1
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Camilleri E, Kruijt M, den Exter PL, Cannegieter SC, van Rein N, Cobbaert CM, van Vlijmen BJM, Ruhaak LR. Quantitative protein mass spectrometry for multiplex measurement of coagulation and fibrinolytic proteins towards clinical application: What, why and how? Thromb Res 2024; 241:109090. [PMID: 39032389 DOI: 10.1016/j.thromres.2024.109090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2024] [Revised: 06/20/2024] [Accepted: 07/03/2024] [Indexed: 07/23/2024]
Abstract
Plasma proteins involved in coagulation and fibrinolysis are essential to hemostasis. Consequently, their circulating levels and functionality are critical in bleeding and thrombosis development. Well-established laboratory tests to assess these are available; however, said tests do not allow high multiplicity, require large volumes of plasma and are often costly. A novel technology to quantify plasma proteins is quantitative protein mass spectrometry (QPMS). Aided by stable isotope-labeled internal standards a large number of proteins can be quantified in one single analytical run requiring <30 μL of plasma. This provides an opportunity to improve insight in the etiology and prognosis of bleeding and thrombotic disorders, in which the balance between different proteins plays a crucial role. This manuscript aims to give an overview of the QPMS potential applications in thrombosis and hemostasis research (quantifying the 38 proteins assigned to coagulation and fibrinolysis by the KEGG database), but also to explore the potential and hurdles if designed for clinical practice. Advantages and limitations of QPMS are described and strategies for improved analysis are proposed, using as an example the test requirements for antithrombin. Application of this technology in the future could represent a step towards individualized patient care.
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Affiliation(s)
- Eleonora Camilleri
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Mirjam Kruijt
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Paul L den Exter
- Department of Internal Medicine, Division of Thrombosis and Hemostasis, Leiden University Medical Center, Leiden, the Netherlands
| | - Suzanne C Cannegieter
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands; Department of Internal Medicine, Division of Thrombosis and Hemostasis, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Nienke van Rein
- Department of Clinical Epidemiology, Leiden University Medical Center, Leiden, the Netherlands; Department of Pharmacy, Leiden University Medical Center, Leiden, the Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
| | - Bart J M van Vlijmen
- Department of Internal Medicine, Division of Thrombosis and Hemostasis, Leiden University Medical Center, Leiden, the Netherlands; Einthoven Laboratory for Vascular and Regenerative Medicine, Leiden University Medical Center, Leiden, the Netherlands.
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, the Netherlands
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2
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Torkamannejad S, Chang G, Aroge FA, Sun B. Single Isotopologue for In-Sample Calibration and Absolute Quantitation by LC-MS/MS. J Proteome Res 2024; 23:1351-1359. [PMID: 38445850 DOI: 10.1021/acs.jproteome.3c00848] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2024]
Abstract
Targeted mass spectrometry (MS)-based absolute quantitative analysis has been increasingly used in biomarker discovery. The ability to accurately measure the masses by MS enabled the use of isotope-incorporated surrogates having virtually identical physiochemical properties with the target analytes as calibrators. Such a unique capacity allowed for accurate in-sample calibration. Current in-sample calibration uses multiple isotopologues or structural analogues for both the surrogate and the internal standard. Here, we simplified this common practice by using endogenous light peptides as the internal standards and used a mathematical deduction of "heavy matching light, HML" to directly quantify an endogenous analyte. This method provides all necessary assay performance parameters in the authentic matrix, including the lower limit of quantitation (LLOQ) and intercept of the calibration curve, by using only a single isotopologue of the analyte. This method can be applied to the quantitation of proteins, peptides, and small molecules. Using this method, we quantified the efficiency of heart tissue digestion and recovery using sodium deoxycholate as a detergent and two spiked exogenous proteins as mimics of heart proteins. The results demonstrated the robustness of the assay.
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Affiliation(s)
- Soroush Torkamannejad
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Ge Chang
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
| | - Fabusuyi A Aroge
- School of Mechatronic Systems Engineering, Simon Fraser University, Surrey, British Columbia V3T0A3, Canada
| | - Bingyun Sun
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia V5A1S6, Canada
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3
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Sleumer B, Kema IP, van de Merbel NC. Quantitative bioanalysis of proteins by digestion and LC-MS/MS: the use of multiple signature peptides. Bioanalysis 2023; 15:1203-1216. [PMID: 37724471 DOI: 10.4155/bio-2023-0129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/20/2023] Open
Abstract
The use of multiple signature peptides for the quantification of proteins by digestion and LC-MS/MS is reviewed and evaluated here. A distinction is made based on the purpose of the use of multiple peptides: confirmation of the protein concentration, discrimination between different protein forms or species and in vivo biotransformation. Most reports that describe methods with at least two peptides use these for confirmation, but it is not always mentioned how the peptides are used and how possible differences in concentration between the peptides are handled. Differences in concentration are often reported in the case of monitoring different protein forms or in vivo biotransformation, and this offers insight into the biological fate of the protein.
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Affiliation(s)
- Bas Sleumer
- ICON Bioanalytical Laboratories, Amerikaweg 18, 9407 TK, Assen, The Netherlands
- Department of Analytical Biochemistry, University of Groningen, A Deusinglaan 1, 9700 AV Groningen, The Netherlands
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, EA61, PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Ido P Kema
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, EA61, PO Box 30.001, 9700 RB Groningen, The Netherlands
| | - Nico C van de Merbel
- ICON Bioanalytical Laboratories, Amerikaweg 18, 9407 TK, Assen, The Netherlands
- Department of Analytical Biochemistry, University of Groningen, A Deusinglaan 1, 9700 AV Groningen, The Netherlands
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4
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Woessmann J, Petrosius V, Üresin N, Kotol D, Aragon-Fernandez P, Hober A, auf dem Keller U, Edfors F, Schoof EM. Assessing the Role of Trypsin in Quantitative Plasma and Single-Cell Proteomics toward Clinical Application. Anal Chem 2023; 95:13649-13658. [PMID: 37639361 PMCID: PMC10500548 DOI: 10.1021/acs.analchem.3c02543] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Accepted: 08/08/2023] [Indexed: 08/31/2023]
Abstract
Mass spectrometry-based bottom-up proteomics is rapidly evolving and routinely applied in large-scale biomedical studies. Proteases are a central component of every bottom-up proteomics experiment, digesting proteins into peptides. Trypsin has been the most widely applied protease in proteomics due to its characteristics. With ever-larger cohort sizes and possible future clinical application of mass spectrometry-based proteomics, the technical impact of trypsin becomes increasingly relevant. To assess possible biases introduced by trypsin digestion, we evaluated the impact of eight commercially available trypsins in a variety of bottom-up proteomics experiments and across a range of protease concentrations and storage times. To investigate the universal impact of these technical attributes, we included bulk HeLa cell lysate, human plasma, and single HEK293 cells, which were analyzed over a range of selected reaction monitoring (SRM), data-independent acquisition (DIA), and data-dependent acquisition (DDA) instrument methods on three LC-MS instruments. The quantification methods employed encompassed both label-free approaches and absolute quantification utilizing spike-in heavy-labeled recombinant protein fragment standards. Based on this extensive data set, we report variations between commercial trypsins, their source, and their concentration. Furthermore, we provide suggestions on the handling of trypsin in large-scale studies.
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Affiliation(s)
- Jakob Woessmann
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kgs. Lyngby, Denmark
- Science
for Life Laboratory, KTH—Royal Institute
of Technology, SE-171 65 Solna, Sweden
- Department
of Protein Science, KTH—Royal Institute
of Technology, SE-106 91 Stockholm, Sweden
| | - Valdemaras Petrosius
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Nil Üresin
- The
Finsen Laboratory, Rigshospitalet, Faculty of Health Sciences, University of Copenhagen, 2200 Copenhagen, Denmark
- Biotech
Research and Innovation Centre (BRIC), University
of Copenhagen, 2200 Copenhagen, Denmark
| | - David Kotol
- Science
for Life Laboratory, KTH—Royal Institute
of Technology, SE-171 65 Solna, Sweden
- Department
of Protein Science, KTH—Royal Institute
of Technology, SE-106 91 Stockholm, Sweden
| | - Pedro Aragon-Fernandez
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Andreas Hober
- Science
for Life Laboratory, KTH—Royal Institute
of Technology, SE-171 65 Solna, Sweden
- Department
of Protein Science, KTH—Royal Institute
of Technology, SE-106 91 Stockholm, Sweden
| | - Ulrich auf dem Keller
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Fredrik Edfors
- Science
for Life Laboratory, KTH—Royal Institute
of Technology, SE-171 65 Solna, Sweden
- Department
of Protein Science, KTH—Royal Institute
of Technology, SE-106 91 Stockholm, Sweden
| | - Erwin M. Schoof
- Department
of Biotechnology and Biomedicine, Technical
University of Denmark, 2800 Kgs. Lyngby, Denmark
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5
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Smit NPM, Romijn FPHTM, van Ham VJJ, Reijnders E, Cobbaert CM, Ruhaak LR. Quantitative protein mass-spectrometry requires a standardized pre-analytical phase. Clin Chem Lab Med 2023; 61:55-66. [PMID: 36069790 DOI: 10.1515/cclm-2022-0735] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 08/21/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Quantitative protein mass-spectrometry (QPMS) in blood depends on tryptic digestion of proteins and subsequent measurement of representing peptides. Whether serum and plasma can be used interchangeably and whether in-vitro anticoagulants affect the recovery is unknown. In our laboratory serum samples are the preferred matrix for QPMS measurement of multiple apolipoproteins. In this study, we investigated the effect of different matrices on apolipoprotein quantification by mass spectrometry. METHODS Blood samples were collected from 44 healthy donors in Beckton Dickinson blood tubes simultaneously for serum (with/without gel) and plasma (heparin, citrate or EDTA). Nine apolipoproteins were quantified according to standard operating procedure using value-assigned native serum calibrators for quantitation. Tryptic digestion kinetics were investigated in the different matrices by following formation of peptides for each apolipoprotein in time, up to 22 h. RESULTS In citrate plasma recovery of apolipoproteins showed an overall reduction with a bias of -14.6%. For heparin plasma only -0.3% bias was found compared to serum, whereas for EDTA-plasma reduction was more pronounced (-5.3% bias) and variable with >14% reduction for peptides of apoA-I, A-II and C-III. Digestion kinetics revealed that especially slow forming peptides showed reduced formation in EDTA-plasma. CONCLUSIONS Plasma anticoagulants affect QPMS test results. Heparin plasma showed comparable results to serum. Reduced concentrations in citrate plasma can be explained by dilution, whereas reduced recovery in EDTA-plasma is dependent on altered proteolytic digestion efficiency. The results highlight the importance of a standardized pre-analytical phase for accurate QPMS applications in clinical chemistry.
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Affiliation(s)
- Nico P M Smit
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Esther Reijnders
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
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6
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Fernández-Metzler C, Ackermann B, Garofolo F, Arnold ME, DeSilva B, Gu H, Laterza O, Mao Y, Rose M, Vazvaei-Smith F, Steenwyk R. Biomarker Assay Validation by Mass Spectrometry. AAPS J 2022; 24:66. [PMID: 35534647 DOI: 10.1208/s12248-022-00707-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Accepted: 03/31/2022] [Indexed: 11/30/2022] Open
Abstract
Decades of discussion and publication have gone into the guidance from the scientific community and the regulatory agencies on the use and validation of pharmacokinetic and toxicokinetic assays by chromatographic and ligand binding assays for the measurement of drugs and metabolites. These assay validations are well described in the FDA Guidance on Bioanalytical Methods Validation (BMV, 2018). While the BMV included biomarker assay validation, the focus was on understanding the challenges posed in validating biomarker assays and the importance of having reliable biomarker assays when used for regulatory submissions, rather than definition of the appropriate experiments to be performed. Different from PK bioanalysis, analysis of biomarkers can be challenging due to the presence of target analyte(s) in the control matrices used for calibrator and quality control sample preparation, and greater difficulty in procuring appropriate reference standards representative of the endogenous molecule. Several papers have been published offering recommendations for biomarker assay validation. The situational nature of biomarker applications necessitates fit-for-purpose (FFP) assay validation. A unifying theme for FFP analysis is that method validation requirements be consistent with the proposed context of use (COU) for any given biomarker. This communication provides specific recommendations for biomarker assay validation (BAV) by LC-MS, for both small and large molecule biomarkers. The consensus recommendations include creation of a validation plan that contains definition of the COU of the assay, use of the PK assay validation elements that support the COU, and definition of assay validation elements adapted to fit biomarker assays and the acceptance criteria for both.
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Affiliation(s)
| | - Brad Ackermann
- Eli Lilly & Company, Lilly Corporate Center, Indianapolis, IN, 46285, USA
| | - Fabio Garofolo
- BRI - a Frontage Company, 8898 Heather St, Vancouver, British Columbia, V6P 3S8, Canada
| | - Mark E Arnold
- Labcorp Drug Development, 221 Tulip Tree Drive, Westampton, NJ, 08060-5511, USA
| | - Binodh DeSilva
- Bristol-Myers Squibb Co., Route 206 & Province Line Road, Princeton, NJ, 08543, USA
| | - Huidong Gu
- Bristol-Myers Squibb Co., Route 206 & Province Line Road, Princeton, NJ, 08543, USA
| | - Omar Laterza
- Merck and Co Inc., 90 E Scott Ave, Rahway, NJ, 07065, USA
| | - Yan Mao
- Boehringer-Ingelheim Pharmaceuticals, 900 Ridgebury Road, Ridgefield, CT, 06877, USA
| | - Mark Rose
- Gossamer Bio Inc., 3013 Science Park Road, Suite 200, San Diego, CA, 92121, USA
| | | | - Rick Steenwyk
- Pfizer-Retired, 8739 N Homestead Circle, Irons, MI, 49644, USA
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7
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Rappold BA. Review of the Use of Liquid Chromatography-Tandem Mass Spectrometry in Clinical Laboratories: Part I-Development. Ann Lab Med 2022; 42:121-140. [PMID: 34635606 PMCID: PMC8548246 DOI: 10.3343/alm.2022.42.2.121] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Revised: 06/25/2021] [Accepted: 09/28/2021] [Indexed: 11/19/2022] Open
Abstract
The process of method development for a diagnostic assay based on liquid chromatography-tandem mass spectrometry (LC-MS/MS) involves several disparate technologies and specialties. Additionally, method development details are typically not disclosed in journal publications. Method developers may need to search widely for pertinent information on their assay(s). This review summarizes the current practices and procedures in method development. Additionally, it probes aspects of method development that are generally not discussed, such as how exactly to calibrate an assay or where to place quality controls, using examples from the literature. This review intends to provide a comprehensive resource and induce critical thinking around the experiments for and execution of developing a clinically meaningful LC-MS/MS assay.
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Affiliation(s)
- Brian A. Rappold
- Laboratory Corporation of America Holdings, Research Triangle Park, NC, USA
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8
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Yang H, Cao Z, Mou R, Cao Z, Chen M. Quantification of rice α‐globulin allergen using liquid chromatography–tandem mass spectrometry combined with cysteine‐specific modifier and extended stable isotope‐labeled peptide. J FOOD PROCESS PRES 2022. [DOI: 10.1111/jfpp.16362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Huan Yang
- Jiangxi Agricultural University Nanchang 330000 People's Republic of China
- Rice Product Quality Inspection and Supervision Center Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou 310006 People's Republic of China
| | - Zhao‐yun Cao
- Rice Product Quality Inspection and Supervision Center Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou 310006 People's Republic of China
| | - Ren‐xiang Mou
- Rice Product Quality Inspection and Supervision Center Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou 310006 People's Republic of China
| | - Zhen‐zhen Cao
- Rice Product Quality Inspection and Supervision Center Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou 310006 People's Republic of China
| | - Ming‐xue Chen
- Rice Product Quality Inspection and Supervision Center Ministry of Agriculture and Rural Affairs China National Rice Research Institute Hangzhou 310006 People's Republic of China
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9
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Rogatsky E. Pandora box of BCA assay. Investigation of the accuracy and linearity of the microplate bicinchoninic protein assay: Analytical challenges and method modifications to minimize systematic errors. Anal Biochem 2021; 631:114321. [PMID: 34343481 DOI: 10.1016/j.ab.2021.114321] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 07/22/2021] [Accepted: 07/28/2021] [Indexed: 11/17/2022]
Abstract
Bicinchoninic colorimetric assay is very widely used for total protein quantitative analysis. We report that bicinchoninic (BCA) total protein assay linearity range and the assay sensitivity are counterbalancing factors. BCA assay true linear range may be considerably narrower than the manufacturer's advertised 20-2000 μg/ml and therefore the choice of the assay calibration range should not solely be dictated by the general recommendations of the user guide, but by the test specific needs and subsequent assay quality control. Expanding the BCA assay range up to 2000 μg/ml comes together with unavoidable heavy negative biases at low protein concentrations. The negative bias at low protein concentration only exacerbates with longer incubation time and/or increased sample to working reagent ratio. To minimize the lack of accuracy at low protein concentration of a wide range BCA assay, we proposing an alternative approach: a two-step incubation and calibration. With a minimum of extra work, the two-step incubation/calibration approach is devoid of the standard BCA workflow disadvantages and biases.
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10
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Smit NPM, Ruhaak LR, Romijn FPHTM, Pieterse MM, van der Burgt YEM, Cobbaert CM. The Time Has Come for Quantitative Protein Mass Spectrometry Tests That Target Unmet Clinical Needs. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:636-647. [PMID: 33522792 PMCID: PMC7944566 DOI: 10.1021/jasms.0c00379] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 12/22/2020] [Accepted: 01/19/2021] [Indexed: 05/04/2023]
Abstract
Protein mass spectrometry (MS) is an enabling technology that is ideally suited for precision diagnostics. In contrast to immunoassays with indirect readouts, MS quantifications are multiplexed and include identification of proteoforms in a direct manner. Although widely used for routine measurements of drugs and metabolites, the number of clinical MS-based protein applications is limited. In this paper, we share our experience and aim to take away the concerns that have kept laboratory medicine from implementing quantitative protein MS. To ensure added value of new medical tests and guarantee accurate test results, five key elements of test evaluation have been established by a working group within the European Federation for Clinical Chemistry and Laboratory Medicine. Moreover, it is emphasized to identify clinical gaps in the contemporary clinical pathways before test development is started. We demonstrate that quantitative protein MS tests that provide an additional layer of clinical information have robust performance and meet long-term desirable analytical performance specifications as exemplified by our own experience. Yet, the adoption of quantitative protein MS tests into medical laboratories is seriously hampered due to its complexity, lack of robotization and high initial investment costs. Successful and widespread implementation in medical laboratories requires uptake and automation of this next generation protein technology by the In-Vitro Diagnostics industry. Also, training curricula of lab workers and lab specialists should include education on enabling technologies for transitioning to precision medicine by quantitative protein MS tests.
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Affiliation(s)
- Nico P. M. Smit
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - L. Renee Ruhaak
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Fred P. H. T. M. Romijn
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Mervin M. Pieterse
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Yuri E. M. van der Burgt
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Christa M. Cobbaert
- Department of Clinical Chemistry and
Laboratory Medicine, Leiden University Medical
Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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11
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Cobbaert CM, Althaus H, Begcevic Brkovic I, Ceglarek U, Coassin S, Delatour V, Deprez L, Dikaios I, Dittrich J, Hoofnagle AN, Kostner GM, Kronenberg F, Kuklenyik Z, Prinzing U, Vesper HW, Zegers I, Ruhaak LR. Towards an SI-Traceable Reference Measurement System for Seven Serum Apolipoproteins Using Bottom-Up Quantitative Proteomics: Conceptual Approach Enabled by Cross-Disciplinary/Cross-Sector Collaboration. Clin Chem 2021; 67:478-489. [PMID: 33331636 DOI: 10.1093/clinchem/hvaa239] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 09/15/2020] [Indexed: 12/15/2022]
Abstract
Current dyslipidemia management in patients with atherosclerotic cardiovascular disease (ASCVD) is based on traditional serum lipids. Yet, there is some indication from basic research that serum apolipoproteins A-I, (a), B, C-I, C-II, C-III, and E may give better pathophysiological insight into the root causes of dyslipidemia. To facilitate the future adoption of clinical serum apolipoprotein (apo) profiling for precision medicine, strategies for accurate testing should be developed in advance. Recent discoveries in basic science and translational medicine set the stage for the IFCC Working Group on Apolipoproteins by Mass Spectrometry. Main drivers were the convergence of unmet clinical needs in cardiovascular disease (CVD) patients with enabling technology and metrology. First, the residual cardiovascular risk after accounting for established risk factors demonstrates that the current lipid panel is too limited to capture the full complexity of lipid metabolism in patients. Second, there is a need for accurate test results in highly polymorphic and atherogenic apolipoproteins such as apo(a). Third, sufficient robustness of mass spectrometry technology allows reproducible protein quantification at the molecular level. Fourth, several calibration hierarchies in the revised ISO 17511:2020 guideline facilitate metrological traceability of test results, the highest achievable standard being traceability to SI. This article outlines the conceptual approach aimed at achieving a novel, multiplexed Reference Measurement System (RMS) for seven apolipoproteins based on isotope dilution mass spectrometry and peptide-based calibration. This RMS should enable standardization of existing and emerging apolipoprotein assays to SI, within allowable limits of measurement uncertainty, through a sustainable network of Reference Laboratories.
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Affiliation(s)
- Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Harald Althaus
- Siemens Healthcare Diagnostics Products GmbH, Marburg, Germany
| | - Ilijana Begcevic Brkovic
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig,Germany.,LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig,Germany.,LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Stefan Coassin
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Liesbet Deprez
- European Commission, Joint Research Centre (JRC), Geel, Belgium
| | - Ioannis Dikaios
- European Commission, Joint Research Centre (JRC), Geel, Belgium
| | - Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig,Germany.,LIFE-Leipzig Research Center for Civilization Diseases, University of Leipzig, Leipzig, Germany
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Gerhard M Kostner
- Gottfried Schatz Research Center (for Cell Signaling, Metabolism and Aging), Division of Molecular Biology and Biochemistry, Medical University of Graz, Graz, Austria
| | - Florian Kronenberg
- Institute of Genetic Epidemiology, Department of Genetics and Pharmacology, Medical University of Innsbruck, Innsbruck, Austria
| | - Zsusanna Kuklenyik
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA
| | | | - Hubert W Vesper
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA
| | - Ingrid Zegers
- Laboratoire National de Métrologie et d'Essais, Paris, France
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
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12
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de Haan N, Wuhrer M, Ruhaak L. Mass spectrometry in clinical glycomics: The path from biomarker identification to clinical implementation. CLINICAL MASS SPECTROMETRY (DEL MAR, CALIF.) 2020; 18:1-12. [PMID: 34820521 PMCID: PMC8600986 DOI: 10.1016/j.clinms.2020.08.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 08/18/2020] [Accepted: 08/21/2020] [Indexed: 02/01/2023]
Abstract
Over the past decades, the genome and proteome have been widely explored for biomarker discovery and personalized medicine. However, there is still a large need for improved diagnostics and stratification strategies for a wide range of diseases. Post-translational modification of proteins by glycosylation affects protein structure and function, and glycosylation has been implicated in many prevalent human diseases. Numerous proteins for which the plasma levels are nowadays evaluated in clinical practice are glycoproteins. While the glycosylation of these proteins often changes with disease, their glycosylation status is largely ignored in the clinical setting. Hence, the implementation of glycomic markers in the clinic is still in its infancy. This is for a large part caused by the high complexity of protein glycosylation itself and of the analytical techniques required for their robust quantification. Mass spectrometry-based workflows are particularly suitable for the quantification of glycans and glycoproteins, but still require advances for their transformation from a biomedical research setting to a clinical laboratory. In this review, we describe why and how glycomics is expected to find its role in clinical tests and the status of current mass spectrometry-based methods for clinical glycomics.
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Affiliation(s)
- N. de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - M. Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - L.R. Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
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13
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Mendoza-Porras O, Pires PRL, Goswami H, Meirelles FV, Colgrave ML, Wijffels G. Cytokines in the grass, a lesson learnt: Measuring cytokines in plasma using multiple reaction monitoring mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8723. [PMID: 31922636 DOI: 10.1002/rcm.8723] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 01/08/2020] [Accepted: 01/09/2020] [Indexed: 06/10/2023]
Abstract
RATIONALE Cytokines are cell regulatory molecules of high importance as indicators for homeostasis and pathology in many species. The current method to measure cytokines in body fluids is reagent dependent, requiring highly specific paired antibodies. METHODS A liquid chromatography/multiple reaction monitoring mass spectrometry (LC/MRM-MS)-based approach was developed to simultaneously establish the limits of detection (LODs) and quantification (LOQs) for recombinant cytokines IL-1β, IL-6, IFNγ and TNFα as pure standards and in bovine sera. All experimental LC/MRM-MS data are available at CSIRO Data Access Portal repository under identifier doi.org/10.25919/5de8a0232a862. RESULTS The present method enabled LODs and LOQs as low as 1.05 and 1.12 fmol/μL in the experiment comprised of pure standards. Comparable results were obtained in the experiment where digested cytokines were mixed with pre-digested sera proteins. The intrinsic matrix effects were evident when intact cytokines were co-digested within undiluted and undigested sera decreasing the ability to detect and quantify cytokines by 10,000-fold compared with pure standards and pre-digested sera. CONCLUSIONS The developed LC/MRM-MS method provided insights into the difficulties in detecting the target peptides when embedded in complex matrices. Nonetheless, the method may potentially be readily applied in biomarker-focused research interrogating fluids of lesser complexity such as synovial fluid, cerebrospinal fluid and tissue culture media.
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Affiliation(s)
- Omar Mendoza-Porras
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
| | - Pedro R L Pires
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
- University of São Paulo, Av Duque de Caxais Morte 225, Jardim Elite, São Paulo, Brazil
| | - Hareshwar Goswami
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
| | - Flavio V Meirelles
- University of São Paulo, Av Duque de Caxais Morte 225, Jardim Elite, São Paulo, Brazil
| | - Michelle L Colgrave
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
| | - Gene Wijffels
- CSIRO Agriculture and Food, 306 Carmody Rd, St Lucia, Queensland, 4067, Australia
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14
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van der Burgt YEM, Siliakus KM, Cobbaert CM, Ruhaak LR. HILIC-MRM-MS for Linkage-Specific Separation of Sialylated Glycopeptides to Quantify Prostate-Specific Antigen Proteoforms. J Proteome Res 2020; 19:2708-2716. [PMID: 32142289 PMCID: PMC8280738 DOI: 10.1021/acs.jproteome.0c00050] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
![]()
Elevated serum prostate-specific
antigen (PSA) levels in body fluids
may indicate prostate cancer (PCa), but it is noted that the clinical
performance is rather poor. Specificity and sensitivity values of
20 and 94% at a cutoff value of 4.1 ng/mL, respectively, result in
overdiagnosis and unnecessary interventions. Previous exploratory
studies have indicated that the glycosylation of PSA potentially leads
to improved PCa diagnosis based on qualitative analyses. However,
the applied methods are not suited for a quantitative evaluation or
implementation in a medical laboratory. Therefore, in this proof-of-principle
study, we have evaluated the use of hydrophilic interaction liquid
chromatography (HILIC) in combination with targeted quantitative mass
spectrometry for the sialic acid linkage-specific analysis of PSA
glyco-proteoforms based on either trypsin or ArgC peptides. The efficiency
of PSA proteolysis was optimized as well as the glycopeptide separation
conditions (buffer type, strength, and pH). The HILIC-based analysis
of PSA glyco-proteoforms presented here has the potential for the
clinical validation of patient cohorts. The method shows the feasibility
of the use of a HILIC stationary phase for the separation of isomeric
glycopeptides to detect specific glyco-proteoforms. This is the first
step toward the development and evaluation of PSA glyco-proteoforms
for use in a clinical chemistry setting aiming for improved PCa diagnosis
or screening.
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Affiliation(s)
- Yuri E M van der Burgt
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Kasper M Siliakus
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA Leiden, The Netherlands
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15
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Wang X, Zhang F, Li H, Xiao P, Su F, Xu B, Sun W, Song D. Purity determination of synthetic glucagon using a mass balance approach. Sci Rep 2020; 10:4423. [PMID: 32157163 PMCID: PMC7064584 DOI: 10.1038/s41598-020-61109-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 02/07/2020] [Indexed: 12/01/2022] Open
Abstract
Due to the widespread use of synthetic peptide drugs, their quantification and the analysis of impurities have become increasingly important in clinical and medical settings. Moreover, quantifying proteins using synthetic peptides as internal or external standards is a general approach, and the key to this approach is the knowing purities of the peptides. In this paper, synthetic glucagon was quantified using a mass balance method. The impurities in glucagon were analyzed and then accurately quantified separately. Karl Fischer (KF) titration and ion chromatography (IC) were used to determine the water and trifluoroacetic acid (TFA) contents in the samples, respectively. Furthermore, the inorganic ion content in the samples was determined by inductively coupled plasma mass spectrometry (ICP-MS). The sequence of peptide impurities was identified by a Thermo Fisher Orbitrap mass. Samples were determined to be 896.36 ± 0.68 mg/g after subtracting all impurity masses from the sample mass. The result can be traced to SI units.
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Affiliation(s)
- Xinxue Wang
- National Institute of Metrology, China/Division of Chemical Metrology and Analytical Science, Beijing, China.,Beijing University of Chemical Technology, Beijing, China
| | - Fangyan Zhang
- National Institute of Metrology, China/Division of Chemical Metrology and Analytical Science, Beijing, China.,Beijing University of Chemical Technology, Beijing, China
| | - Hongmei Li
- National Institute of Metrology, China/Division of Chemical Metrology and Analytical Science, Beijing, China.
| | - Peng Xiao
- National Institute of Metrology, China/Division of Chemical Metrology and Analytical Science, Beijing, China
| | - Fuhai Su
- National Institute of Metrology, China/Division of Chemical Metrology and Analytical Science, Beijing, China
| | - Bei Xu
- National Institute of Metrology, China/Division of Chemical Metrology and Analytical Science, Beijing, China
| | - Wei Sun
- Beijing University of Chemical Technology, Beijing, China
| | - Dewei Song
- National Institute of Metrology, China/Division of Chemical Metrology and Analytical Science, Beijing, China.
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16
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Neubert H, Shuford CM, Olah TV, Garofolo F, Schultz GA, Jones BR, Amaravadi L, Laterza OF, Xu K, Ackermann BL. Protein Biomarker Quantification by Immunoaffinity Liquid Chromatography–Tandem Mass Spectrometry: Current State and Future Vision. Clin Chem 2020; 66:282-301. [DOI: 10.1093/clinchem/hvz022] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 11/12/2019] [Indexed: 12/19/2022]
Abstract
Abstract
Immunoaffinity–mass spectrometry (IA-MS) is an emerging analytical genre with several advantages for profiling and determination of protein biomarkers. Because IA-MS combines affinity capture, analogous to ligand binding assays (LBAs), with mass spectrometry (MS) detection, this platform is often described using the term hybrid methods. The purpose of this report is to provide an overview of the principles of IA-MS and to demonstrate, through application, the unique power and potential of this technology. By combining target immunoaffinity enrichment with the use of stable isotope-labeled internal standards and MS detection, IA-MS achieves high sensitivity while providing unparalleled specificity for the quantification of protein biomarkers in fluids and tissues. In recent years, significant uptake of IA-MS has occurred in the pharmaceutical industry, particularly in the early stages of clinical development, enabling biomarker measurement previously considered unattainable. By comparison, IA-MS adoption by CLIA laboratories has occurred more slowly. Current barriers to IA-MS use and opportunities for expanded adoption are discussed. The path forward involves identifying applications for which IA-MS is the best option compared with LBA or MS technologies alone. IA-MS will continue to benefit from advances in reagent generation, more sensitive and higher throughput MS technologies, and continued growth in use by the broader analytical community. Collectively, the pursuit of these opportunities will secure expanded long-term use of IA-MS for clinical applications.
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17
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Valdés A, Bergström Lind S. Mass Spectrometry-Based Analysis of Time-Resolved Proteome Quantification. Proteomics 2019; 20:e1800425. [PMID: 31652013 DOI: 10.1002/pmic.201800425] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2019] [Revised: 09/20/2019] [Indexed: 11/09/2022]
Abstract
The aspect of time is essential in biological processes and thus it is important to be able to monitor signaling molecules through time. Proteins are key players in cellular signaling and they respond to many stimuli and change their expression in many time-dependent processes. Mass spectrometry (MS) is an important tool for studying proteins, including their posttranslational modifications and their interaction partners-both in qualitative and quantitative ways. In order to distinguish the different trends over time, proteins, modification sites, and interacting proteins must be compared between different time points, and therefore relative quantification is preferred. In this review, the progress and challenges for MS-based analysis of time-resolved proteome dynamics are discussed. Further, aspects on model systems, technologies, sampling frequencies, and presentation of the dynamic data are discussed.
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Affiliation(s)
- Alberto Valdés
- Department of Analytical Chemistry, Physical Chemistry and Chemical Engineering, University of Alcalá, Ctra. Madrid-Barcelona, Km. 33.600, 28871, Alcalá de Henares, Madrid, Spain
| | - Sara Bergström Lind
- Department of Chemistry-BMC, Analytical Chemistry, Uppsala University, Box 599, 75124, Uppsala, Sweden
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18
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Renee Ruhaak L, van der Laarse A, Cobbaert CM. Apolipoprotein profiling as a personalized approach to the diagnosis and treatment of dyslipidaemia. Ann Clin Biochem 2019; 56:338-356. [PMID: 30889974 PMCID: PMC6595551 DOI: 10.1177/0004563219827620] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/31/2018] [Indexed: 01/08/2023]
Abstract
An elevated low-density lipoprotein cholesterol concentration is a classical risk factor for cardiovascular disease. This has led to pharmacotherapy in patients with atherosclerotic heart disease or high heart disease risk with statins to reduce serum low-density lipoprotein cholesterol. Even in patients in whom the target levels of low-density lipoprotein cholesterol are reached, there remains a significant residual cardiovascular risk; this is due, in part, to a focus on low-density lipoprotein cholesterol alone and neglect of other important aspects of lipoprotein metabolism. A more refined lipoprotein analysis will provide additional information on the accumulation of very low-density lipoproteins, intermediate density lipoproteins, chylomicrons, chylomicron-remnants and Lp(a) concentrations. Instead of measuring the cholesterol and triglyceride content of the lipoproteins, measurement of their apolipoproteins (apos) is more informative. Apos are either specific for a particular lipoprotein or for a group of lipoproteins. In particular measurement of apos in atherogenic particles is more biologically meaningful than the measurement of the cholesterol concentration contained in these particles. Applying apo profiling will not only improve characterization of the lipoprotein abnormality, but will also improve definition of therapeutic targets. Apo profiling aligns with the concept of precision medicine by which an individual patient is not treated as 'average' patient by the average (dose of) therapy. This concept of precision medicine fits the unmet clinical need for stratified cardiovascular medicine. The requirements for clinical application of proteomics, including apo profiling, can now be met using robust mass spectrometry technology which offers desirable analytical performance and standardization.
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Affiliation(s)
- L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Arnoud van der Laarse
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
- Department of Cardiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
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19
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Zhou M, Duong DM, Johnson ECB, Dai J, Lah JJ, Levey AI, Seyfried NT. Mass Spectrometry-Based Quantification of Tau in Human Cerebrospinal Fluid Using a Complementary Tryptic Peptide Standard. J Proteome Res 2019; 18:2422-2432. [PMID: 30983353 DOI: 10.1021/acs.jproteome.8b00920] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Here, we report a method for the generation of complementary tryptic (CompTryp) isotope-labeled peptide standards for the relative and absolute quantification of proteins by mass spectrometry (MS). These standards can be digested in parallel with either trypsin (Tryp-C) or trypsin-N (Tryp-N), to generate peptides that significantly overlap in primary sequence having C- and N-terminal arginine and lysine residues, respectively. As a proof of concept, an isotope-labeled CompTryp standard was synthesized for Tau, a well-established biomarker in Alzheimer's disease (AD), which included both N- and C-terminal heavy isotope-labeled (15N and 13C) arginine residues and flanking amino acid sequences to monitor proteolytic digestion. Despite having the exact same mass, the N- and C-terminal heavy Tau peptides are distinguishable by retention time and MS/MS fragmentation profiles. The isotope-labeled Tau CompTryp standard was added to human cerebrospinal fluid (CSF) followed by parallel digestion with Tryp-N and Tryp-C. The native and isotope-labeled peptide pairs were quantified by parallel reaction monitoring (PRM) in a single assay. Notably, both tryptic peptides were effective at quantifying Tau in human CSF, and both showed a significant difference in CSF Tau levels between AD and controls. Treating these CompTryp Tau peptide measurements as independent replicates also improved the coefficient of variation and correlation with Tau immunoassays. More broadly, we propose that CompTryp standards can be generated for any protein of interest, providing an efficient method to improve the robustness and reproducibility for MS analysis of clinical and research samples.
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Affiliation(s)
| | | | | | - Jingting Dai
- Department of Neurology, Second Xiangya Hospital , Central South University , Changsha , Hunan 410078 , China
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20
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Korte R, Oberleitner D, Brockmeyer J. Determination of food allergens by LC-MS: Impacts of sample preparation, food matrix, and thermal processing on peptide detectability and quantification. J Proteomics 2018; 196:131-140. [PMID: 30408562 DOI: 10.1016/j.jprot.2018.11.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2018] [Revised: 10/17/2018] [Accepted: 11/02/2018] [Indexed: 01/02/2023]
Abstract
Food allergies are a growing worldwide concern and the contamination of products with food allergens represents a significant health risk to allergic consumers. With the introduction of reference doses, quantitative methods are needed for the monitoring of allergen levels, and the potential of LC-MS/MS is of hugely growing interest. In this study, we demonstrate that relevant food matrices (bakery products and chocolates) and thermal food processing substantially influence the quantification of 18 marker peptides from various nut and peanut allergens via targeted proteomics. In addition, we characterize the individual release kinetics of marker peptides and provide examples for metastable marker peptide candidates. Matrix recovery rates overall ranged between 15 and 250% with the observed variation being linked to the individual peptide structure as well as to specific matrix interferences. In contrast, thermal processing considerably influences the detectability of allergens on the protein level as different marker peptides from the identical parent allergen are similarly affected, leading to a loss in signal of up to 83% in extreme cases after a 45-min simulated baking. Provided data are finally used for evaluation of different calibrators as well as the overall potential and challenges of LC-MS for the absolute quantification of food allergens. SIGNIFICANCE: With the scientific discussion moving towards a risk-based management of food allergens, including the establishment of threshold doses, robust methods for the absolute quantification of allergens in food samples are urgently needed. Because the currently used antibody- and DNA-based technologies show severe limitations in terms of specificity and reproducibility, LC-MS has emerged as a promising alternative. Its application to absolute quantification, however, first requires an understanding of the various impacts that affect quantification results, including different food matrices, sample preparation, and thermal processing of foodstuffs. Knowledge of these factors, which are assessed as part of a comprehensive survey in this study, is also an important prerequisite to evaluate means of calibration for an LC-MS-based quantification of food allergens.
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Affiliation(s)
- Robin Korte
- Institute of Food Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, Münster 48149, Germany
| | - Daniela Oberleitner
- Institute of Food Chemistry, Westfälische Wilhelms-Universität Münster, Corrensstraße 45, Münster 48149, Germany
| | - Jens Brockmeyer
- Institute of Biochemistry and Technical Biochemistry, Department of Food Chemistry, University of Stuttgart, Allmandring 5b, Stuttgart 70569, Germany.
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21
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Ali N, Ljunggren S, Karlsson HM, Wierzbicka A, Pagels J, Isaxon C, Gudmundsson A, Rissler J, Nielsen J, Lindh CH, Kåredal M. Comprehensive proteome analysis of nasal lavage samples after controlled exposure to welding nanoparticles shows an induced acute phase and a nuclear receptor, LXR/RXR, activation that influence the status of the extracellular matrix. Clin Proteomics 2018; 15:20. [PMID: 29760600 PMCID: PMC5946400 DOI: 10.1186/s12014-018-9196-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 05/02/2018] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Epidemiological studies have shown that many welders experience respiratory symptoms. During the welding process a large number of airborne nanosized particles are generated, which might be inhaled and deposited in the respiratory tract. Knowledge of the underlying mechanisms behind observed symptoms is still partly lacking, although inflammation is suggested to play a central role. The aim of this study was to investigate the effects of welding fume particle exposure on the proteome expression level in welders suffering from respiratory symptoms, and changes in protein mediators in nasal lavage samples were analyzed. Such mediators will be helpful to clarify the pathomechanisms behind welding fume particle-induced effects. METHODS In an exposure chamber, 11 welders with work-related symptoms in the lower airways during the last month were exposed to mild-steel welding fume particles (1 mg/m3) and to filtered air, respectively, in a double-blind manner. Nasal lavage samples were collected before, immediately after, and the day after exposure. The proteins in the nasal lavage were analyzed with two different mass spectrometry approaches, label-free discovery shotgun LC-MS/MS and a targeted selected reaction monitoring LC-MS/MS analyzing 130 proteins and four in vivo peptide degradation products. RESULTS The analysis revealed 30 significantly changed proteins that were associated with two main pathways; activation of acute phase response signaling and activation of LXR/RXR, which is a nuclear receptor family involved in lipid signaling. Connective tissue proteins and proteins controlling the degradation of such tissues, including two different matrix metalloprotease proteins, MMP8 and MMP9, were among the significantly changed enzymes and were identified as important key players in the pathways. CONCLUSION Exposure to mild-steel welding fume particles causes measurable changes on the proteome level in nasal lavage matrix in exposed welders, although no clinical symptoms were manifested. The results suggested that the exposure causes an immediate effect on the proteome level involving acute phase proteins and mediators regulating lipid signaling. Proteases involved in maintaining the balance between the formation and degradation of extracellular matrix proteins are important key proteins in the induced effects.
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Affiliation(s)
- Neserin Ali
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Stefan Ljunggren
- Occupational and Environmental Medicine Center, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Helen M. Karlsson
- Occupational and Environmental Medicine Center, Department of Clinical and Experimental Medicine, Linköping University, Linköping, Sweden
| | - Aneta Wierzbicka
- Department of Design Sciences, Ergonomics and Aerosol Technology, Lund University, Lund, Sweden
| | - Joakim Pagels
- Department of Design Sciences, Ergonomics and Aerosol Technology, Lund University, Lund, Sweden
| | - Christina Isaxon
- Department of Design Sciences, Ergonomics and Aerosol Technology, Lund University, Lund, Sweden
| | - Anders Gudmundsson
- Department of Design Sciences, Ergonomics and Aerosol Technology, Lund University, Lund, Sweden
| | - Jenny Rissler
- Department of Design Sciences, Ergonomics and Aerosol Technology, Lund University, Lund, Sweden
| | - Jörn Nielsen
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Christian H. Lindh
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
| | - Monica Kåredal
- Division of Occupational and Environmental Medicine, Lund University, Lund, Sweden
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22
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Zheng YZ, DeMarco ML. Manipulating trypsin digestion conditions to accelerate proteolysis and simplify digestion workflows in development of protein mass spectrometric assays for the clinical laboratory. CLINICAL MASS SPECTROMETRY (DEL MAR, CALIF.) 2017; 6:1-12. [PMID: 39193414 PMCID: PMC11322774 DOI: 10.1016/j.clinms.2017.10.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2017] [Revised: 10/09/2017] [Accepted: 10/17/2017] [Indexed: 01/15/2023]
Abstract
For ease of measurement and accurate identification of proteins by mass spectrometry, protein targets are commonly cleaved into peptides. Protein digestion is a critical step in sample preparation, yielding peptides amenable to both chromatographic separation and mass spectrometric analysis. Trypsin is the most extensively used protease due to its high cleavage specificity; however, it can yield highly variable digestion profiles and is dependent on several factors including digestion buffer, denaturant, trypsin quality selected, and composition/complexity of the sample matrix. Historically, trypsin digestion protocols have relied on lengthy digestion times-which are unsuitable for many clinical applications-to ensure effective proteolysis. Here, we performed an iterative and comprehensive evaluation of digestion conditions for five structurally diverse proteins in plasma and serum: apolipoprotein A-1, retinol-binding protein 4, transthyretin, complement component 9 and C-reactive protein. Conditions were monitored for improvements in signal intensity, reproducibility of digestion profile, and rate of release of proteolytic peptides. This approach yielded an optimized digestion protocol for detection of all five proteins in a single workflow requiring a brief 20 min digestion, without the use of chemical denaturants or reduction/alkylation steps, and only 1 μl of plasma. It is our hope that this data can accelerate the development phase of targeted mass spectrometric protein assays by identifying practical approaches to accelerate and simplify digestion protocols for clinical applications and assist with the selection of tryptic peptides for protein quantitation.
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Affiliation(s)
- Yu Zi Zheng
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Mari L. DeMarco
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
- Department of Pathology and Laboratory Medicine, St. Paul’s Hospital, Providence Health Care, Vancouver, Canada
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23
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Ji H, Wang J, Ju S, Cong H, Wang X, Su J, Wang H. Quantification of cystatin-C in human serum by stable isotope dilution liquid chromatography electrospray ionization tandem mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci 2017; 1059:49-55. [DOI: 10.1016/j.jchromb.2017.04.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 03/06/2017] [Accepted: 04/02/2017] [Indexed: 10/19/2022]
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24
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Shuford CM, Walters JJ, Holland PM, Sreenivasan U, Askari N, Ray K, Grant RP. Absolute Protein Quantification by Mass Spectrometry: Not as Simple as Advertised. Anal Chem 2017; 89:7406-7415. [DOI: 10.1021/acs.analchem.7b00858] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Christopher M. Shuford
- Center
for Esoteric
Testing, Laboratory Corporation of America Holdings, Burlington, North Carolina 27215, United States
| | | | - Patricia M. Holland
- Center
for Esoteric
Testing, Laboratory Corporation of America Holdings, Burlington, North Carolina 27215, United States
| | | | | | - Kevin Ray
- MilliporeSigma, Saint Louis, Missouri 63103, United States
| | - Russell P. Grant
- Center
for Esoteric
Testing, Laboratory Corporation of America Holdings, Burlington, North Carolina 27215, United States
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25
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van den Broek I, Romijn FPHTM, Nouta J, van der Laarse A, Drijfhout JW, Smit NPM, van der Burgt YEM, Cobbaert CM. Automated Multiplex LC-MS/MS Assay for Quantifying Serum Apolipoproteins A-I, B, C-I, C-II, C-III, and E with Qualitative Apolipoprotein E Phenotyping. Clin Chem 2016; 62:188-97. [DOI: 10.1373/clinchem.2015.246702] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 11/03/2015] [Indexed: 12/31/2022]
Abstract
Abstract
BACKGROUND
Direct and calculated measures of lipoprotein fractions for cardiovascular risk assessment suffer from analytical inaccuracy in certain dyslipidemic and pathological states, most commonly hypertriglyceridemia. LC-MS/MS has proven suitable for multiplexed quantification and phenotyping of apolipoproteins. We developed and provisionally validated an automated assay for quantification of apolipoprotein (apo) A-I, B, C-I, C-II, C-III, and E and simultaneous qualitative assessment of apoE phenotypes.
METHODS
We used 5 value-assigned human serum pools for external calibration. Serum proteins were denatured, reduced, and alkylated according to standard mass spectrometry–based proteomics procedures. After trypsin digestion, peptides were analyzed by LC-MS/MS. For each peptide, we measured 2 transitions. We compared LC-MS/MS results to those obtained by an immunoturbidimetric assay or ELISA.
RESULTS
Intraassay CVs were 2.3%–5.5%, and total CVs were 2.5%–5.9%. The LC-MS/MS assay correlated (R = 0.975–0.995) with immunoturbidimetric assays with Conformité Européenne marking for apoA-I, apoB, apoC-II, apoC-III, and apoE in normotriglyceridemic (n = 54) and hypertriglyceridemic (n = 46) sera. Results were interchangeable for apoA-I ≤3.0 g/L (Deming slope 1.014) and for apoB-100 ≤1.8 g/L (Deming slope 1.016) and were traceable to higher-order standards.
CONCLUSIONS
The multiplex format provides an opportunity for new diagnostic and pathophysiologic insights into types of dyslipidemia and allows a more personalized approach for diagnosis and treatment of lipid abnormalities.
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Affiliation(s)
| | | | - Jan Nouta
- Department of Clinical Chemistry and Laboratory Medicine
| | | | | | - Nico P M Smit
- Department of Clinical Chemistry and Laboratory Medicine
| | - Yuri E M van der Burgt
- Department of Clinical Chemistry and Laboratory Medicine
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, the Netherlands
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Harwood MD, Achour B, Neuhoff S, Russell MR, Carlson G, Warhurst G. In Vitro-In Vivo Extrapolation Scaling Factors for Intestinal P-Glycoprotein and Breast Cancer Resistance Protein: Part I: A Cross-Laboratory Comparison of Transporter-Protein Abundances and Relative Expression Factors in Human Intestine and Caco-2 Cells. ACTA ACUST UNITED AC 2015; 44:297-307. [PMID: 26631742 DOI: 10.1124/dmd.115.067371] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Accepted: 12/01/2015] [Indexed: 12/22/2022]
Abstract
Over the last 5 years the quantification of transporter-protein absolute abundances has dramatically increased in parallel to the expanded use of in vitro-in vivo extrapolation (IVIVE) and physiologically based pharmacokinetics (PBPK)-linked models, for decision-making in pharmaceutical company drug development pipelines and regulatory submissions. Although several research groups have developed laboratory-specific proteomic workflows, it is unclear if the large range of reported variability is founded on true interindividual variability or experimental variability resulting from sample preparation or the proteomic methodology used. To assess the potential for methodological bias on end-point abundance quantification, two independent laboratories, the University of Manchester (UoM) and Bertin Pharma (BPh), employing different proteomic workflows, quantified the absolute abundances of Na/K-ATPase, P-gp, and breast cancer resistance protein (BCRP) in the same set of biologic samples from human intestinal and Caco-2 cell membranes. Across all samples, P-gp abundances were significantly correlated (P = 0.04, Rs = 0.72) with a 2.4-fold higher abundance (P = 0.001) generated at UoM compared with BPh. There was a systematically higher BCRP abundance in Caco-2 cell samples quantified by BPh compared with UoM, but not in human intestinal samples. Consequently, a similar intestinal relative expression factor (REF), derived from distal jejunum and Caco-2 monolayer samples, between laboratories was found for P-gp. However, a 2-fold higher intestinal REF was generated by UoM (2.22) versus BPh (1.11). We demonstrate that differences in absolute protein abundance are evident between laboratories and they probably result from laboratory-specific methodologies relating to peptide choice.
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Affiliation(s)
- Matthew D Harwood
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Brahim Achour
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Sibylle Neuhoff
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Matthew R Russell
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Gordon Carlson
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
| | - Geoffrey Warhurst
- Gut Barrier Group, Inflammation and Repair, University of Manchester, Salford Royal NHS Trust, Salford, United Kingdom (M.D.H., G.C., G.W.); Centre for Applied Pharmacokinetic Research, Manchester Pharmacy School, Stopford Building, Manchester, United Kingdom (B.A., M.R.R., A.R-H.); Simcyp Limited (a Certara Company), Sheffield (M.D.H., S.N., A.R-H.), United Kingdom
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van den Broek I, Blokland M, Nessen MA, Sterk S. Current trends in mass spectrometry of peptides and proteins: Application to veterinary and sports-doping control. MASS SPECTROMETRY REVIEWS 2015; 34:571-594. [PMID: 24375671 DOI: 10.1002/mas.21419] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Revised: 11/12/2013] [Accepted: 11/12/2013] [Indexed: 06/03/2023]
Abstract
Detection of misuse of peptides and proteins as growth promoters is a major issue for sport and food regulatory agencies. The limitations of current analytical detection strategies for this class of compounds, in combination with their efficacy in growth-promoting effects, make peptide and protein drugs highly susceptible to abuse by either athletes or farmers who seek for products to illicitly enhance muscle growth. Mass spectrometry (MS) for qualitative analysis of peptides and proteins is well-established, particularly due to tremendous efforts in the proteomics community. Similarly, due to advancements in targeted proteomic strategies and the rapid growth of protein-based biopharmaceuticals, MS for quantitative analysis of peptides and proteins is becoming more widely accepted. These continuous advances in MS instrumentation and MS-based methodologies offer enormous opportunities for detection and confirmation of peptides and proteins. Therefore, MS seems to be the method of choice to improve the qualitative and quantitative analysis of peptide and proteins with growth-promoting properties. This review aims to address the opportunities of MS for peptide and protein analysis in veterinary control and sports-doping control with a particular focus on detection of illicit growth promotion. An overview of potential peptide and protein targets, including their amino acid sequence characteristics and current MS-based detection strategies is, therefore, provided. Furthermore, improvements of current and new detection strategies with state-of-the-art MS instrumentation are discussed for qualitative and quantitative approaches.
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Affiliation(s)
- Irene van den Broek
- RIKILT Wageningen UR, Institute of Food Safety, Akkermaalsbos 2, 6708, WB, Wageningen, The Netherlands
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center (LUMC), Albinusdreef 2, 2333, ZA, Leiden, The Netherlands
| | - Marco Blokland
- RIKILT Wageningen UR, Institute of Food Safety, Akkermaalsbos 2, 6708, WB, Wageningen, The Netherlands
| | - Merel A Nessen
- RIKILT Wageningen UR, Institute of Food Safety, Akkermaalsbos 2, 6708, WB, Wageningen, The Netherlands
| | - Saskia Sterk
- RIKILT Wageningen UR, Institute of Food Safety, Akkermaalsbos 2, 6708, WB, Wageningen, The Netherlands
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Serum apolipoprotein A-1 quantification by LC-MS with a SILAC internal standard reveals reduced levels in smokers. Bioanalysis 2015; 7:2895-911. [PMID: 26394123 PMCID: PMC4737526 DOI: 10.4155/bio.15.195] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Background: Absolute quantification of protein biomarkers such as serum apolipoprotein A1 by both immunoassays and LC–MS can provide misleading results. Results: Recombinant ApoA-1 internal standard was prepared using stable isotope labeling by amino acids in cell culture with [13C615N2]-lysine and [13C915N1]-tyrosine in human cells. A stable isotope dilution LC–MS method for serum ApoA-1 was validated and levels analyzed for 50 nonsmokers and 50 smokers. Conclusion: The concentration of ApoA-1 in nonsmokers was 169.4 mg/dl with an 18.4% reduction to 138.2 mg/dl in smokers. The validated assay will have clinical utility for assessing effects of smoking cessation and therapeutic or dietary interventions in high-risk populations.
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Hill RC, Oman TJ, Shan G, Schafer B, Eble J, Chen C. Development and Validation of a Multiplexed Protein Quantitation Assay for the Determination of Three Recombinant Proteins in Soybean Tissues by Liquid Chromatography with Tandem Mass Spectrometry. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2015; 63:7450-61. [PMID: 26237374 DOI: 10.1021/acs.jafc.5b03083] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Currently, traditional immunochemistry technologies such as enzyme-linked immunosorbent assays (ELISA) are the predominant analytical tool used to measure levels of recombinant proteins expressed in genetically engineered (GE) plants. Recent advances in agricultural biotechnology have created a need to develop methods capable of selectively detecting and quantifying multiple proteins in complex matrices because of increasing numbers of transgenic proteins being coexpressed or "stacked" to achieve tolerance to multiple herbicides or to provide multiple modes of action for insect control. A multiplexing analytical method utilizing liquid chromatography with tandem mass spectrometry (LC-MS/MS) has been developed and validated to quantify three herbicide-tolerant proteins in soybean tissues: aryloxyalkanoate dioxygenase (AAD-12), 5-enol-pyruvylshikimate-3-phosphate synthase (2mEPSPS), and phosphinothricin acetyltransferase (PAT). Results from the validation showed high recovery and precision over multiple analysts and laboratories. Results from this method were comparable to those obtained with ELISA with respect to protein quantitation, and the described method was demonstrated to be suitable for multiplex quantitation of transgenic proteins in GE crops.
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Affiliation(s)
- Ryan C Hill
- Dow AgroSciences, LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Trent J Oman
- Dow AgroSciences, LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Guomin Shan
- Dow AgroSciences, LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Barry Schafer
- Dow AgroSciences, LLC , 9330 Zionsville Road, Indianapolis, Indiana 46268, United States
| | - Julie Eble
- Critical Path Services, LLC , 3070 McCann Farm Drive, Garnet Valley, Pennsylvania 19060, United States
| | - Cynthia Chen
- Critical Path Services, LLC , 3070 McCann Farm Drive, Garnet Valley, Pennsylvania 19060, United States
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30
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LC–MS-based quantification of intact proteins: perspective for clinical and bioanalytical applications. Bioanalysis 2015; 7:1943-58. [DOI: 10.4155/bio.15.113] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bioanalytical LC–MS for protein quantification is traditionally based on enzymatic digestion of the target protein followed by absolute quantification of a specific signature peptide relative to a stable-isotope labeled analog. The enzymatic digestion, nonetheless, limits rapid method development, sample throughput and turnaround time, and, moreover, makes that essential information regarding the biological function of the intact protein is lost. The recent advancements in high-resolution MS instrumentation and improved sample preparation techniques dedicated to protein clean-up raise the question to what extent LC–MS can be applied for quantitative bioanalysis of intact proteins. This review provides an overview of current and potential applications of LC–MS for intact protein quantification as well as the main limitations and challenges for broad application.
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31
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Faria M, Halquist MS, Yuan M, Mylott W, Jenkins RG, Karnes HT. Comparison of a stable isotope labeled (SIL) peptide and an extended SIL peptide as internal standards to track digestion variability of an unstable signature peptide during quantification of a cancer biomarker, human osteopontin, from plasma using capillary microflow LC-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 1001:156-68. [PMID: 26279007 DOI: 10.1016/j.jchromb.2015.05.040] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Revised: 04/30/2015] [Accepted: 05/10/2015] [Indexed: 10/23/2022]
Abstract
Human osteopontin (hOPN) is a secreted plasma protein which is elevated in various cancers and is indicative of poor prognosis. Here we describe investigations involving an extended peptide internal standard to track an unstable signature peptide followed by further method development and validation for quantitative measurement of hOPN from plasma using microflow liquid chromatography and tandem mass spectrometry (MFLC-MS/MS). A biologically relevant tryptic peptide 'GDSVVYGLR' was used as a signature peptide for this method. The optimized method involved immunocapture of the analyte protein using hOPN specific antibodies followed by trypsin digestion to obtain the signature peptide. Analysis was carried out on a Waters IonKey/MS system using a flow rate of 2.5μL/min. Immunocapture buffer was used as a surrogate matrix for the validation studies. The method was validated over a range of 25-600ng/mL. Intra-assay and inter-assay accuracies were within ±13%. Intra-assay and inter-assay precision were within 17%. A stable isotope labeled (SIL) peptide GDSVVYGLR* and an extended SIL peptide TYDGRGDSVV*YGLRSKSKKF were evaluated as internal standards (IS) to account for signature peptide digestion instability and variability. Inherent digestion variability i.e., under controlled conditions, was within ±20% with both IS peptides. In digestion variability studies, where trypsin activity was varied (20-180%), the use of the extended SIL peptide as an internal standard limited the variability to within ±30% of the normalized response. Alternatively, when the SIL peptide was used as the internal standard, the variability ranged from -67.4% to 50.6% of the normalized response. The applicability of the validated method was demonstrated by quantification of OPN from plasma samples obtained from 10 healthy individuals and 10 breast cancer patients. The plasma OPN concentrations in healthy individuals ranged from 38 to 85ng/mL with a mean concentration of 55.4±15.3ng/mL. A 1.5-12 fold increase in OPN concentrations, ranging from 85 to 637ng/mL, was seen in breast cancer patient samples.
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Affiliation(s)
- Morse Faria
- Department of Pharmaceutics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Matthew S Halquist
- Department of Pharmaceutics, Virginia Commonwealth University, Richmond, VA 23298, USA
| | - Moucun Yuan
- Chromatographic Sciences, PPD, 2244 Dabney Road, Richmond, VA 23230, USA
| | - William Mylott
- Chromatographic Sciences, PPD, 2244 Dabney Road, Richmond, VA 23230, USA
| | - Rand G Jenkins
- Chromatographic Sciences, PPD, 2244 Dabney Road, Richmond, VA 23230, USA
| | - H Thomas Karnes
- Department of Pharmaceutics, Virginia Commonwealth University, Richmond, VA 23298, USA.
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32
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Scott KB, Turko IV, Phinney KW. Quantitative Performance of Internal Standard Platforms for Absolute Protein Quantification Using Multiple Reaction Monitoring-Mass Spectrometry. Anal Chem 2015; 87:4429-35. [DOI: 10.1021/acs.analchem.5b00331] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kerry Bauer Scott
- Biomolecular
Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Illarion V. Turko
- Biomolecular
Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
- Institute for Bioscience and Biotechnology Research, 9600 Gudelsky Drive, Rockville, Maryland 20850, United States
| | - Karen W. Phinney
- Biomolecular
Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Gaithersburg, Maryland 20899, United States
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33
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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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34
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Scherl A. Clinical protein mass spectrometry. Methods 2015; 81:3-14. [PMID: 25752846 DOI: 10.1016/j.ymeth.2015.02.015] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 12/26/2022] Open
Abstract
Quantitative protein analysis is routinely performed in clinical chemistry laboratories for diagnosis, therapeutic monitoring, and prognosis. Today, protein assays are mostly performed either with non-specific detection methods or immunoassays. Mass spectrometry (MS) is a very specific analytical method potentially very well suited for clinical laboratories. Its unique advantage relies in the high specificity of the detection. Any protein sequence variant, the presence of a post-translational modification or degradation will differ in mass and structure, and these differences will appear in the mass spectrum of the protein. On the other hand, protein MS is a relatively young technique, demanding specialized personnel and expensive instrumentation. Many scientists and opinion leaders predict MS to replace immunoassays for routine protein analysis, but there are only few protein MS applications routinely used in clinical chemistry laboratories today. The present review consists of a didactical introduction summarizing the pros and cons of MS assays compared to immunoassays, the different instrumentations, and various MS protein assays that have been proposed and/or are used in clinical laboratories. An important distinction is made between full length protein analysis (top-down method) and peptide analysis after enzymatic digestion of the proteins (bottom-up method) and its implication for the protein assay. The document ends with an outlook on what type of analyses could be used in the future, and for what type of applications MS has a clear advantage compared to immunoassays.
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Affiliation(s)
- Alexander Scherl
- Department of Human Protein Science, Faculty of Medicine, University of Geneva, Geneva, Switzerland; Department of Genetic and Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.
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35
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Fleurbaaij F, van Leeuwen HC, Klychnikov OI, Kuijper EJ, Hensbergen PJ. Mass Spectrometry in Clinical Microbiology and Infectious Diseases. Chromatographia 2015. [DOI: 10.1007/s10337-014-2839-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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36
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van den Broek I, Romijn FPHTM, Smit NPM, van der Laarse A, Drijfhout JW, van der Burgt YEM, Cobbaert CM. Quantifying protein measurands by peptide measurements: where do errors arise? J Proteome Res 2015; 14:928-42. [PMID: 25494833 DOI: 10.1021/pr5011179] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Clinically actionable quantification of protein biomarkers by mass spectrometry (MS) requires analytical performance in concordance with quality specifications for diagnostic tests. Laboratory-developed tests should, therefore, be validated in accordance with EN ISO 15189:2012 guidelines for medical laboratories to demonstrate competence and traceability along the entire workflow, including the selected standardization strategy and the phases before, during, and after proteolysis. In this study, bias and imprecision of a previously developed MS method for quantification of serum apolipoproteins A-I (Apo A-I) and B (Apo B) were thoroughly validated according to Clinical and Laboratory Standards Institute (CLSI) guidelines EP15-A2 and EP09-A3, using 100 patient sera and either stable-isotope labeled (SIL) peptides or SIL-Apo A-I as internal standard. The systematic overview of error components assigned sample preparation before the first 4 h of proteolysis as major source (∼85%) of within-sample imprecision without external calibration. No improvement in imprecision was observed with the use of SIL-Apo A-I instead of SIL-peptides. On the contrary, when the use of SIL-Apo A-I was combined with external calibration, imprecision improved significantly (from ∼9% to ∼6%) as a result of the normalization for matrix effects on linearity. A between-sample validation of bias in 100 patient sera further supported the presence of matrix effects on digestion completeness and additionally demonstrated specimen-specific biases associated with modified peptide sequences or alterations in protease activity. In conclusion, the presented overview of bias and imprecision components contributes to a better understanding of the sources of errors in MS-based protein quantification and provides valuable recommendations to assess and control analytical quality in concordance with the requirements for clinical use.
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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
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Bladergroen MR, van der Burgt YEM. Solid-phase extraction strategies to surmount body fluid sample complexity in high-throughput mass spectrometry-based proteomics. JOURNAL OF ANALYTICAL METHODS IN CHEMISTRY 2015; 2015:250131. [PMID: 25692071 PMCID: PMC4322654 DOI: 10.1155/2015/250131] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Revised: 01/08/2015] [Accepted: 01/08/2015] [Indexed: 05/08/2023]
Abstract
For large-scale and standardized applications in mass spectrometry- (MS-) based proteomics automation of each step is essential. Here we present high-throughput sample preparation solutions for balancing the speed of current MS-acquisitions and the time needed for analytical workup of body fluids. The discussed workflows reduce body fluid sample complexity and apply for both bottom-up proteomics experiments and top-down protein characterization approaches. Various sample preparation methods that involve solid-phase extraction (SPE) including affinity enrichment strategies have been automated. Obtained peptide and protein fractions can be mass analyzed by direct infusion into an electrospray ionization (ESI) source or by means of matrix-assisted laser desorption ionization (MALDI) without further need of time-consuming liquid chromatography (LC) separations.
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Affiliation(s)
- Marco R. Bladergroen
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, Netherlands
| | - Yuri E. M. van der Burgt
- Leiden University Medical Center (LUMC), Center for Proteomics and Metabolomics, P.O. Box 9600, 2300 RC Leiden, Netherlands
- *Yuri E. M. van der Burgt:
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38
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Smit NPM, Romijn FPHTM, van den Broek I, Drijfhout JW, Haex M, van der Laarse A, van der Burgt YEM, Cobbaert CM. Metrological traceability in mass spectrometry-based targeted protein quantitation: a proof-of-principle study for serum apolipoproteins A-I and B100. J Proteomics 2014; 109:143-61. [PMID: 24972322 DOI: 10.1016/j.jprot.2014.06.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2014] [Revised: 05/22/2014] [Accepted: 06/16/2014] [Indexed: 12/23/2022]
Abstract
UNLABELLED In this study, we have followed up on previous liquid chromatography (LC) multiple reaction monitoring (MRM) mass spectrometry (MS) approaches for measurement of apolipoprotein (apo) A-I and apo B100 in serum aiming for implementation of a multiplexed assay in a clinical chemistry laboratory with full metrological traceability. Signature peptides were selected and detected by dynamic MRM, and stable isotope labeled (SIL)-peptides were used as internal standards. Five apo A-I and four apo B100 peptides were measured in serum digests with linearity (R(2)>0.992) in the physiologically relevant concentration ranges. Linearity with regard to protein concentration was ascertained at five concentration levels (R(2)>0.926 and R(2)>0.965, for the apo A-I and apo B100 peptides, respectively). Three native value-assigned sera were used as external calibrators for further method verification. Imprecision values on sample preparation and LC-MS/MS acquisition were below the established minimal specifications for apo A-I and apo B100 (5.0% and 5.3%, respectively). Correlation of LC-MS/MS results with immunoturbidimetric assay results, for normo- and hypertriglyceridemic samples, showed R(2)>0.944 for apo A-I and R(2)>0.964 for apo B100. This LC-MS/MS method has potential for clinical application in normo- and dyslipidemic patients. BIOLOGICAL SIGNIFICANCE Measurement of apo A-I and apo B100 may offer an alternative to high and low density lipoprotein cholesterol (HDL-c and LDL-c) methods for cardiovascular disease risk assessment in dyslipidemic patients [1]. An LC-MS/MS method for apo A-I and apo B100 has the advantage of antibody independent and specific detection of protein signature peptides. The introduction of an LC-MS/MS method for apo A-I and apo B100 can serve as an example for many existing and newly developed (multiplex) biomarker methods in quantitative clinical chemistry proteomics (qCCP). Such LC-MS/MS methods should meet basic clinical chemistry principles with regard to test evaluation [2]. Criteria for imprecision should be pre-defined, e.g., based on biological variation. The use of commutable and traceable serum-based calibrators will improve inter-laboratory reproducibility of LC-MS/MS methods and may contribute to a more rapid transition of biomarker discovery to clinical utility with benefit for the patient treatment and improvement of general health care.
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Affiliation(s)
- Nico P M Smit
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
| | - Fred P H T M Romijn
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Irene van den Broek
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Jan W Drijfhout
- Department of Immunohematology and Bloodtransfusion, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Martin Haex
- Agilent Technologies Netherlands B.V., Amstelveen, The Netherlands
| | - Arnoud van der Laarse
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Christa M Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
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Acosta-Martin AE, Lane L. Combining bioinformatics and MS-based proteomics: clinical implications. Expert Rev Proteomics 2014; 11:269-84. [PMID: 24720436 DOI: 10.1586/14789450.2014.900446] [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: 12/17/2022]
Abstract
Clinical proteomics research aims at i) discovery of protein biomarkers for screening, diagnosis and prognosis of disease, ii) discovery of protein therapeutic targets for improvement of disease prevention, treatment and follow-up, and iii) development of mass spectrometry (MS)-based assays that could be implemented in clinical chemistry, microbiology or hematology laboratories. MS has been increasingly applied in clinical proteomics studies for the identification and quantification of proteins. Bioinformatics plays a key role in the exploitation of MS data in several aspects such as the generation and curation of protein sequence databases, the development of appropriate software for MS data treatment and integration with other omics data and the establishment of adequate standard files for data sharing. In this article, we discuss the main MS approaches and bioinformatics solutions that are currently applied to accomplish the objectives of clinical proteomic research.
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