| | - Inger Oulie
- Department Pharmacy
- University of Oslo
- 0316 Oslo
- Norway
| | | | - Elisabeth Paus
- Department of Medical Biochemistry
- Norwegian Radium Hospital
- Oslo University Hospital
- Norway
| | - Léon Reubsaet
- Department Pharmacy
- University of Oslo
- 0316 Oslo
- Norway
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9
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Koss KM, Tsui C, Unsworth LD. Enzymatic Activity in Fractal Networks of Self-Assembling Peptides. Biomacromolecules 2018; 20:422-434. [DOI: 10.1021/acs.biomac.8b01496] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kyle M. Koss
- Department of Chemical and Materials Engineering, University of Alberta, 13-390 Floor - Donadeo Innovation Centre for Engineering
(ICE), 9211-116 Street NW, Edmonton, AB T6G 1H9, Canada
| | - Christopher Tsui
- Department of Chemical and Materials Engineering, University of Alberta, 13-390 Floor - Donadeo Innovation Centre for Engineering
(ICE), 9211-116 Street NW, Edmonton, AB T6G 1H9, Canada
| | - Larry D. Unsworth
- Department of Chemical and Materials Engineering, University of Alberta, 13-390 Floor - Donadeo Innovation Centre for Engineering
(ICE), 9211-116 Street NW, Edmonton, AB T6G 1H9, Canada
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10
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Zahedi RP, Parker CE, Borchers CH. Immuno-MALDI-TOF-MS in the Clinic. Clin Chem 2018; 64:1271-1272. [PMID: 30018057 DOI: 10.1373/clinchem.2018.292136] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 06/25/2018] [Indexed: 01/17/2023]
Affiliation(s)
- René P Zahedi
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada.,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - Carol E Parker
- University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada
| | - Christoph H Borchers
- Segal Cancer Proteomics Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, Quebec, Canada; .,Gerald Bronfman Department of Oncology, Jewish General Hospital, McGill University, Montréal, Quebec, Canada.,University of Victoria-Genome British Columbia Proteomics Centre, University of Victoria, Victoria, British Columbia, Canada.,Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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11
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Mohammed Y, Pan J, Zhang S, Han J, Borchers CH. ExSTA: External Standard Addition Method for Accurate High-Throughput Quantitation in Targeted Proteomics Experiments. Proteomics Clin Appl 2018; 12:1600180. [PMID: 28895300 PMCID: PMC6084352 DOI: 10.1002/prca.201600180] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Revised: 08/09/2017] [Indexed: 11/08/2022]
Abstract
PURPOSE Targeted proteomics using MRM with stable-isotope-labeled internal-standard (SIS) peptides is the current method of choice for protein quantitation in complex biological matrices. Better quantitation can be achieved with the internal standard-addition method, where successive increments of synthesized natural form (NAT) of the endogenous analyte are added to each sample, a response curve is generated, and the endogenous concentration is determined at the x-intercept. Internal NAT-addition, however, requires multiple analyses of each sample, resulting in increased sample consumption and analysis time. EXPERIMENTAL DESIGN To compare the following three methods, an MRM assay for 34 high-to-moderate abundance human plasma proteins is used: classical internal SIS-addition, internal NAT-addition, and external NAT-addition-generated in buffer using NAT and SIS peptides. Using endogenous-free chicken plasma, the accuracy is also evaluated. RESULTS The internal NAT-addition outperforms the other two in precision and accuracy. However, the curves derived by internal vs. external NAT-addition differ by only ≈3.8% in slope, providing comparable accuracies and precision with good CV values. CONCLUSIONS AND CLINICAL RELEVANCE While the internal NAT-addition method may be "ideal", this new external NAT-addition can be used to determine the concentration of high-to-moderate abundance endogenous plasma proteins, providing a robust and cost-effective alternative for clinical analyses or other high-throughput applications.
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Affiliation(s)
- Yassene Mohammed
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
- Center for Proteomics and MetabolomicsLeiden University Medical CenterLeidenthe Netherlands
| | - Jingxi Pan
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
| | - Suping Zhang
- MRM Proteomics Inc.VictoriaBritish ColumbiaCanada
| | - Jun Han
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
| | - Christoph H. Borchers
- University of Victoria ‐ Genome British Columbia Proteomics CentreVictoriaCanada
- University of VictoriaDepartment of Biochemistry and MicrobiologyVictoriaBCCanada
- Gerald Bronfman Department of OncologyJewish General HospitalMcGill UniversityMontrealQuebecCanada
- Proteomics CentreSegal Cancer CentreLady Davis InstituteJewish General HospitalMcGill UniversityMontrealQuebecCanada
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12
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Preece RL, Han SYS, Bahn S. Proteomic approaches to identify blood-based biomarkers for depression and bipolar disorders. Expert Rev Proteomics 2018; 15:325-340. [DOI: 10.1080/14789450.2018.1444483] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Rhian Lauren Preece
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Sung Yeon Sarah Han
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Sabine Bahn
- Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
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13
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Klont F, Ten Hacken NHT, Horvatovich P, Bakker SJL, Bischoff R. Assuring Consistent Performance of an Insulin-Like Growth Factor 1 MALDImmunoassay by Monitoring Measurement Quality Indicators. Anal Chem 2017; 89:6188-6195. [PMID: 28467045 PMCID: PMC5463271 DOI: 10.1021/acs.analchem.7b01125] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Analytical
methods based on mass spectrometry (MS) have been successfully
applied in biomarker discovery studies, while the role of MS in translating
biomarker candidates to clinical diagnostics is less pronounced. MALDImmunoassays—methods
that combine immunoaffinity enrichment with matrix-assisted laser
desorption ionization time-of-flight (MALDI-TOF) mass spectrometric
detection—are attractive analytical approaches for large-scale
sample analysis by virtue of their ease of operation and high-throughput
capabilities. Despite this fact, MALDImmunoassays are not widely used
in clinical diagnostics, which is mainly due to the limited availability
of internal standards that can adequately correct for variability
in sample preparation and the MALDI process itself. Here we present
a novel MALDImmunoassay for quantification of insulin-like growth
factor 1 (IGF1) in human plasma. Reliable IGF1 quantification in the
range of 10–1000 ng/mL was achieved by employing 15N-IGF1 as internal standard, which proved to be an essential feature
of the IGF1 MALDImmunoassay. The method was validated according to
U.S. Food and Drug Administration (FDA) guidelines, which included
demonstrating the effectiveness of IGF1/IGF binding protein (IGF1/IGFBP)
complex dissociation using sodium dodecyl sulfate (SDS). Furthermore,
the MALDImmunoassay compared well with the IDS-iSYS IGF1 immunoassay
with high correlation (R2 = 0.99), although
substantially lower levels were reported by the MALDImmunoassay. The
method was tested on >1000 samples from a cohort of renal transplant
recipients to assess its performance in a clinical setting. On the
basis of this study, we identified readouts to monitor the quality
of the measurements. Our work shows that MALDI-TOF mass spectrometry
is suitable for quantitative biomarker analysis provided that an appropriate
internal standard is used and that readouts are monitored to assess
the quality of the measurements.
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Affiliation(s)
- Frank Klont
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | - Péter Horvatovich
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
| | | | - Rainer Bischoff
- Analytical Biochemistry, Department of Pharmacy, University of Groningen , Antonius Deusinglaan 1, 9713 AV Groningen, The Netherlands
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14
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Li H, Han J, Pan J, Liu T, Parker CE, Borchers CH. Current trends in quantitative proteomics - an update. JOURNAL OF MASS SPECTROMETRY : JMS 2017; 52:319-341. [PMID: 28418607 DOI: 10.1002/jms.3932] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/28/2017] [Accepted: 04/06/2017] [Indexed: 05/11/2023]
Abstract
Proteins can provide insights into biological processes at the functional level, so they are very promising biomarker candidates. The quantification of proteins in biological samples has been routinely used for the diagnosis of diseases and monitoring the treatment. Although large-scale protein quantification in complex samples is still a challenging task, a great amount of effort has been made to advance the technologies that enable quantitative proteomics. Seven years ago, in 2009, we wrote an article about the current trends in quantitative proteomics. In writing this current paper, we realized that, today, we have an even wider selection of potential tools for quantitative proteomics. These tools include new derivatization reagents, novel sampling formats, new types of analyzers and scanning techniques, and recently developed software to assist in assay development and data analysis. In this review article, we will discuss these innovative methods, and their current and potential applications in proteomics. Copyright © 2017 John Wiley & Sons, Ltd.
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Affiliation(s)
- H Li
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - J Han
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - J Pan
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - T Liu
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - C E Parker
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
| | - C H Borchers
- University of Victoria - Genome British Columbia Proteomics Centre, University of Victoria, Victoria, BC, V8Z 7X8, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8P 5C2, Canada
- Proteomics Centre, Segal Cancer Centre, Lady Davis Institute, Jewish General Hospital, McGill University, Montreal, QC, H3T 1E2, Canada
- Gerald Bronfman Department of Oncology, Jewish General Hospital, Montreal, Quebec, H3T 1E2, Canada
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15
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Li H, Popp R, Borchers CH. Affinity-mass spectrometric technologies for quantitative proteomics in biological fluids. Trends Analyt Chem 2017. [DOI: 10.1016/j.trac.2017.02.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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16
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Percy AJ, Michaud SA, Jardim A, Sinclair NJ, Zhang S, Mohammed Y, Palmer AL, Hardie DB, Yang J, LeBlanc AM, Borchers CH. Multiplexed MRM-based assays for the quantitation of proteins in mouse plasma and heart tissue. Proteomics 2016; 17. [DOI: 10.1002/pmic.201600097] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2016] [Revised: 08/14/2016] [Accepted: 09/28/2016] [Indexed: 12/30/2022]
Affiliation(s)
- Andrew J. Percy
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Sarah A. Michaud
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Armando Jardim
- Institute of Parasitology; McGill University; Montreal QC Canada
| | - Nicholas J. Sinclair
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Suping Zhang
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Yassene Mohammed
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
- Center for Proteomics and Metabolomics; Leiden University Medical Center; ZA Leiden Netherlands
| | - Andrea L. Palmer
- MRM Proteomics; , Vancouver Island Technology Park; Victoria BC Canada
| | - Darryl B. Hardie
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Juncong Yang
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Andre M. LeBlanc
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
| | - Christoph H. Borchers
- University of Victoria-Genome British Columbia Proteomics Centre; , Vancouver Island Technology Park; Victoria BC Canada
- Department of Biochemistry and Microbiology; University of Victoria; Victoria BC Canada
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17
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High precision quantification of human plasma proteins using the automated SISCAPA Immuno-MS workflow. N Biotechnol 2016; 33:494-502. [DOI: 10.1016/j.nbt.2015.12.008] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 12/22/2015] [Accepted: 12/29/2015] [Indexed: 11/24/2022]
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18
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Shi T, Song E, Nie S, Rodland KD, Liu T, Qian WJ, Smith RD. Advances in targeted proteomics and applications to biomedical research. Proteomics 2016; 16:2160-82. [PMID: 27302376 PMCID: PMC5051956 DOI: 10.1002/pmic.201500449] [Citation(s) in RCA: 145] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Revised: 05/09/2016] [Accepted: 06/10/2016] [Indexed: 12/17/2022]
Abstract
Targeted proteomics technique has emerged as a powerful protein quantification tool in systems biology, biomedical research, and increasing for clinical applications. The most widely used targeted proteomics approach, selected reaction monitoring (SRM), also known as multiple reaction monitoring (MRM), can be used for quantification of cellular signaling networks and preclinical verification of candidate protein biomarkers. As an extension to our previous review on advances in SRM sensitivity (Shi et al., Proteomics, 12, 1074-1092, 2012) herein we review recent advances in the method and technology for further enhancing SRM sensitivity (from 2012 to present), and highlighting its broad biomedical applications in human bodily fluids, tissue and cell lines. Furthermore, we also review two recently introduced targeted proteomics approaches, parallel reaction monitoring (PRM) and data-independent acquisition (DIA) with targeted data extraction on fast scanning high-resolution accurate-mass (HR/AM) instruments. Such HR/AM targeted quantification with monitoring all target product ions addresses SRM limitations effectively in specificity and multiplexing; whereas when compared to SRM, PRM and DIA are still in the infancy with a limited number of applications. Thus, for HR/AM targeted quantification we focus our discussion on method development, data processing and analysis, and its advantages and limitations in targeted proteomics. Finally, general perspectives on the potential of achieving both high sensitivity and high sample throughput for large-scale quantification of hundreds of target proteins are discussed.
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Affiliation(s)
- Tujin Shi
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Ehwang Song
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Song Nie
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Karin D Rodland
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Tao Liu
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Wei-Jun Qian
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
| | - Richard D Smith
- Biological Sciences Division and Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA
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19
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Percy AJ, Byrns S, Pennington SR, Holmes DT, Anderson NL, Agreste TM, Duffy MA. Clinical translation of MS-based, quantitative plasma proteomics: status, challenges, requirements, and potential. Expert Rev Proteomics 2016; 13:673-84. [DOI: 10.1080/14789450.2016.1205950] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Andrew J. Percy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
| | - Simon Byrns
- Department of Surgery, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB, Canada
| | - Stephen R. Pennington
- Department of Pathology, School of Medicine, UCD Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Daniel T. Holmes
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - N. Leigh Anderson
- Department of Clinical Biomarkers, SISCAPA Assay Technologies, Inc., Washington, DC, USA
| | - Tasha M. Agreste
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
| | - Maureen A. Duffy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA, USA
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20
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Sabbagh B, Mindt S, Neumaier M, Findeisen P. Clinical applications of MS-based protein quantification. Proteomics Clin Appl 2016; 10:323-45. [DOI: 10.1002/prca.201500116] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Revised: 11/18/2015] [Accepted: 12/30/2015] [Indexed: 12/14/2022]
Affiliation(s)
- Bassel Sabbagh
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Sonani Mindt
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Michael Neumaier
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
| | - Peter Findeisen
- Institute for Clinical Chemistry; Medical Faculty Mannheim of the University of Heidelberg; University Hospital Mannheim; Mannheim Germany
- MVZ Labor Dr. Limbach und Kollegen; Heidelberg Germany
- Working Group Proteomics of the German United Society for Clinical Chemistry and Laboratory Medicine e.V. (DGKL); Bonn Germany
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21
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Percy AJ, Yang J, Chambers AG, Mohammed Y, Miliotis T, Borchers CH. Protocol for Standardizing High-to-Moderate Abundance Protein Biomarker Assessments Through an MRM-with-Standard-Peptides Quantitative Approach. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2016; 919:515-530. [DOI: 10.1007/978-3-319-41448-5_24] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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22
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Fredolini C, Byström S, Pin E, Edfors F, Tamburro D, Iglesias MJ, Häggmark A, Hong MG, Uhlen M, Nilsson P, Schwenk JM. Immunocapture strategies in translational proteomics. Expert Rev Proteomics 2015; 13:83-98. [PMID: 26558424 PMCID: PMC4732419 DOI: 10.1586/14789450.2016.1111141] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Aiming at clinical studies of human diseases, antibody-assisted assays have been applied to biomarker discovery and toward a streamlined translation from patient profiling to assays supporting personalized treatments. In recent years, integrated strategies to couple and combine antibodies with mass spectrometry-based proteomic efforts have emerged, allowing for novel possibilities in basic and clinical research. Described in this review are some of the field's current and emerging immunocapture approaches from an affinity proteomics perspective. Discussed are some of their advantages, pitfalls and opportunities for the next phase in clinical and translational proteomics.
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Affiliation(s)
- Claudia Fredolini
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Sanna Byström
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Elisa Pin
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Fredrik Edfors
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Davide Tamburro
- Department of Oncology-Pathology, Clinical Proteomics Mass Spectrometry, SciLifeLab, Karolinska Institutet, Solna, Sweden
| | - Maria Jesus Iglesias
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Anna Häggmark
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Mun-Gwan Hong
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Mathias Uhlen
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Peter Nilsson
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
| | - Jochen M Schwenk
- Affinity Proteomics, SciLifeLab, School of Biotechnology, KTH - Royal Institute of Technology, Solna, Sweden
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23
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Boström T, Takanen JO, Hober S. Antibodies as means for selective mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1021:3-13. [PMID: 26565067 DOI: 10.1016/j.jchromb.2015.10.042] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 10/15/2015] [Accepted: 10/23/2015] [Indexed: 01/21/2023]
Abstract
For protein analysis of biological samples, two major strategies are used today; mass spectrometry (MS) and antibody-based methods. Each strategy offers advantages and drawbacks. However, combining the two using an immunoenrichment step with MS analysis brings together the benefits of each method resulting in increased sensitivity, faster analysis and possibility of higher degrees of multiplexing. The immunoenrichment can be performed either on protein or peptide level and quantification standards can be added in order to enable determination of the absolute protein concentration in the sample. The combination of immunoenrichment and MS holds great promise for the future in both proteomics and clinical diagnostics. This review describes different setups of immunoenrichment coupled to mass spectrometry and how these can be utilized in various applications.
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Affiliation(s)
- Tove Boström
- School of Biotechnology, Division of Protein Technology, KTH-Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Jenny Ottosson Takanen
- School of Biotechnology, Division of Proteomics and Nanobiotechnology, KTH-Royal Institute ofTechnology, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Sophia Hober
- School of Biotechnology, Division of Protein Technology, KTH-Royal Institute of Technology, AlbaNova University Center, SE-106 91 Stockholm, Sweden.
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24
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Smolira A, Hałas S, Wessely-Szponder J. Quantification of the PR-39 cathelicidin compound in porcine blood by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1811-1816. [PMID: 26331932 DOI: 10.1002/rcm.7284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2015] [Accepted: 07/20/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE The PR-39 porcine cathelicidin occurs naturally in animal neutrophils. Its main function is antimicrobial activity, which potentially can be used in antibiotic treatments in veterinary medicine. Investigations concerning such a use require the detection and quantification of PR-39 in a given sample. The aim of this work is to determine the concentration of PR-39 contained in porcine blood. METHODS Prior to matrix-assisted laser desorption/ionization (MALDI) analysis, the porcine blood sample was subjected to crude extraction in order to release the active form of PR-39 from the neutrophil granules. Next, gel filtration chromatography was performed to separate PR-39 from other cathelicidins present in porcine blood. Positive ion MALDI time-of-flight (TOF) mass spectra of the resulting portion of lyophilisate with unknown PR-39 content were acquired in linear mode. To quantify PR-39 in the lyophilisate sample, the standard addition method was applied. The PR-39 concentration obtained in the lyophilisate sample was then converted into the peptide concentration in porcine blood. RESULTS The linear fit function of the constructed calibration curve indicates an excellent correlation between the PR-39 peak intensity and the added quantity of synthetic PR-39 (R(2) = 0.994) and a low relative standard deviation of the slope = 1.98%. From the x-intercept of the straight line, we estimated the PR-39 concentration in porcine blood to be 20.5 ± 4.6 ng/mL. CONCLUSIONS The MALDI method was successfully applied for the quantitative analysis of PR-39 found in porcine blood. Compared with other available methods, it is relatively easy, inexpensive and not time-consuming. Despite the method having lower accuracy than the enzyme-linked immunosorbent assay (ELISA), the results obtained here, by a much simpler method, are in good agreement with the literature data.
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Affiliation(s)
- Anna Smolira
- Mass Spectrometry Laboratory, Institute of Physics, Maria Curie Sklodowska University, Pl. M. Curie-Skłodowskiej 1, 20-031, Lublin, Poland
| | - Stanisław Hałas
- Mass Spectrometry Laboratory, Institute of Physics, Maria Curie Sklodowska University, Pl. M. Curie-Skłodowskiej 1, 20-031, Lublin, Poland
| | - Joanna Wessely-Szponder
- Department of Pathophysiology, Chair of Preclinical Veterinary Sciences, Faculty of Veterinary Medicine, University of Life Sciences, Akademicka 12, 20-033, Lublin, Poland
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25
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Lorey M, Adler B, Yan H, Soliymani R, Ekström S, Yli-Kauhaluoma J, Laurell T, Baumann M. Mass-Tag Enhanced Immuno-Laser Desorption/Ionization Mass Spectrometry for Sensitive Detection of Intact Protein Antigens. Anal Chem 2015; 87:5255-62. [DOI: 10.1021/acs.analchem.5b00304] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Affiliation(s)
- Martina Lorey
- Meilahti
Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63, FI-00014 University of Helsinki, Finland
- Institute
of Biotechnology, University of Helsinki, P.O. Box 65, Helsinki FI-00014, Finland
- Unit
of Systems Toxicology, Finnish Institute of Occupational Health, Topeliuksenkatu 41 b, FI-00250 Helsinki, Finland
| | - Belinda Adler
- Department
of Biomedical Engineering, Faculty of Engineering, Lund University, P.O. Box 118, SE-21100 Lund, Sweden
| | - Hong Yan
- Department
of Biomedical Engineering, Faculty of Engineering, Lund University, P.O. Box 118, SE-21100 Lund, Sweden
| | - Rabah Soliymani
- Meilahti
Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63, FI-00014 University of Helsinki, Finland
| | - Simon Ekström
- Department
of Biomedical Engineering, Faculty of Engineering, Lund University, P.O. Box 118, SE-21100 Lund, Sweden
| | - Jari Yli-Kauhaluoma
- Division
of Pharmaceutical Chemistry and Technology, Faculty of Pharmacy, University of Helsinki, P.O. Box 56, Viikinkaari 5 E, FI-00014 University of Helsinki, Finland
| | - Thomas Laurell
- Department
of Biomedical Engineering, Faculty of Engineering, Lund University, P.O. Box 118, SE-21100 Lund, Sweden
- Department
of Biomedical Engineering, Dongguk University, 202 Science Building Phildong 3ga. Joong-Gu Seoul, Republic of Korea
| | - Marc Baumann
- Meilahti
Clinical Proteomics Core Facility, University of Helsinki, P.O. Box 63, FI-00014 University of Helsinki, Finland
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26
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Hartmann EM, Colquhoun DR, Schwab KJ, Halden RU. Absolute quantification of norovirus capsid protein in food, water, and soil using synthetic peptides with electrospray and MALDI mass spectrometry. JOURNAL OF HAZARDOUS MATERIALS 2015; 286:525-32. [PMID: 25603302 PMCID: PMC4369174 DOI: 10.1016/j.jhazmat.2014.12.055] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Revised: 12/20/2014] [Accepted: 12/27/2014] [Indexed: 05/16/2023]
Abstract
Norovirus infections are one of the most prominent public health problems of microbial origin in the U.S. and other industrialized countries. Surveillance is necessary to prevent secondary infection, confirm successful cleanup after outbreaks, and track the causative agent. Quantitative mass spectrometry, based on absolute quantitation with stable-isotope labeled peptides, is a promising tool for norovirus monitoring because of its speed, sensitivity, and robustness in the face of environmental inhibitors. In the current study, we present two new methods for the detection of the norovirus genogroup I capsid protein using electrospray and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. The peptide TLDPIEVPLEDVR was used to quantify norovirus-like particles down to 500 attomoles with electrospray and 100 attomoles with MALDI. With MALDI, we also demonstrate a detection limit of 1 femtomole and a quantitative dynamic range of 5 orders of magnitude in the presence of an environmental matrix effect. Due to the rapid processing time and applicability to a wide range of environmental sample types (bacterial lysate, produce, milk, soil, and groundwater), mass spectrometry-based absolute quantitation has a strong potential for use in public health and environmental sciences.
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Affiliation(s)
- Erica M Hartmann
- Center for Environmental Security and Security Defense Systems Initiative, The Biodesign Institute, Arizona State University, 781 E. Terrace Mall, Tempe, AZ 85287-5904, USA
| | - David R Colquhoun
- Department of Environmental Health Sciences, The Johns Hopkins University, Bloomberg School of Public Health, 615 N. Wolfe St., Baltimore, MD 21205, USA
| | - Kellogg J Schwab
- Department of Environmental Health Sciences, The Johns Hopkins University, Bloomberg School of Public Health, 615 N. Wolfe St., Baltimore, MD 21205, USA
| | - Rolf U Halden
- Center for Environmental Security and Security Defense Systems Initiative, The Biodesign Institute, Arizona State University, 781 E. Terrace Mall, Tempe, AZ 85287-5904, USA; Department of Environmental Health Sciences, The Johns Hopkins University, Bloomberg School of Public Health, 615 N. Wolfe St., Baltimore, MD 21205, USA.
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27
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van den Broek I, Nouta J, Razavi M, Yip R, Bladergroen MR, Romijn FPHTM, Smit NPM, Drews O, Paape R, Suckau D, Deelder AM, van der Burgt YEM, Pearson TW, Anderson NL, Cobbaert CM. Quantification of serum apolipoproteins A-I and B-100 in clinical samples using an automated SISCAPA-MALDI-TOF-MS workflow. Methods 2015; 81:74-85. [PMID: 25766926 DOI: 10.1016/j.ymeth.2015.03.001] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Revised: 03/01/2015] [Accepted: 03/02/2015] [Indexed: 01/09/2023] Open
Abstract
A fully automated workflow was developed and validated for simultaneous quantification of the cardiovascular disease risk markers apolipoproteins A-I (apoA-I) and B-100 (apoB-100) in clinical sera. By coupling of stable-isotope standards and capture by anti-peptide antibodies (SISCAPA) for enrichment of proteotypic peptides from serum digests to matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) MS detection, the standardized platform enabled rapid, liquid chromatography-free quantification at a relatively high throughput of 96 samples in 12h. The average imprecision in normo- and triglyceridemic serum pools was 3.8% for apoA-I and 4.2% for apoB-100 (4 replicates over 5 days). If stored properly, the MALDI target containing enriched apoA-1 and apoB-100 peptides could be re-analyzed without any effect on bias or imprecision for at least 7 days after initial analysis. Validation of the workflow revealed excellent linearity for daily calibration with external, serum-based calibrators (R(2) of 0.984 for apoA-I and 0.976 for apoB-100 as average over five days), and absence of matrix effects or interference from triglycerides, protein content, hemolysates, or bilirubins. Quantification of apoA-I in 93 normo- and hypertriglyceridemic clinical sera showed good agreement with immunoturbidimetric analysis (slope = 1.01, R(2) = 0.95, mean bias = 4.0%). Measurement of apoB-100 in the same clinical sera using both methods, however, revealed several outliers in SISCAPA-MALDI-TOF-MS measurements, possibly as a result of the lower MALDI-TOF-MS signal intensity (slope = 1.09, R(2) = 0.91, mean bias = 2.0%). The combination of analytical performance, rapid cycle time and automation potential validate the SISCAPA-MALDI-TOF-MS platform as a valuable approach for standardized and high-throughput quantification of apoA-I and apoB-100 in large sample cohorts.
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Affiliation(s)
- Irene van den Broek
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands.
| | - Jan Nouta
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Morteza Razavi
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC 20009, USA
| | - Richard Yip
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC 20009, USA
| | - Marco R Bladergroen
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Nico P M Smit
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Oliver Drews
- Bruker Daltonics GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Rainer Paape
- Bruker Daltonics GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - Detlev Suckau
- Bruker Daltonics GmbH, Fahrenheitstraße 4, 28359 Bremen, Germany
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Terry W Pearson
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC 20009, USA
| | - N Leigh Anderson
- SISCAPA Assay Technologies Inc., Box 53309, Washington, DC 20009, USA
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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28
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Cho YT, Su H, Wu WJ, Wu DC, Hou MF, Kuo CH, Shiea J. Biomarker Characterization by MALDI-TOF/MS. Adv Clin Chem 2015; 69:209-54. [PMID: 25934363 DOI: 10.1016/bs.acc.2015.01.001] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometric techniques frequently used in clinical diagnosis, such as gas chromatography-mass spectrometry, liquid chromatography-mass spectrometry, ambient ionization mass spectrometry, and matrix-assisted laser desorption ionization/time-of-flight mass spectrometry (MALDI-TOF/MS), are discussed. Due to its ability to rapidly detect large biomolecules in trace amounts, MALDI-TOF/MS is an ideal tool for characterizing disease biomarkers in biologic samples. Clinical applications of MS for the identification and characterization of microorganisms, DNA fragments, tissues, and biofluids are introduced. Approaches for using MALDI-TOF/MS to detect various disease biomarkers including peptides, proteins, and lipids in biological fluids are further discussed. Finally, various sample pretreatment methods which improve the detection efficiency of disease biomarkers are introduced.
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Affiliation(s)
- Yi-Tzu Cho
- Department of Cosmetic Applications and Management, Yuh-Ing Junior College of Health Care & Management, Kaohsiung, Taiwan
| | - Hung Su
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan
| | - Wen-Jeng Wu
- Department of Urology, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Deng-Chyang Wu
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Ming-Feng Hou
- Department of Surgery, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan
| | - Chao-Hung Kuo
- Division of Gastroenterology, Department of Internal Medicine, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan
| | - Jentaie Shiea
- Department of Chemistry, National Sun Yat-sen University, Kaohsiung, Taiwan; Center for Stem Cell Research, Kaohsiung Medical University, Kaohsiung, Taiwan; Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung, Taiwan; Department of Medicinal and Applied Chemistry, Kaohsiung Medical University, Kaohsiung, Taiwan.
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29
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Abstract
Glycans on proteins and lipids are known to alter with malignant transformation. The study of these may contribute to the discovery of biomarkers and treatment targets as well as understanding of cancer biology. We here describe the change of glycosylation specifically defining colorectal cancer with view on N-glycans, O-glycans, and glycosphingolipid glycans in colorectal cancer cells and tissues as well as patient sera. Glycan alterations observed in colon cancer include increased β1,6-branching and correlating higher abundance of (poly-)N-acetyllactosamine extensions of N-glycans as well as an increase in (truncated) high-mannose type glycans, while bisected structures decrease. Colorectal cancer-associated O-glycan changes are predominated by reduced expression of core 3 and 4 glycans, whereas higher levels of core 1 glycans, (sialyl) T-antigen, (sialyl) Tn-antigen, and a generally higher density of O-glycans are observed. Specific changes for glycosphingolipid glycans are lower abundances of disialylated structures as well as globo-type glycosphingolipid glycans with exception of Gb3. In general, alterations affecting all discussed glycan types are increased sialylation, fucosylation as well as (sialyl) Lewis-type antigens and type-2 chain glycans. As a consequence, interactions with glycan-binding proteins can be affected and the biological function and cellular consequences of the altered glycosylation with regard to tumorigenesis, metastasis, modulation of immunity, and resistance to antitumor therapy will be discussed. Finally, analytical approaches aiding in the field of glycomics will be reviewed with focus on binding assays and mass spectrometry.
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Affiliation(s)
- Stephanie Holst
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands; Department of Molecular Cell Biology and Immunology, VU University Medical Center, Amsterdam, The Netherlands; Division of BioAnalytical Chemistry, VU University, Amsterdam, The Netherlands
| | - Yoann Rombouts
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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30
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Säll A, Carlsson F, Olsson N, Wingren C, Ohlin M, Persson H, Waldemarson S. AFFIRM--a multiplexed immunoaffinity platform that combines recombinant antibody fragments and LC-SRM analysis. J Proteome Res 2014; 13:5837-47. [PMID: 25337893 DOI: 10.1021/pr500757s] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Targeted measurements of low abundance proteins in complex mixtures are in high demand in many areas, not the least in clinical applications measuring biomarkers. We here present the novel platform AFFIRM (AFFInity sRM) that utilizes the power of antibody fragments (scFv) to efficiently enrich for target proteins from a complex background and the exquisite specificity of SRM-MS based detection. To demonstrate the ability of AFFIRM, three target proteins of interest were measured in a serum background in single-plexed and multiplexed experiments in a concentration range of 5-1000 ng/mL. Linear responses were demonstrated down to low ng/mL concentrations with high reproducibility. The platform allows for high throughput measurements in 96-well format, and all steps are amendable to automation and scale-up. We believe the use of recombinant antibody technology in combination with SRM MS analysis provides a powerful way to reach sensitivity, specificity, and reproducibility as well as the opportunity to build resources for fast on-demand implementation of novel assays.
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Affiliation(s)
- Anna Säll
- Department of Immunotechnology, Lund University , Medicon Village (House 406), SE-223 81 Lund, Sweden
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Wang D, Baudys J, Krilich J, Smith TJ, Barr JR, Kalb SR. A two-stage multiplex method for quantitative analysis of botulinum neurotoxins type A, B, E, and F by MALDI-TOF mass spectrometry. Anal Chem 2014; 86:10847-54. [PMID: 25285509 DOI: 10.1021/ac502948v] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
In this publication, we report on the development of a quantitative enzymatic method for the detection of four botulinum neurotoxin (BoNT) serotypes responsible for human botulism by MALDI-TOF mass spectrometry. Factors that might affect the linearity and dynamic range for detection of BoNT cleavage products were initially examined, including the amount of peptide substrate and internal standard, the timing of cleavage reaction, and the components in the reaction solution. It was found that a long incubation time produced sensitive results, but was not capable of determining higher toxin concentrations, whereas a short incubation time was less sensitive so that lower toxin concentrations were not detected. In order to overcome these limitations, a two-stage analysis strategy was applied. The first stage analysis involved a short incubation period (e.g., 30 min). If no toxin was detected at this stage, the cleavage reaction was allowed to continue and the samples were analyzed at a second time point (4 h), so that toxin levels lower than 1 mouse LD50 or 55 attomoles per milliliter (55 amol/mL) could be quantified. By combining the results from two-stage quantification, 4 or 5 orders of magnitude in dynamic range were achieved for the detection of the serotypes of BoNT/A, BoNT/B, BoNT/E, or BoNT/F. The effect of multiplexing the assay by mixing substrates for different BoNT serotypes into a single reaction was also investigated in order to reduce the numbers of the cleavage reactions and save valuable clinical samples.
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Affiliation(s)
- Dongxia Wang
- Division of Laboratory Sciences, National Center for Environmental Health, Centers for Disease Control and Prevention , Atlanta, Georgia 30341, United States
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An automated assay for the clinical measurement of plasma renin activity by immuno-MALDI (iMALDI). BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:547-58. [PMID: 25461795 DOI: 10.1016/j.bbapap.2014.10.008] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 09/26/2014] [Accepted: 10/09/2014] [Indexed: 11/24/2022]
Abstract
Plasma renin activity (PRA) is essential for the screening and diagnosis of primary aldosteronism (PA), a form of secondary hypertension, which affects approximately 100 million people worldwide. It is commonly determined by radioimmunoassay (RIA) and, more recently, by relatively low-throughput LC-MS/MS methods. In order to circumvent the negative aspects of RIAs (radioisotopes, cross-reactivity) and the low throughput of LC-MS based methods, we have developed a high-throughput immuno-MALDI (iMALDI)-based assay for PRA determination using an Agilent Bravo for automated liquid handling and a Bruker Microflex LRF instrument for MALDI analysis, with the goal of implementing the assay in clinical laboratories. The current assay allows PRA determination of 29 patient samples (192 immuno-captures), within ~6 to 7h, using a 3-hour Ang I generation period, at a 7.5-fold faster analysis time than LC-MS/MS. The assay is performed on 350μL of plasma, and has a linear range from 0.08 to 5.3ng/L/s in the reflector mode, and 0.04 to 5.3ng/L/s in the linear mode. The analytical precision is 2.0 to 9.7% CV in the reflector mode, and 1.5 to 14.3% CV in the linear mode. A method comparison to a clinically employed LC-MS/MS assay for PRA determination showed excellent correlation within the linear range, with an R(2) value of ≥0.98. This automated high throughput iMALDI platform has clinically suitable sensitivity, precision, linear range, and correlation with the standard method for PRA determination. Furthermore, the developed workflow based on the iMALDI technology can be used for the determination of other proteomic biomarkers. This article is part of a Special Issue entitled: Medical Proteomics.
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Ritorto MS, Ewan R, Perez-Oliva AB, Knebel A, Buhrlage SJ, Wightman M, Kelly SM, Wood NT, Virdee S, Gray NS, Morrice NA, Alessi DR, Trost M. Screening of DUB activity and specificity by MALDI-TOF mass spectrometry. Nat Commun 2014; 5:4763. [PMID: 25159004 PMCID: PMC4147353 DOI: 10.1038/ncomms5763] [Citation(s) in RCA: 240] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 07/21/2014] [Indexed: 12/22/2022] Open
Abstract
Deubiquitylases (DUBs) are key regulators of the ubiquitin system which cleave ubiquitin moieties from proteins and polyubiquitin chains. Several DUBs have been implicated in various diseases and are attractive drug targets. We have developed a sensitive and fast assay to quantify in vitro DUB enzyme activity using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. Unlike other current assays, this method uses unmodified substrates, such as diubiquitin topoisomers. By analysing 42 human DUBs against all diubiquitin topoisomers we provide an extensive characterization of DUB activity and specificity. Our results confirm the high specificity of many members of the OTU and JAB/MPN/Mov34 metalloenzyme DUB families and highlight that all USPs tested display low linkage selectivity. We also demonstrate that this assay can be deployed to assess the potency and specificity of DUB inhibitors by profiling 11 compounds against a panel of 32 DUBs. Deubiquitylases (DUBs) remove ubiquitin chains from proteins. Here the authors develop a mass spectrometry-based DUB activity screen using unmodified diubiquitin isomers to characterize substrate specificity for 42 human DUBs, and assess the potency and selectivity of 11 DUB inhibitors.
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Affiliation(s)
- Maria Stella Ritorto
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Richard Ewan
- 1] MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK [2]
| | - Ana B Perez-Oliva
- 1] MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK [2]
| | - Axel Knebel
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Sara J Buhrlage
- 1] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA [2] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, SGM 628, Boston, Massachusetts 02115, USA
| | - Melanie Wightman
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Sharon M Kelly
- Institute of Molecular Cell and Systems Biology, University of Glasgow, Glasgow G12 8QQ, Scotland, UK
| | - Nicola T Wood
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Satpal Virdee
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Nathanael S Gray
- 1] Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, Massachusetts 02115, USA [2] Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 250 Longwood Avenue, SGM 628, Boston, Massachusetts 02115, USA
| | - Nicholas A Morrice
- The Beatson Institute for Cancer Research, Bearsden, Glasgow G61 1BD, Scotland, UK
| | - Dario R Alessi
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
| | - Matthias Trost
- MRC Protein Phosphorylation and Ubiquitylation Unit, University of Dundee, Dundee DD1 5EH, Scotland, UK
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Relative quantitation of glycopeptides based on stable isotope labeling using MALDI-TOF MS. Molecules 2014; 19:9944-61. [PMID: 25010467 PMCID: PMC6271863 DOI: 10.3390/molecules19079944] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 07/01/2014] [Accepted: 07/07/2014] [Indexed: 12/19/2022] Open
Abstract
We have developed an effective, sensitive method for quantitative glycopeptide profiling using stable isotope labeling and MALDI-TOF mass spectrometry (MS). In this study, we synthesized benzoic acid-d0N-succinimidyl ester (BzOSu) and benzoic acid-d5N-succinimidyl ester (d-BzOSu) as light and heavy isotope reagents for stable isotope quantification for the comparative analysis of glycopeptides. Using this approach provided enhanced ionization efficiency in both positive and negative modes by MALDI-TOF MS. These reagents were quantitatively reacted with glycopeptides from human serum IgG (hIgG) at a wide range of concentrations; the labeling efficiency of the glycopeptides showed high reproducibility and a good calibration curve was obtained. To demonstrate the practical utility of this approach, we characterized the structures of glycopeptides from hIgG and from IgG1 produced by myeloma plasma. The glycopeptides were quantitatively analyzed by mixing Bz-labeled IgG1 glycopeptides with d-Bz-labeled hIgG glycopeptides. Glycan structural identification of the hIgG glycopeptides was demonstrated by combining the highly specific recognition of endo-β-N-acetyl glucosaminidases from Streptococcus pyogenes (endoS) or from Streptococcus pneumoniae (endo-D) with MALDI-TOF MS analysis. The obtained data revealed the glycan profile and the ratio of glycan structural isomers containing a galactosylated extension on IgG1, IgG2 and IgG3 glycopetides.
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Anderson L. Six decades searching for meaning in the proteome. J Proteomics 2014; 107:24-30. [PMID: 24642211 DOI: 10.1016/j.jprot.2014.03.005] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2014] [Accepted: 03/04/2014] [Indexed: 11/26/2022]
Abstract
This review describes one thread in a fabric of developments leading to the present state of proteomics, stretching over 60years and ending with a prediction for 2024. While composed largely of personal reminiscences, the story offers some instructive successes and failures, and appears to be nearing the long-sought goal of deep insights into real biology. This article is part of a Special Issue entitled: 20 Years of Proteomics in memory of Viatliano Pallini. Guest Editors: Luca Bini , Juan J. Calvete, Natacha Turck, Denis Hochstrasser and Jean-Charles Sanchez.
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Affiliation(s)
- Leigh Anderson
- SISCAPA Assay Technologies, Inc., P.O. Box 53309, Washington, DC 20009, USA.
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Whiteaker JR, Zhao L, Frisch C, Ylera F, Harth S, Knappik A, Paulovich AG. High-affinity recombinant antibody fragments (Fabs) can be applied in peptide enrichment immuno-MRM assays. J Proteome Res 2014; 13:2187-96. [PMID: 24568200 PMCID: PMC3993957 DOI: 10.1021/pr4009404] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
High-affinity
antibodies binding to linear peptides in solution
are a prerequisite for performing immuno-MRM, an emerging technology
for protein quantitation with high precision and specificity using
peptide immunoaffinity enrichment coupled to stable isotope dilution
and targeted mass spectrometry. Recombinant antibodies can be generated
from appropriate libraries in high-throughput in an automated laboratory
and thus may offer advantages over conventional monoclonal antibodies.
However, recombinant antibodies are typically obtained as fragments
(Fab or scFv) expressed from E. coli, and it is not
known whether these antibody formats are compatible with the established
protocols and whether the affinities necessary for immunocapture of
small linear peptides can be achieved with this technology. Hence,
we performed a feasibility study to ask: (a) whether it is feasible
to isolate high-affinity Fabs to small linear antigens and (b) whether
it is feasible to incorporate antibody fragments into robust, quantitative
immuno-MRM assays. We describe successful isolation of high-affinity
Fab fragments against short (tryptic) peptides from a human combinatorial
Fab library. We analytically characterize three immuno-MRM assays
using recombinant Fabs, full-length IgGs constructed from these Fabs,
or traditional monoclonals. We show that the antibody fragments show
similar performance compared with traditional mouse- or rabbit-derived
monoclonal antibodies. The data establish feasibility of isolating
and incorporating high-affinity Fabs into peptide immuno-MRM assays.
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Affiliation(s)
- Jeffrey R Whiteaker
- Fred Hutchinson Cancer Research Center , 1100 Fairview Avenue North, Seattle, Washington 98109, United States
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Camenzind AG, van der Gugten JG, Popp R, Holmes DT, Borchers CH. Development and evaluation of an immuno-MALDI (iMALDI) assay for angiotensin I and the diagnosis of secondary hypertension. Clin Proteomics 2013; 10:20. [PMID: 24359218 PMCID: PMC4081661 DOI: 10.1186/1559-0275-10-20] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/13/2013] [Indexed: 11/10/2022] Open
Abstract
Plasma renin activity (PRA) is an essential analytical tool for screening and diagnosis of secondary forms of hypertension. Typically, PRA is measured by competitive radioimmunoassay, but there are significant drawbacks to this technique including non-specificity, long analysis times, narrow calibration range, and the requirement for radionucleotides. In this paper, we report a method for plasma renin activity determination by immuno-MALDI mass spectrometry detection. This method overcomes the issues of non-specificity and long analytical times present with RIA, and does not require the use of radionucleotides. As an initial methodological evaluation, plasma renin activity results obtained by radioimmunoassay, LC/ESI-MS/MS, and immuno-MALDI on 64 samples from an outpatient primary aldosteronism screening program have been compared. A strong correlation was found between immuno-MALDI and radioimmunoassay (R2 = 0.9412, 62/64 within the 95% CI of the Bland-Altman plot), and iMALDI and LC/ESI-MS/MS (R2 = 0.9471, 62/64 within the 95% CI of the Bland-Altman plot). Technical replicates showed a 4.8% CV, while inter- and intra-day replicates showed CVs of 17.3% and 17.2% respectively. We have developed an assay capable of measuring PRA without the use of radionucleotides. This immuno-MALDI approach affords the specificity of MS while avoiding the long analytical run times and technical problems associated with HPLC. With the use of robotic sample preparation to optimize precision, this assay should be adaptable to clinical environments.
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Affiliation(s)
- Alexander G Camenzind
- Genome British Columbia Proteomics Centre, University of Victoria, 3101-4464 Markham St, Victoria, BC V8Z 7X8, Canada
| | - Jessica Grace van der Gugten
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Robert Popp
- Genome British Columbia Proteomics Centre, University of Victoria, 3101-4464 Markham St, Victoria, BC V8Z 7X8, Canada
| | - Daniel T Holmes
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, University of British Columbia, 1081 Burrard Street, Vancouver, BC V6Z 1Y6, Canada
| | - Christoph H Borchers
- Genome British Columbia Proteomics Centre, University of Victoria, 3101-4464 Markham St, Victoria, BC V8Z 7X8, Canada
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8P 5C2, Canada
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Razavi M, Johnson LDS, Lum JJ, Kruppa G, Anderson NL, Pearson TW. Quantification of a Proteotypic Peptide from Protein C Inhibitor by Liquid Chromatography–Free SISCAPA-MALDI Mass Spectrometry: Application to Identification of Recurrence of Prostate Cancer. Clin Chem 2013; 59:1514-22. [DOI: 10.1373/clinchem.2012.199786] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND
Biomarker validation remains one of the most challenging constraints to the development of new diagnostic assays. To facilitate biomarker validation, we previously developed a chromatography-free stable isotope standards and capture by antipeptide antibodies (SISCAPA)-MALDI assay allowing rapid, high-throughput quantification of protein analytes in large sample sets. Here we applied this assay to the measurement of a surrogate proteotypic peptide from protein C inhibitor (PCI) in sera from patients with prostate cancer.
METHODS
A 2-plex SISCAPA-MALDI assay for quantification of proteotypic peptides from PCI and soluble transferrin receptor (sTfR) was used to measure these peptides in 159 trypsin-digested sera collected from 51 patients with prostate cancer. These patients had been treated with radiation with or without neoadjuvant androgen deprivation.
RESULTS
Patients who experienced biochemical recurrence of prostate cancer showed decreased serum concentrations of the PCI peptide analyte within 18 months of treatment. The PCI peptide concentrations remained increased in the sera of patients who did not experience cancer recurrence. Prostate-specific antigen concentrations had no predictive value during the same time period.
CONCLUSIONS
The high-throughput, liquid chromatography–free SISCAPA-MALDI assay is capable of rapid quantification of proteotypic PCI and sTfR peptide analytes in complex serum samples. Decreased serum concentrations of the PCI peptide were found to be related to recurrence of prostate cancer in patients treated with radiation with or without hormone therapy. However, a larger cohort of patients will be required for unequivocal validation of the PCI peptide as a biomarker for clinical use.
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Affiliation(s)
- Morteza Razavi
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
| | - Lisa DS Johnson
- Trev & Joyce Deeley Research Centre, BC Cancer Agency, Victoria, British Columbia, Canada
| | - Julian J Lum
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
- Trev & Joyce Deeley Research Centre, BC Cancer Agency, Victoria, British Columbia, Canada
| | | | | | - Terry W Pearson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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Ostermann KM, Dieplinger R, Lutsch NM, Strupat K, Metz TF, Mechtler TP, Kasper DC. Matrix-assisted laser desorption/ionization for simultaneous quantitation of (acyl-)carnitines and organic acids in dried blood spots. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:1497-1504. [PMID: 23722684 DOI: 10.1002/rcm.6597] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2013] [Revised: 04/11/2013] [Accepted: 04/12/2013] [Indexed: 06/02/2023]
Abstract
RATIONALE Screening for inborn errors of metabolism using mass spectrometry is part of nationwide newborn screening programs and involves the detection of disease relevant (acyl-)carnitines and organic acids from dried blood spots. Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-MS) is a well-established tool for proteomics approaches. In recent years, this technique has become more and more integrated in analysis and identification of small metabolites and disease biomarkers in daily clinical laboratories. METHODS We used a combination of both MALDI and high-resolution accurate mass (HR/AM) mass spectrometry using a linear ion trap-Orbitrap for the identification of small molecules from dried blood spots that serve as biomarkers for inborn errors of metabolism. The levels of detected metabolite species were compared between healthy newborns and affected patients with various inborn errors of metabolism using isotopically labeled internal standards and new bioinformatics software, respectively. RESULTS (Acyl-)carnitine levels from normal and affected patients could be quantified and differentiated. Additionally, using the high resolving power of full scan Orbitrap mass spectrometry and novel software tools we demonstrated the identification and quantification of disease-specific organic acids. CONCLUSIONS MALDI-HR/AM and full scan spectra to obtain information for the metabolic status of patients is a promising complementary approach to electrospray ionization mass spectrometry by simplified sample preparation, facilitating the screening of hundreds of metabolites from small sample volumes.
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Affiliation(s)
- Katharina M Ostermann
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
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40
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Krüger T, Lehmann T, Rhode H. Effect of quality characteristics of single sample preparation steps in the precision and coverage of proteomic studies—A review. Anal Chim Acta 2013; 776:1-10. [DOI: 10.1016/j.aca.2013.01.020] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2012] [Revised: 01/10/2013] [Accepted: 01/11/2013] [Indexed: 11/25/2022]
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L.S. Tang N, Poon T, Poon TCW. Advances in MALDI mass spectrometry in clinical diagnostic applications. Top Curr Chem (Cham) 2013; 336:139-75. [PMID: 23563502 PMCID: PMC7121589 DOI: 10.1007/128_2012_413] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The concept of matrix-assisted laser desorption/ionization mass spectrometry (MALDI MS) was first reported in 1985. Since then, MALDI MS technologies have been evolving, and successfully used in genome, proteome, metabolome, and clinical diagnostic research. These technologies are high-throughput and sensitive. Emerging evidence has shown that they are not only useful in qualitative and quantitative analyses of proteins, but also of other types of biomolecules, such as DNA, glycans, and metabolites. Recently, parallel fragmentation monitoring (PFM), which is a method comparable to selected reaction monitoring, has been reported. This highlights the potentials of MALDI-TOF/TOF tandem MS in quantification of metabolites. Here we critically review the applications of the major MALDI MS technologies, including MALDI-TOF MS, MALDI-TOF/TOF MS, SALDI-TOF MS, MALDI-QqQ MS, and SELDI-TOF MS, to the discovery and quantification of disease biomarkers in biological specimens, especially those in plasma/serum specimens. Using SELDI-TOF MS as an example, the presence of systemic bias in biomarker discovery studies employing MALDI-TOF MS and its possible solutions are also discussed in this chapter. The concepts of MALDI, SALDI, SELDI, and PFM are complementary to each other. Theoretically, all these technologies can be combined, leading to the next generation of the MALDI MS technologies. Real applications of MALDI MS technologies in clinical diagnostics should be forthcoming.
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Affiliation(s)
- Nelson L.S. Tang
- grid.10784.3a0000000419370482Dept. of Chemical Pathology and Lab. of Genetics of Disease Suscept., The Chinese University of Hong Kong, Hong Kong, People's Republic of China
| | - Terence Poon
- grid.10784.3a0000000419370482Department of Paediatrics and Proteomics Laboratory, The Chinese University of Hong Kong, Hong Kong, People's Republic of China
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42
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Roth MJ, Maresh EM, Plymire DA, Zhang J, Corbett JR, Robbins R, Patrie SM. Surface preparation strategies for improved parallelization and reproducible MALDI-TOF MS ligand binding assays. ACS APPLIED MATERIALS & INTERFACES 2013; 5:6-10. [PMID: 23249094 DOI: 10.1021/am3024756] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Immunoassays are employed in academia and the healthcare and biotech industries for high-throughput, quantitative screens of biomolecules. We have developed monolayer-based immunoassays for MALDI-TOF MS. To improve parallelization, we adapted the workflow to photolithography-generated arrays. Our work shows Parylene-C coatings provide excellent "solvent pinning" for reagents and biofluids, enabling sensitive MS detection of immobilized components. With a unique MALDI-matrix crystallization technique we show routine interassay RSD <10% at picomolar concentrations and highlight platform compatibility for relative and label-free quantitation applications. Parylene-arrays provide high sample densities and promise screening throughputs exceeding 1000 samples/h with modern liquid-handlers and MALDI-TOF systems.
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Hammarström B, Yan H, Nilsson J, Ekström S. Efficient sample preparation in immuno-matrix-assisted laser desorption/ionization mass spectrometry using acoustic trapping. BIOMICROFLUIDICS 2013; 7:24107. [PMID: 24404012 PMCID: PMC3625219 DOI: 10.1063/1.4798473] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2012] [Accepted: 03/14/2013] [Indexed: 05/15/2023]
Abstract
Acoustic trapping of minute bead amounts against fluid flow allows for easy automation of multiple assay steps, using a convenient aspirate/dispense format. Here, a method based on acoustic trapping that allows sample preparation for immuno-matrix-assisted laser desorption/ionization mass spectrometry using only half a million 2.8 μm antibody covered beads is presented. The acoustic trapping is done in 200 × 2000 μm(2) glass capillaries and provides highly efficient binding and washing conditions, as shown by complete removal of detergents and sample processing times of 5-10 min. The versatility of the method is demonstrated using an antibody against Angiotensin I (Ang I), a peptide hormone involved in hypotension. Using this model system, the acoustic trapping was efficient in enriching Angiotensin at 400 pM spiked in plasma samples.
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Affiliation(s)
- Björn Hammarström
- Department of Measurement Technology and Industrial Electrical Engineering, Lund University, Lund, Sweden
| | - Hong Yan
- Department of Measurement Technology and Industrial Electrical Engineering, Lund University, Lund, Sweden
| | - Johan Nilsson
- Department of Measurement Technology and Industrial Electrical Engineering, Lund University, Lund, Sweden
| | - Simon Ekström
- Department of Measurement Technology and Industrial Electrical Engineering, Lund University, Lund, Sweden ; Lund University, CREATE Health, Lund, Sweden
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MS-based approaches to unravel the molecular complexity of proprotein-derived biomarkers and support their quantification: the examples of B-type natriuretic peptide and apelin peptides. Bioanalysis 2012; 4:2851-63. [DOI: 10.4155/bio.12.259] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The specific forms of described protein biomarkers that occur in human blood are not yet fully established. Even though B-type natriuretic peptide (BNP) and N-terminal proBNP are now well known markers of heart failure and other cardiac disorders, several studies yielded highly controversial results reporting various truncated, multimerized or modified forms in human blood. Similar discrepancies were observed for other biomarkers also originating from proproteins, such as the apelin peptides. The drawback of most of these studies is that they used methods with low resolving power, such as immunoassays after HPLC separation. MS-based techniques may be able to avoid such flaws. In this review, we discuss the usefulness of MS-based approaches for the characterization of circulating forms of peptide biomarkers that originate from a given proprotein. Two particular examples are discussed in detail: BNP-related peptides and some more putative biomarkers of heart failure, the apelin peptides.
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45
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Razavi M, Frick LE, LaMarr WA, Pope ME, Miller CA, Anderson NL, Pearson TW. High-throughput SISCAPA quantitation of peptides from human plasma digests by ultrafast, liquid chromatography-free mass spectrometry. J Proteome Res 2012; 11:5642-9. [PMID: 23126378 DOI: 10.1021/pr300652v] [Citation(s) in RCA: 81] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
We investigated the utility of an SPE-MS/MS platform in combination with a modified SISCAPA workflow for chromatography-free MRM analysis of proteotypic peptides in digested human plasma. This combination of SISCAPA and SPE-MS/MS technology allows sensitive, MRM-based quantification of peptides from plasma digests with a sample cycle time of ∼7 s, a 300-fold improvement over typical MRM analyses with analysis times of 30-40 min that use liquid chromatography upstream of MS. The optimized system includes capture and enrichment to near purity of target proteotypic peptides using rigorously selected, high affinity, antipeptide monoclonal antibodies and reduction of background peptides using a novel treatment of magnetic bead immunoadsorbents. Using this method, we have successfully quantitated LPS-binding protein and mesothelin (concentrations of ∼5000 ng/mL and ∼10 ng/mL, respectively) in human plasma. The method eliminates the need for upstream liquid-chromatography and can be multiplexed, thus facilitating quantitative analysis of proteins, including biomarkers, in large sample sets. The method is ideal for high-throughput biomarker validation after affinity enrichment and has the potential for applications in clinical laboratories.
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Affiliation(s)
- Morteza Razavi
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, Canada
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46
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Roth MJ, Kim J, Maresh EM, Plymire DA, Corbett JR, Zhang J, Patrie SM. Thin-layer matrix sublimation with vapor-sorption induced co-crystallization for sensitive and reproducible SAMDI-TOF MS analysis of protein biosensors. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:1661-1669. [PMID: 22847391 DOI: 10.1007/s13361-012-0442-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2012] [Revised: 06/19/2012] [Accepted: 06/22/2012] [Indexed: 06/01/2023]
Abstract
Coupling immunoassays on self-assembled monolayers (SAMs) to matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry (MS) provides improved assay selectivity compared with traditional photometric detection techniques. We show that thin-layer-transfer (TLT) of α-cyano-4-hydroxycinnaminic acid (CHCA) MALDI matrix via vacuum sublimation followed by organic solvent-based vapor-sorption induced co-crystallization (VIC) results in unique matrix/analyte co-crystallization tendencies that optimizes assay reproducibility and sensitivity. Unique matrix crystal morphologies resulted from VIC solvent vapors, indicating nucleation and crystal growth characteristics depend upon VIC parameters. We observed that CHCA microcrystals generated by methanol VIC resulted in >10× better sensitivity, increased analyte charging, and improved precision compared with dried droplet measurements. The uniformity of matrix/analyte co-crystallization across planar immunoassays directed at intact proteins yielded low spectral variation for single shot replicates (18.5 % relative standard deviation, RSD) and signal averaged spectra (<10 % RSD). We envision that TLT and VIC for MALDI-TOF will enable high-throughput, reproducible array-based immunoassays for protein molecular diagnostic assays in diverse biochemical and clinical applications.
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Affiliation(s)
- Michael J Roth
- Department of Pathology, University of Texas Southwestern Medical Center, Dallas, 75390, USA
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47
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Lesur A, Varesio E, Domon B, Hopfgartner G. Peptides Quantification by Liquid Chromatography with Matrix-Assisted Laser Desorption/Ionization and Selected Reaction Monitoring Detection. J Proteome Res 2012; 11:4972-82. [DOI: 10.1021/pr300514u] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Antoine Lesur
- Life Sciences Mass Spectrometry,
School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Emmanuel Varesio
- Life Sciences Mass Spectrometry,
School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
| | - Bruno Domon
- Luxembourg Clinical Proteomics Center, Luxembourg
| | - Gérard Hopfgartner
- Life Sciences Mass Spectrometry,
School of Pharmaceutical Sciences, University of Geneva, University of Lausanne, Geneva, Switzerland
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48
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Surface plasmon resonance imaging in arrays coupled with mass spectrometry (SUPRA–MS): proof of concept of on-chip characterization of a potential breast cancer marker in human plasma. Anal Bioanal Chem 2012; 404:423-32. [DOI: 10.1007/s00216-012-6130-4] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2012] [Revised: 05/19/2012] [Accepted: 05/20/2012] [Indexed: 01/20/2023]
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