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Mi W, Zhang X, Wang B, Sun R, Ma S, Hu Z, Dai X. Absolute protein quantification based on calibrated particle counting using electrospray-differential mobility analysis. Anal Chim Acta 2024; 1304:342534. [PMID: 38637035 DOI: 10.1016/j.aca.2024.342534] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/13/2024] [Accepted: 03/25/2024] [Indexed: 04/20/2024]
Abstract
The traceability of in vitro diagnostics or drug products is based on the accurate quantification of proteins. In this study, we developed an absolute quantification approach for proteins. This method is based on calibrated particle counting using electrospray-differential mobility analysis (ES-DMA) coupled with a condensation particle counter (CPC). The absolute concentration of proteins was quantified with the observed protein particle number measured with ES-DMA-CPC, and the detection efficiency was determined by calibrators. The measurement performance and quantitative level were verified using two certificated reference materials, BSA and NIMCmAb. The linear regression fit for the detection efficiency values of three reference materials and one highly purified protein (myoglobin, BSA, NIMCmAb and fibrinogen) indicated that the detection efficiency and the particle size distribution of these proteins exhibited a linear relationship. Moreover, to explore the suitability of the detection efficiency-particle size curve for protein quantification, the concentrations of three typical proteinaceous particles, including two high molecular weight proteins (NIST reference material 8671 and D-dimer) and one protein complex (glutathione S-transferase dimer), were determined. This work suggests that this calibrated particle counting method is an efficient approach for nondestructive, rapid and accurate quantification of proteins, especially for measuring proteinaceous particles with tremendous size and without reference standards.
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Affiliation(s)
- Wei Mi
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China.
| | - Xinyi Zhang
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China
| | - Bin Wang
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China
| | - Ruixue Sun
- College of Life Sciences, China Jiliang University, Xueyuan Street 258, Hangzhou, 310018, China
| | - Shangying Ma
- College of Life Sciences, China Jiliang University, Xueyuan Street 258, Hangzhou, 310018, China
| | - Zhishang Hu
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China.
| | - Xinhua Dai
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China.
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2
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Mi W, Zhang X, Tian X, Sun R, Ma S, Hu Z, Dai X. Development of a potential primary method for protein quantification via electrospray differential mobility analysis. Talanta 2024; 266:124797. [PMID: 37541009 DOI: 10.1016/j.talanta.2023.124797] [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: 01/26/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 08/06/2023]
Abstract
Accurate protein quantification is the basis for establishing the metrological traceability of in vitro diagnostics or drug products. In this study, we established and validated a potential primary method for protein quantification based on electrospray-differential mobility analysis coupled with a condensation particle counter (ES-DMA-CPC). The analytical performance of this method was assessed using the certified reference material NIMCmAb, and the uncertainty of measurement was evaluated. The method was applied to the quantification of three other protein reference materials and one highly purified protein, including myoglobin, bovine serum albumin, IgG monoclonal antibody, and one highly purified fibrinogen, with a molecular weight range between 17 kDa and 340 kDa. In addition, when compared with isotope dilution mass spectrometry (IDMS) and UV‒VIS spectrophotometry approaches, the ES-DMA-CPC method showed good agreement with IDMS method for the quantification of these protein reference materials. Our proposed method provided an accurate quantification of proteins, especially those with large molecular weights. Moreover, our method could be a potential primary method for protein quantification and serve as a complement to IDMS method.
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Affiliation(s)
- Wei Mi
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China.
| | - Xinyi Zhang
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China
| | - Xiangrong Tian
- College of Biology and Environmental Science, JiShou University, Renming South Road 120, Jishou, Hunan, 416000, China
| | - Ruixue Sun
- College of Life Sciences, China Jiliang University, Xueyuan Street 258, Hangzhou, 310018, China
| | - Shangying Ma
- College of Life Sciences, China Jiliang University, Xueyuan Street 258, Hangzhou, 310018, China
| | - Zhishang Hu
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China.
| | - Xinhua Dai
- National Institute of Metrology, No.18 Beisanhuan Donglu, Beijing, 100029, China.
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3
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Lundeen RA, Kennedy JJ, Murillo OD, Ivey RG, Zhao L, Schoenherr RM, Hoofnagle AN, Wang P, Whiteaker JR, Paulovich AG. Monitoring Both Extended and Tryptic Forms of Stable Isotope-Labeled Standard Peptides Provides an Internal Quality Control of Proteolytic Digestion in Targeted Mass Spectrometry-Based Assays. Mol Cell Proteomics 2023; 22:100621. [PMID: 37478973 PMCID: PMC10458721 DOI: 10.1016/j.mcpro.2023.100621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/23/2023] Open
Abstract
Targeted mass spectrometry (MS)-based proteomic assays, such as multiplexed multiple reaction monitoring (MRM)-MS assays, enable sensitive and specific quantification of proteotypic peptides as stoichiometric surrogates for proteins. Efforts are underway to expand the use of MRM-MS assays in clinical environments, which requires a reliable strategy to monitor proteolytic digestion efficiency within individual samples. Towards this goal, extended stable isotope-labeled standard (SIS) peptides (hE), which incorporate native proteolytic cleavage sites, can be spiked into protein lysates prior to proteolytic (trypsin) digestion, and release of the tryptic SIS peptide (hT) can be monitored. However, hT measurements alone cannot monitor the extent of digestion and may be confounded by matrix effects specific to individual patient samples; therefore, they are not sufficient to monitor sample-to-sample digestion variability. We hypothesized that measuring undigested hE, along with its paired hT, would improve detection of digestion issues compared to only measuring hT. We tested the ratio of the SIS pair measurements, or hE/hT, as a quality control (QC) metric of trypsin digestion for two MRM assays: a direct-MRM (398 targets) and an immuno-MRM (126 targets requiring immunoaffinity peptide enrichment) assay, with extended SIS peptides observable for 54% (216) and 62% (78) of the targets, respectively. We evaluated the quantitative bias for each target in a series of experiments that adversely affected proteolytic digestion (e.g., variable digestion times, pH, and temperature). We identified a subset of SIS pairs (36 for the direct-MRM, 7 for the immuno-MRM assay) for which the hE/hT ratio reliably detected inefficient digestion that resulted in decreased assay sensitivity and unreliable endogenous quantification. The hE/hT ratio was more responsive to a decrease in digestion efficiency than a metric based on hT measurements alone. For clinical-grade MRM-MS assays, this study describes a ready-to-use QC panel and also provides a road map for designing custom QC panels.
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Affiliation(s)
- Rachel A Lundeen
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Jacob J Kennedy
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Oscar D Murillo
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Richard G Ivey
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Lei Zhao
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Regine M Schoenherr
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA; Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Pei Wang
- Department of Genetics and Genomic Sciences, Mount Sinai Hospital, New York, New York, USA
| | - Jeffrey R Whiteaker
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
| | - Amanda G Paulovich
- Translational Science and Therapeutics Division, Fred Hutchinson Cancer Center, Seattle, Washington, USA.
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4
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Kilpatrick LE, Bouillon R, Davis WC, Henderson CM, Hoofnagle AN, Pauwels S, Vanderschueren D, Waelkens E, Wildiers H, Yen JH, Phinney KW. The influence of proteoforms: assessing the accuracy of total vitamin D-binding protein quantification by proteolysis and LC-MS/MS. Clin Chem Lab Med 2023; 61:78-85. [PMID: 36279170 DOI: 10.1515/cclm-2022-0642] [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: 07/05/2022] [Accepted: 09/26/2022] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Vitamin D-binding protein (VDBP), a serum transport protein for 25-hydroxyvitamin D [25(OH)D], has three common proteoforms which have co-localized amino acid variations and glycosylation. A monoclonal immunoassay was found to differentially detect VDBP proteoforms and methods using liquid chromatography-tandem mass spectrometry (LC-MS/MS) might be able to overcome this limitation. Previously developed multiple reaction monitoring LC-MS/MS methods for total VDBP quantification represent an opportunity to probe the potential effects of proteoforms on proteolysis, instrument response and quantification accuracy. METHODS VDBP was purified from homozygous human donors and quantified using proteolysis or acid hydrolysis and LC-MS/MS. An interlaboratory comparison was performed using pooled human plasma [Standard Reference Material® 1950 (SRM 1950) Metabolites in Frozen Human Plasma] and analyses with different LC-MS/MS methods in two laboratories. RESULTS Several shared peptides from purified proteoforms were found to give reproducible concentrations [≤2.7% coefficient of variation (CV)] and linear instrument responses (R2≥0.9971) when added to human serum. Total VDBP concentrations from proteolysis or amino acid analysis (AAA) of purified proteoforms had ≤1.92% CV. SRM 1950, containing multiple proteoforms, quantified in two laboratories resulted in total VDBP concentrations with 7.05% CV. CONCLUSIONS VDBP proteoforms were not found to cause bias during quantification by LC-MS/MS, thus demonstrating that a family of proteins can be accurately quantified using shared peptides. A reference value was assigned for total VDBP in SRM 1950, which may be used to standardize methods and improve the accuracy of VDBP quantification in research and clinical samples.
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Affiliation(s)
- Lisa E Kilpatrick
- Material Measurement Laboratory, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Roger Bouillon
- Laboratory of Clinical and Experimental Endocrinology, Department of Chronic Diseases, Metabolism and Ageing, KU Leuven, Leuven, Belgium
| | - W Clay Davis
- Hollings Marine Laboratory, National Institute of Standards and Technology, Charleston, SC, USA
| | - Clark M Henderson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA.,Seagen, Inc., Bothell, WA, USA
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA, USA
| | - Steven Pauwels
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Dirk Vanderschueren
- Department of Laboratory Medicine, University Hospitals Leuven, Leuven, Belgium
| | - Etienne Waelkens
- Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Hans Wildiers
- Department of General Medical Oncology, University Hospitals Leuven, Leuven, Belgium
| | - James H Yen
- Statistical Engineering Division, Information Technology Laboratory, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Karen W Phinney
- Material Measurement Laboratory, Biomolecular Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
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Rzagalinski I, Bogdanova A, Raghuraman BK, Geertsma ER, Hersemann L, Ziemssen T, Shevchenko A. FastCAT Accelerates Absolute Quantification of Proteins Using Multiple Short Nonpurified Chimeric Standards. J Proteome Res 2022; 21:1408-1417. [PMID: 35561006 PMCID: PMC9171895 DOI: 10.1021/acs.jproteome.2c00014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022]
Abstract
![]()
Absolute (molar)
quantification of clinically relevant proteins
determines their reference values in liquid and solid biopsies. The
FastCAT (for Fast-track QconCAT) method employs multiple short (<50
kDa), stable-isotope labeled chimeric proteins (CPs) composed of concatenated
quantotypic (Q)-peptides representing the quantified proteins. Each
CP also comprises scrambled sequences of reference (R)-peptides that
relate its abundance to a single protein standard (bovine serum albumin,
BSA). FastCAT not only alleviates the need to purify CP or use sodium
dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) but
also improves the accuracy, precision, and dynamic range of the absolute
quantification by grouping Q-peptides according to the expected abundance
of the target proteins. We benchmarked FastCAT against the reference
method of MS Western and tested it in the direct molar quantification
of neurological markers in human cerebrospinal fluid at the low ng/mL
level.
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Affiliation(s)
- Ignacy Rzagalinski
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Aliona Bogdanova
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | | | - Eric R Geertsma
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Lena Hersemann
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
| | - Tjalf Ziemssen
- Center of Clinical Neuroscience, Department of Neurology, University Hospital Carl Gustav Carus, Technical University of Dresden, 01307 Dresden, Germany
| | - Andrej Shevchenko
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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6
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Affinity capture in bottom-up protein analysis - Overview of current status of proteolytic peptide capture using antibodies and molecularly imprinted polymers. Anal Chim Acta 2021; 1182:338714. [PMID: 34602193 DOI: 10.1016/j.aca.2021.338714] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 05/27/2021] [Accepted: 05/28/2021] [Indexed: 12/17/2022]
Abstract
Antibody-based affinity capture has become the gold standard in sample preparation for determination of low-abundance protein biomarkers in biological matrices prior to liquid chromatography-mass spectrometry (LC-MS) determination. This comprises both capture of intact proteins prior to the digestion step and capture of proteolytic peptides after digestion of the sample. The latter can be performed both using antibodies specifically developed to capture target proteolytic peptides, as well as by the less explored use of anti-protein antibodies to capture the proteolytic epitope peptide. Molecularly imprinted polymers (MIPs), also called plastic antibodies are another affinity-based approach emerging as sample preparation technique in LC-MS based protein biomarker analysis. The current review gives a critical and comprehensive overview of proteolytic peptide capture using antibodies and MIPs in LC-MS based protein biomarker determination during the last five years. The main emphasis is on capture of non-modified peptides, while a brief overview of affinity capture of peptides containing post-translational modifications (PTMs) is provided.
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7
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Application of middle-down approach in quantitation and catabolite identification of protein by LC-high-resolution mass spectrometry. Bioanalysis 2021; 13:465-479. [PMID: 33719526 DOI: 10.4155/bio-2020-0315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Aim: To further enhance the detection sensitivity and increase resolving power of top-down intact protein bioanalysis, middle-down approach was explored. Materials & methods: An monoclonal antibody (mAb) was used as a model protein to evaluate quantitative bioanalytical assay performance and a disulfide linked dimer protein was investigated for its pharmacokinetics properties and catabolism in vivo by middle-down approach. Results & Conclusion: For quantitation of the mAb, different subunits generated by middle-down approach provided different level of signal improvement in biological samples with Lc and half Fc giving five-times better sensitivity than intact mAb. For the dimer protein, middle-down analysis by reduction enabled effective differentiation of the unchanged protein and its oxidized form, and clearly elucidated their respective proteolytic catabolites.
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8
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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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9
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Burdman I, Burckhardt BB. Human prorenin determination by hybrid immunocapture liquid chromatography/mass spectrometry: A mixed-solvent-triggered digestion utilizing D-optimal design. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8932. [PMID: 32845569 DOI: 10.1002/rcm.8932] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 08/03/2020] [Accepted: 08/17/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Human prorenin, representing the precursor of mature renin, has been discussed as a potential biomarker, e.g. in diagnosing primary hyperaldosteronism or diabetes-induced nephropathy. Currently, only immunoassays are available for prorenin quantification. As the similarity of prorenin to active renin impedes its accurate determination by immunoassay, mass spectrometry appears as an accurate alternative for differentiation of that protein. METHODS Immunoaffinity purification plus a mixed-solvent-triggered digestion was combined with liquid chromatography/mass spectrometry (LC/MS) to enable a fast, sensitive, and less laboratory-intensive approach to the quantification of prorenin. Statistical experimental planning, which is known as Design of Experiments (DOE), was used to identify the optimal conditions for the generation of the signature peptides within a manageable number of experiments. The efficiency of the mixed-solvent-triggered digestion by trypsin was investigated using four different organic solvents: acetonitrile, acetone, tetrahydrofuran and methanol. RESULTS By utilizing a D-optimal design, we found that the optimal mixed-solvent type for the generation of both signature peptides was acetonitrile at a concentration of 84% and an incubation temperature of 16°C. Using the mixed-solvent-triggered digestion, the procedure time allowed a fast analysis of active renin and prorenin with a short digestion time of 98 min. This optimized mixed-solvent-triggered digestion procedure was applied to detect renin and prorenin successfully in human plasma by the newly developed hybrid approach. CONCLUSIONS The identification of unique surrogates for human prorenin enabled the mass spectrometric differentiation between the two similar proteins. The novel hybrid approach successfully proved its ability to purify, detect and distinguish between prorenin and active renin in human plasma.
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Affiliation(s)
- Ilja Burdman
- Institute of Clinical Pharmacy and Pharmacotherapy, Heinrich Heine University, Universitaetsstr. 1, Dusseldorf, Germany
| | - Bjoern B Burckhardt
- Institute of Clinical Pharmacy and Pharmacotherapy, Heinrich Heine University, Universitaetsstr. 1, Dusseldorf, Germany
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10
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Bottom-up sample preparation for the LC-MS/MS quantification of anti-cancer monoclonal antibodies in bio matrices. Bioanalysis 2020; 12:1405-1425. [PMID: 32975434 DOI: 10.4155/bio-2020-0204] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Therapeutic monoclonal antibodies (mAbs) are rapidly taking over the treatment of many malignancies, and an astonishing number of mAbs is in development. This causes a high demand for quantification of mAbs in biomatrices both for measuring therapeutic mAb concentrations and to support pharmacokinetics and pharmacodynamics studies. Conventionally, ligand-binding assays are used for these purposes, but LC-MS is gaining popularity. Although intact (top-down) and subunit (middle-down) mAb quantification is reported, signature peptide (bottom-up) quantification is currently most advantageous. This review provides an overview of the reported bottom-up mAb quantification methods in biomatrices as well as general recommendations regarding signature peptide and internal standard selection, reagent use and optimization of digestion in bottom-up quantification methods.
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11
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Geisslitz S, Longin CFH, Koehler P, Scherf KA. Comparative quantitative LC-MS/MS analysis of 13 amylase/trypsin inhibitors in ancient and modern Triticum species. Sci Rep 2020; 10:14570. [PMID: 32883982 PMCID: PMC7471314 DOI: 10.1038/s41598-020-71413-z] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/10/2020] [Indexed: 12/16/2022] Open
Abstract
Amylase/trypsin inhibitors (ATIs) are major wheat allergens and they are also implicated in causing non-celiac gluten sensitivity and worsening other inflammatory conditions. With only few studies on ATI contents in different Triticum species available so far, we developed a targeted liquid chromatography-tandem mass spectrometry (LC–MS/MS) method based on stable isotope dilution assays to quantitate the 13 most important ATIs in a well-defined sample set of eight cultivars of common wheat and durum wheat (modern species), as well as spelt, emmer and einkorn (ancient species) grown at three locations in Germany, respectively. Only few ATIs with low contents were detected in einkorn. In contrast, spelt had the highest total ATI contents. Emmer and common wheat had similar total ATI contents, with durum wheat having lower contents than common wheat. Due to the lack of correlation, it was not possible to estimate ATI contents based on crude protein contents. The wheat species had a higher influence on ATI contents than the growing location and the heritability of this trait was high. Despite comparatively low intra-species variability, some cultivars were identified that may be promising candidates for breeding for naturally low ATI contents.
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Affiliation(s)
- Sabrina Geisslitz
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Strasse 34, 85354, Freising, Germany.,Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Adenauerring 20 a, 76131, Karlsruhe, Germany
| | - C Friedrich H Longin
- State Plant Breeding Institute, University of Hohenheim, 70599, Stuttgart, Germany
| | - Peter Koehler
- biotask AG, Schelztorstrasse 54-56, 73728, Esslingen am Neckar, Germany
| | - Katharina Anne Scherf
- Leibniz-Institute for Food Systems Biology at the Technical University of Munich, Lise-Meitner-Strasse 34, 85354, Freising, Germany. .,Department of Bioactive and Functional Food Chemistry, Institute of Applied Biosciences, Karlsruhe Institute of Technology (KIT), Adenauerring 20 a, 76131, Karlsruhe, Germany.
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12
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Lin Z, Ren Y, Shi Z, Zhang K, Yang H, Liu S, Hao P. Evaluation and minimization of nonspecific tryptic cleavages in proteomic sample preparation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8733. [PMID: 32031715 DOI: 10.1002/rcm.8733] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/16/2020] [Accepted: 01/17/2020] [Indexed: 06/10/2023]
Abstract
UNLABELLED High specificity of trypsin is a prerequisite for accurate identification and quantification of proteins in shotgun proteomics. It is important to minimize nonspecific enzymatic cleavages during proteomic sample preparation. METHODS In this study, protein extraction and trypsin digestion conditions were extensively evaluated using the less-complex Escherichia coli lysates to improve the sensitivity of detecting low-abundance nonspecific peptides by liquid chromatography/tandem mass spectrometry. RESULTS Trypsin digestion buffers and digestion times were proved to have a significant effect on nonspecific cleavages. The triethylammonium bicarbonate buffer induces significantly lower nonspecific cleavages than the other two buffers, but a freshly prepared urea solution does not induce more than sodium dodecyl sulfate. Because prolonged trypsin digestion resulted in a considerable number of nonspecific cleavages, an optimized 2-h protocol was developed with 45.2% less semispecific tryptic peptides but 18.5% more unmodified peptides identified than the commonly used 16-h protocol. CONCLUSIONS The significant decrease in nonspecific cleavages and artificial modifications improves the accuracy of protein quantification and the identification of low-abundance proteins, and it is especially useful for studying protein posttranslational modifications. For trypsin digestion, the proposed 2-h protocol can potentially be a replacement for the traditional 16-h protocol.
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Affiliation(s)
| | - Yan Ren
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Zhaomei Shi
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
| | | | - Huanming Yang
- BGI-Shenzhen, Shenzhen, Guangdong, China
- James D. Watson Institute of Genome Sciences, Hangzhou, China
| | - Siqi Liu
- BGI-Shenzhen, Shenzhen, Guangdong, China
| | - Piliang Hao
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
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13
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Na CH, Sathe G, Rosenthal LS, Moghekar AR, Dawson VL, Dawson TM, Pandey A. Development of a novel method for the quantification of tyrosine 39 phosphorylated α- and β-synuclein in human cerebrospinal fluid. Clin Proteomics 2020; 17:13. [PMID: 32390785 PMCID: PMC7197159 DOI: 10.1186/s12014-020-09277-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2020] [Accepted: 04/18/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Parkinson's disease (PD) is the second most prevalent neurodegenerative disorder. Biomarkers that can help monitor the progression of PD or response to disease-modifying agents will be invaluable in making appropriate therapeutic decisions. Further, biomarkers that could be used to distinguish PD from other related disorders with PD-like symptoms will be useful for accurate diagnosis and treatment. C-Abl tyrosine kinase is activated in PD resulting in increased phosphorylation of the tyrosine residue at position 39 (Y39) of α-synuclein (α-syn) (pY39 α-syn), which contributes to the death of dopaminergic neurons. Because pY39 α-syn may be pathogenic, monitoring pY39 α-syn could allow us to diagnose presymptomatic PD and help monitor disease progression and response to treatment. We sought to investigate if increased phosphorylation of pY39 α-syn can be detected in the cerebrospinal fluid (CSF) of PD patients by targeted mass spectrometry. METHODS Here, we report a two-step enrichment method in which phosphotyrosine peptides were first enriched with an anti-phosphotyrosine antibody followed by a second round of enrichment by titanium dioxide (TiO2) beads to detect EGVLpYVGSK sequence derived from tyrosine 39 region of α- and β-synuclein (αβ-syn). Accurate quantification was achieved by adding a synthetic heavy version of pY39 αβ-syn peptide before enzymatic digestion. RESULTS Using the developed enrichment methods and optimized parallel reaction monitoring (PRM) assays, we detected pY39 αβ-syn peptide in human CSF and demonstrated that the ratio of pY39 αβ-syn to Y39 αβ-syn was significantly increased in the CSF of patients with PD. CONCLUSIONS We anticipate that this optimized two-step enrichment-based PRM detection method will help monitor c-Abl activation in PD patients and can also be used to quantify other phosphotyrosine peptides of low abundance in biological samples.
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Affiliation(s)
- Chan Hyun Na
- Neurodegeneration Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
| | - Gajanan Sathe
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
- Present Address: Center for Molecular Medicine, National Institute of Mental Health and Neurosciences (NIMHANS), Hosur Road, Bangalore, 560 029 India
| | - Liana S. Rosenthal
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Abhay R. Moghekar
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Valina L. Dawson
- Neurodegeneration Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Ted M. Dawson
- Neurodegeneration Program, Institute for Cell Engineering, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Neurology, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
- Solomon H. Snyder Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
| | - Akhilesh Pandey
- Diana Helis Henry Medical Research Foundation, New Orleans, LA 70130 USA
- Department of Biological Chemistry, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205 USA
- Manipal Academy of Higher Education (MAHE), Manipal, 576104 Karnataka India
- Present Address: Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55902 USA
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14
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van den Broek I, Mastali M, Mouapi K, Bystrom C, Bairey Merz CN, Van Eyk JE. Quality Control and Outlier Detection of Targeted Mass Spectrometry Data from Multiplex Protein Panels. J Proteome Res 2020; 19:2278-2293. [PMID: 32270680 DOI: 10.1021/acs.jproteome.9b00854] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Increased throughput as well as increased multiplexing of liquid chromatography coupled to selected reaction monitoring mass spectrometry (LC-SRM-MS) assays for protein quantification challenges routine data analysis. Despite the measurement of multiple transitions from multiple peptides, for clinical applications a single (quantifier) transition from one (quantifier) signature peptide is used to represent the protein quantity with most data used solely to validate the quantifier result. To support the generation of reliable protein results from multiplexed LC-SRM-MS assays with large sample numbers, we developed a data analysis process for quality control and outlier detection using data from an 11-protein multiplex LC-SRM-MS method for dried blood samples (195 492 chromatographic peaks from 1481 samples * 11 proteins * 2 peptides * 3 transitions * 2 isotopologues). The 2-tiered data analysis process detects outliers for ion transition ratio, peptide ratio, and % difference between duplicates, applying less stringent criteria to samples with a small % difference between duplicates (Tier 1) and more stringent criteria to samples with unassessed or a large % difference between duplicates (Tier 2). After manual peak review, 1127 samples (76%) were selected based on the sample quality. The data analysis process thereafter automatically selected quantifier transitions/peptides, removed quality control failures and outliers (8%), averaged duplicates, and generated a comprehensive report listing 6085 quality controlled protein-level results. The proposed data analysis process serves as a starting point toward standardized data analysis of multiplexed LC-SRM-MS protein assays.
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Affiliation(s)
- Irene van den Broek
- Cedars-Sinai Precision Biomarker Laboratories, Cedars-Sinai Medical Center, 127 S. San Vicente Blvd., Pavilion, 9th Floor, Los Angeles, California 90048, United States
| | - Mitra Mastali
- Cedars-Sinai Precision Biomarker Laboratories, Cedars-Sinai Medical Center, 127 S. San Vicente Blvd., Pavilion, 9th Floor, Los Angeles, California 90048, United States.,Advanced Clinical BioSystems Research Institute, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Kelly Mouapi
- Advanced Clinical BioSystems Research Institute, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Cory Bystrom
- Cedars-Sinai Precision Biomarker Laboratories, Cedars-Sinai Medical Center, 127 S. San Vicente Blvd., Pavilion, 9th Floor, Los Angeles, California 90048, United States
| | - C Noel Bairey Merz
- Barbra Streisand Women's Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
| | - Jennifer E Van Eyk
- Cedars-Sinai Precision Biomarker Laboratories, Cedars-Sinai Medical Center, 127 S. San Vicente Blvd., Pavilion, 9th Floor, Los Angeles, California 90048, United States.,Advanced Clinical BioSystems Research Institute, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States.,Barbra Streisand Women's Heart Center, The Smidt Heart Institute, Cedars-Sinai Medical Center, Los Angeles, California 90048, United States
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15
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Hober A, Edfors F, Ryaboshapkina M, Malmqvist J, Rosengren L, Percy AJ, Lind L, Forsström B, Uhlén M, Oscarsson J, Miliotis T. Absolute Quantification of Apolipoproteins Following Treatment with Omega-3 Carboxylic Acids and Fenofibrate Using a High Precision Stable Isotope-labeled Recombinant Protein Fragments Based SRM Assay. Mol Cell Proteomics 2019; 18:2433-2446. [PMID: 31591263 PMCID: PMC6885709 DOI: 10.1074/mcp.ra119.001765] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Indexed: 11/20/2022] Open
Abstract
Stable isotope-labeled standard (SIS) peptides are used as internal standards in targeted proteomics to provide robust protein quantification, which is required in clinical settings. However, SIS peptides are typically added post trypsin digestion and, as the digestion efficiency can vary significantly between peptides within a protein, the accuracy and precision of the assay may be compromised. These drawbacks can be remedied by a new class of internal standards introduced by the Human Protein Atlas project, which are based on SIS recombinant protein fragments called SIS PrESTs. SIS PrESTs are added initially to the sample and SIS peptides are released on trypsin digestion. The SIS PrEST technology is promising for absolute quantification of protein biomarkers but has not previously been evaluated in a clinical setting. An automated and scalable solid phase extraction workflow for desalting and enrichment of plasma digests was established enabling simultaneous preparation of up to 96 samples. Robust high-precision quantification of 13 apolipoproteins was achieved using a novel multiplex SIS PrEST-based LC-SRM/MS Tier 2 assay in non-depleted human plasma. The assay exhibited inter-day coefficients of variation between 1.5% and 14.5% (median = 3.5%) and was subsequently used to investigate the effects of omega-3 carboxylic acids (OM3-CA) and fenofibrate on these 13 apolipoproteins in human plasma samples from a randomized placebo-controlled trial, EFFECT I (NCT02354976). No significant changes were observed in the OM3-CA arm, whereas treatment with fenofibrate significantly increased apoAII and reduced apoB, apoCI, apoE and apoCIV levels. The reduction in apoCIV following fenofibrate treatment is a novel finding. The study demonstrates that SIS PrESTs can facilitate the generation of robust multiplexed biomarker Tier 2 assays for absolute quantification of proteins in clinical studies.
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Affiliation(s)
- Andreas Hober
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden; Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Fredrik Edfors
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden; Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Maria Ryaboshapkina
- Translational Science, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Jonas Malmqvist
- Translational Science, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Louise Rosengren
- Translational Science, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Andrew J Percy
- Department of Applications Development, Cambridge Isotope Laboratories, Inc., Tewksbury, MA 01876
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Björn Forsström
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden; Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Mathias Uhlén
- Science for Life Laboratory, KTH - Royal Institute of Technology, Stockholm, Sweden; Department of Protein Science, KTH - Royal Institute of Technology, Stockholm, Sweden
| | - Jan Oscarsson
- Global Medicines Development, Cardiovascular, Renal and Metabolism, AstraZeneca, Gothenburg, Sweden
| | - Tasso Miliotis
- Translational Science, Cardiovascular, Renal and Metabolism, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden.
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16
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Toth CA, Kuklenyik Z, Barr JR. Nuts and Bolts of Protein Quantification by Online Trypsin Digestion Coupled LC-MS/MS Analysis. Methods Mol Biol 2019; 1871:295-311. [PMID: 30276747 DOI: 10.1007/978-1-4939-8814-3_19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/14/2023]
Abstract
Protein digestion coupled to liquid chromatography and tandem mass spectrometry (LC-MS/MS) detection enables multiplexed quantification of proteins in complex biological matrices. However, the reproducibility of enzymatic digestion of proteins to produce proteotypic target peptides is a major limiting factor of assay precision. Online digestion using immobilized trypsin addresses this problem through precise control of digestion conditions and time. Because online digestion is typically for a short time, the potential for peptide degradation, a major source of measurement bias, is significantly reduced. Online proteolysis requires minimal sample preparation and is easily coupled to LC-MS/MS systems, further reducing potential method variability. We describe herein a method optimized for the multiplexed quantification of several apolipoproteins in human serum using on-column digestion. We highlight key features of the method that enhance assay accuracy and precision. These include the use of value-assigned serum as calibrators and stable isotope-labeled (SIL) peptide analogs as internal standards. We also comment on practical aspects of column switching valve design, instrument maintenance, tandem mass spectrometry data acquisition, and data processing.
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Affiliation(s)
- Christopher A Toth
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| | - Zsuzsanna Kuklenyik
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - John R Barr
- Division of Laboratory Sciences, Centers for Disease Control and Prevention, Atlanta, GA, USA
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17
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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: 6] [Impact Index Per Article: 1.2] [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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18
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Shi J, Zheng YZ, Sin DD, DeMarco ML. A Streamlined Method for Quantification of Apolipoprotein A1 in Human Plasma by LC-MS/MS. Clin Chem 2018; 64:1782-1784. [DOI: 10.1373/clinchem.2018.293530] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Junyan Shi
- Department of Pathology and Laboratory Medicine University of British Columbia Vancouver, Canada
| | - Yu Zi Zheng
- Department of Pathology and Laboratory Medicine University of British Columbia Vancouver, Canada
| | - Don D Sin
- Centre for Heart Lung Innovation St Paul's Hospital and Department of Medicine (Division of Respiratory 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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19
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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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20
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Rappold BA. Special Considerations for Liquid Chromatography–Tandem Mass Spectrometry Method Development. Clin Lab Med 2018; 38:539-551. [DOI: 10.1016/j.cll.2018.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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21
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Haghighi F, Talebpour Z, Nezhad AS. Towards fully integrated liquid chromatography on a chip: Evolution and evaluation. Trends Analyt Chem 2018. [DOI: 10.1016/j.trac.2018.05.002] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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22
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Bowers JJ, Gunawardena HP, Cornu A, Narvekar AS, Richieu A, Deffieux D, Quideau S, Tharayil N. Rapid Screening of Ellagitannins in Natural Sources via Targeted Reporter Ion Triggered Tandem Mass Spectrometry. Sci Rep 2018; 8:10399. [PMID: 29991731 PMCID: PMC6039434 DOI: 10.1038/s41598-018-27708-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 05/17/2018] [Indexed: 12/18/2022] Open
Abstract
Complex biomolecules present in their natural sources have been difficult to analyze using traditional analytical approaches. Ultrahigh-performance liquid chromatography (UHPLC-MS/MS) methods have the potential to enhance the discovery of a less well characterized and challenging class of biomolecules in plants, the ellagitannins. We present an approach that allows for the screening of ellagitannins by employing higher energy collision dissociation (HCD) to generate reporter ions for classification and collision-induced dissociation (CID) to generate unique fragmentation spectra for isomeric variants of previously unreported species. Ellagitannin anions efficiently form three characteristic reporter ions after HCD fragmentation that allows for the classification of unknown precursors that we call targeted reporter ion triggering (TRT). We demonstrate how a tandem HCD-CID experiment might be used to screen natural sources using UHPLC-MS/MS by application of 22 method conditions from which an optimized data-dependent acquisition (DDA) emerged. The method was verified not to yield false-positive results in complex plant matrices. We were able to identify 154 non-isomeric ellagitannins from strawberry leaves, which is 17 times higher than previously reported in the same matrix. The systematic inclusion of CID spectra for isomers of each species classified as an ellagitannin has never been possible before the development of this approach.
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Affiliation(s)
- Jeremiah J Bowers
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29631, USA
| | - Harsha P Gunawardena
- Janssen Research and Development, The Janssen Pharmaceutical Companies of Johnson and Johnson, Spring House, PA, 19477, USA
| | - Anaëlle Cornu
- University Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Ashwini S Narvekar
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29631, USA
| | - Antoine Richieu
- University Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Denis Deffieux
- University Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Stéphane Quideau
- University Bordeaux, ISM (CNRS-UMR 5255), 351 cours de la Libération, 33405, Talence Cedex, France
| | - Nishanth Tharayil
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC, 29631, USA.
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Zhang X, Dominguez PG, Kumar M, Bygdell J, Miroshnichenko S, Sundberg B, Wingsle G, Niittylä T. Cellulose Synthase Stoichiometry in Aspen Differs from Arabidopsis and Norway Spruce. PLANT PHYSIOLOGY 2018; 177:1096-1107. [PMID: 29760198 PMCID: PMC6053019 DOI: 10.1104/pp.18.00394] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 05/03/2018] [Indexed: 05/02/2023]
Abstract
Cellulose is synthesized at the plasma membrane by cellulose synthase complexes (CSCs) containing cellulose synthases (CESAs). Genetic analysis and CESA isoform quantification indicate that cellulose in the secondary cell walls of Arabidopsis (Arabidopsis thaliana) is synthesized by isoforms CESA4, CESA7, and CESA8 in equimolar amounts. Here, we used quantitative proteomics to investigate whether the CSC model based on Arabidopsis secondary cell wall CESA stoichiometry can be applied to the angiosperm tree aspen (Populus tremula) and the gymnosperm tree Norway spruce (Picea abies). In the developing xylem of aspen, the secondary cell wall CESA stoichiometry was 3:2:1 for PtCESA8a/b:PtCESA4:PtCESA7a/b, while in Norway spruce, the stoichiometry was 1:1:1, as observed previously in Arabidopsis. Furthermore, in aspen tension wood, the secondary cell wall CESA stoichiometry changed to 8:3:1 for PtCESA8a/b:PtCESA4:PtCESA7a/b. PtCESA8b represented 73% of the total secondary cell wall CESA pool, and quantitative polymerase chain reaction analysis of CESA transcripts in cryosectioned tension wood revealed increased PtCESA8b expression during the formation of the cellulose-enriched gelatinous layer, while the transcripts of PtCESA4, PtCESA7a/b, and PtCESA8a decreased. A wide-angle x-ray scattering analysis showed that the shift in CESA stoichiometry in tension wood coincided with an increase in crystalline cellulose microfibril diameter, suggesting that the CSC CESA composition influences microfibril properties. The aspen CESA stoichiometry results raise the possibility of alternative CSC models and suggest that homomeric PtCESA8b complexes are responsible for cellulose biosynthesis in the gelatinous layer in tension wood.
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Affiliation(s)
- Xueyang Zhang
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
| | - Pia Guadalupe Dominguez
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
| | - Manoj Kumar
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
- Faculty of Life Sciences, University of Manchester, Manchester M13 9PT, United Kingdom
| | - Joakim Bygdell
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
| | - Sergey Miroshnichenko
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
| | - Björn Sundberg
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
| | - Gunnar Wingsle
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
| | - Totte Niittylä
- Umeå Plant Science Centre, Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE 901 83 Umea, Sweden
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Vildhede A, Kimoto E, Rodrigues AD, Varma MVS. Quantification of Hepatic Organic Anion Transport Proteins OAT2 and OAT7 in Human Liver Tissue and Primary Hepatocytes. Mol Pharm 2018; 15:3227-3235. [PMID: 29906129 DOI: 10.1021/acs.molpharmaceut.8b00320] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Organic anion transporter (OAT) 2 and OAT7 were recently shown to be involved in the hepatic uptake of drugs; however, there is limited understanding of the population variability in the expression of these transporters in liver. There is also a need to derive relative expression-based scaling factors (REFs) that can be used to bridge in vitro functional data to the in vivo drug disposition. To this end, we quantified OAT2 and OAT7 surrogate peptide abundance in a large number of human liver tissue samples ( n = 52), as well as several single-donor cryopreserved human hepatocyte lots ( n = 30) by a novel, validated liquid chromatography tandem mass spectrometry (LC-MS/MS) method. The average surrogate peptide expression of OAT2 and OAT7 in the liver samples was 1.52 ± 0.57 and 4.63 ± 1.58 fmol/μg membrane protein, respectively. While we noted statistically significant differences ( p < 0.05) in hepatocyte and liver tissue abundances for both OAT2 and OAT7, the differences were relatively small (1.8- and 1.5-fold difference in median values, respectively). Large interindividual variability was noted in the hepatic expression of OAT2 (16-fold in liver tissue and 23-fold in hepatocytes). OAT7, on the other hand, showed less interindividual variability (4-fold) in the livers, but high variability for the hepatocyte lots (27-fold). A significant positive correlation in OAT2 and OAT7 expression was observed, but expression levels were neither associated with age nor sex. In conclusion, our data suggest marked interindividual variability in the hepatic expression of OAT2/7, which may contribute to the pharmacokinetic variability of their substrates. Because both transporters were less abundant in hepatocytes than livers, a REF-based approach is recommended when scaling in vitro hepatocyte transport data to predict hepatic drug clearance and liver exposure of OAT2/7 substrates.
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Affiliation(s)
- Anna Vildhede
- Pharmacokinetics, Dynamics and Metabolism, Medicine Design , Pfizer Worldwide R&D , Groton , Connecticut 06340 , United States
| | - Emi Kimoto
- Pharmacokinetics, Dynamics and Metabolism, Medicine Design , Pfizer Worldwide R&D , Groton , Connecticut 06340 , United States
| | - A David Rodrigues
- Pharmacokinetics, Dynamics and Metabolism, Medicine Design , Pfizer Worldwide R&D , Groton , Connecticut 06340 , United States
| | - Manthena V S Varma
- Pharmacokinetics, Dynamics and Metabolism, Medicine Design , Pfizer Worldwide R&D , Groton , Connecticut 06340 , United States
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25
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Dittrich J, Adam M, Maas H, Hecht M, Reinicke M, Ruhaak LR, Cobbaert C, Engel C, Wirkner K, Löffler M, Thiery J, Ceglarek U. Targeted On-line SPE-LC-MS/MS Assay for the Quantitation of 12 Apolipoproteins from Human Blood. Proteomics 2018; 18. [PMID: 29280342 DOI: 10.1002/pmic.201700279] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Revised: 12/01/2017] [Indexed: 12/22/2022]
Abstract
Laborious sample pretreatment of biological samples represents the most limiting factor for the translation of targeted proteomics assays from research to clinical routine. An optimized method for the simultaneous quantitation of 12 major apolipoproteins (apos) combining on-line SPE and fast LC-MS/MS analysis in 6.5 min total run time was developed, reducing the manual sample pretreatment time of 3 μL serum or plasma by 60%. Within-run and between-day imprecisions below 10 and 15% (n = 10) and high recovery rates (94-131%) were obtained applying the high-throughput setup. High-quality porcine trypsin was used, which outperformed cost-effective bovine trypsin regarding digestion efficiency. Comparisons with immunoassays and another LC-MS/MS assay demonstrated good correlation (Pearson's R: 0.81-0.98). Further, requirements on sample quality concerning sampling, processing, and long-term storage up to 1 year were investigated revealing significant influences of the applied sampling material and coagulant on quantitation results. Apo profiles of 1339 subjects of the LIFE-Adult-Study were associated with lifestyle and physiological parameters as well as establish parameters of lipid metabolism (e.g., triglycerides, cholesterol). Besides gender effects, most significant impact was seen regarding lipid-lowering medication. In conclusion, this novel highly standardized, high-throughput targeted proteomics assay utilizes a fast, simultaneous analysis of 12 apos from least sample amounts.
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Affiliation(s)
- Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany.,LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Melanie Adam
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Hilke Maas
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Max Hecht
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - Madlen Reinicke
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany
| | - L Renee Ruhaak
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Christa Cobbaert
- Department of Clinical Chemistry and Laboratory Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Christoph Engel
- LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany.,Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
| | - Kerstin Wirkner
- LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Markus Löffler
- LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany.,Institute for Medical Informatics, Statistics and Epidemiology, Leipzig University, Leipzig, Germany
| | - Joachim Thiery
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany.,LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
| | - Uta Ceglarek
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany.,LIFE, Leipzig Research Center for Civilization Diseases, Leipzig University, Leipzig, Germany
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26
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Oeckl P, Steinacker P, Otto M. Comparison of Internal Standard Approaches for SRM Analysis of Alpha-Synuclein in Cerebrospinal Fluid. J Proteome Res 2017; 17:516-523. [PMID: 29183121 DOI: 10.1021/acs.jproteome.7b00660] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Absolute protein quantification by selected reaction monitoring (SRM, also MRM) is an alternative to immunoassays, and the gold standard here is the addition of stable-isotope labeled (SIL) proteins (PSAQ). Cerebrospinal fluid (CSF) is the preferred source of biomarkers for neurological diseases, and recent improvements in mass spectrometry enable the quantification of disease-relevant proteins in CSF. We used alpha-synuclein SRM to investigate alternatives to the PSAQ approach in human CSF regarding precision and accuracy, including SIL peptides, winged SIL (WiSIL) peptides, and quantitative protein epitope signature tags (QPrESTs). All approaches yielded precise results in CSF with CV values <15% in several runs for all four measured peptides. PSAQ and QPrEST also showed good accuracy (deviation ≤15%), whereas SIL and WiSIL peptides yielded deviations up to 54% that greatly depended on the measured peptide. Total protein concentration in CSF did not affect precision and accuracy. Thus, our study indicates that all four approaches are suitable for relative quantification of alpha-synuclein in CSF. QPrESTs are a valuable alternative to PSAQ in terms of precision and accuracy, although SIL and WiSIL peptides can yield accurate results as well when peptides are selected consciously.
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Affiliation(s)
- Patrick Oeckl
- Department of Neurology, Ulm University Hospital , D-89081 Ulm, Germany
| | - Petra Steinacker
- Department of Neurology, Ulm University Hospital , D-89081 Ulm, Germany
| | - Markus Otto
- Department of Neurology, Ulm University Hospital , D-89081 Ulm, Germany
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27
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Fu Q, Kowalski MP, Mastali M, Parker SJ, Sobhani K, van den Broek I, Hunter CL, Van Eyk JE. Highly Reproducible Automated Proteomics Sample Preparation Workflow for Quantitative Mass Spectrometry. J Proteome Res 2017; 17:420-428. [PMID: 29083196 DOI: 10.1021/acs.jproteome.7b00623] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Sample preparation for protein quantification by mass spectrometry requires multiple processing steps including denaturation, reduction, alkylation, protease digestion, and peptide cleanup. Scaling these procedures for the analysis of numerous complex biological samples can be tedious and time-consuming, as there are many liquid transfer steps and timed reactions where technical variations can be introduced and propagated. We established an automated sample preparation workflow with a total processing time for 96 samples of 5 h, including a 2 h incubation with trypsin. Peptide cleanup is accomplished by online diversion during the LC/MS/MS analysis. In a selected reaction monitoring (SRM) assay targeting 6 plasma biomarkers and spiked β-galactosidase, mean intraday and interday cyclic voltammograms (CVs) for 5 serum and 5 plasma samples over 5 days were <20%. In a highly multiplexed SRM assay targeting more than 70 proteins, 90% of the transitions from 6 plasma samples repeated on 3 separate days had total CVs below 20%. Similar results were obtained when the workflow was transferred to a second site: 93% of peptides had CVs below 20%. An automated trypsin digestion workflow yields uniformly processed samples in less than 5 h. Reproducible quantification of peptides was observed across replicates, days, instruments, and laboratory sites, demonstrating the broad applicability of this approach.
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Affiliation(s)
- Qin Fu
- Advanced Clinical Biosystems Institute, Heart Institute, Cedars Sinai Medical Center , Los Angeles, California 90048, United States
| | - Michael P Kowalski
- Beckman Coulter Life Sciences, Indianapolis, Indiana 46268, United States
| | - Mitra Mastali
- Advanced Clinical Biosystems Institute, Heart Institute, Cedars Sinai Medical Center , Los Angeles, California 90048, United States
| | - Sarah J Parker
- Advanced Clinical Biosystems Institute, Heart Institute, Cedars Sinai Medical Center , Los Angeles, California 90048, United States
| | - Kimia Sobhani
- Pathology and Laboratory Medicine, Cedars Sinai Medical Center , Los Angeles, California 90048, United States
| | - Irene van den Broek
- Advanced Clinical Biosystems Institute, Heart Institute, Cedars Sinai Medical Center , Los Angeles, California 90048, United States
| | | | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Institute, Heart Institute, Cedars Sinai Medical Center , Los Angeles, California 90048, United States
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28
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van den Broek I, Sobhani K, Van Eyk JE. Advances in quantifying apolipoproteins using LC-MS/MS technology: implications for the clinic. Expert Rev Proteomics 2017; 14:869-880. [PMID: 28870113 DOI: 10.1080/14789450.2017.1374859] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
INTRODUCTION Apolipoproteins play a key role in pre-, pro-, and anti-atherosclerotic processes and have become important circulating biomarkers for the prediction of cardiovascular disease (CVD) risk. Whereas currently clinical immunoassays are not available for most apolipoproteins and lack the capacity for multiplexing, liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) allows simultaneous, highly-specific, and precise quantification of multiple apolipoproteins. Areas covered: We discuss LC-MS/MS methods for quantification of apolipoproteins reported in the literature and highlight key requirements for clinical use. Besides the advances in sample preparation and LC-MS/MS technologies, this overview also discusses advances in proteoform analysis and applications of dried blood/plasma collection. Expert commentary: Standardized quantification using LC-MS/MS technology has been demonstrated for apolipoprotein A-I and B. However, for implementation in clinical CVD risk assessment, LC-MS/MS must bring significant added clinical value in comparison to fast, standardized, and straightforward clinical (immuno)assays. Ongoing advances in accuracy and multiplexing capacity of LC-MS/MS, nonetheless, bear potential to enable standardized and interpretable personalized profiling of a patient's CVD risk by simultaneous quantification of multiple apolipoproteins and -variants. We, moreover, anticipate further personalization of CVD risk assessment by the potential of LC-MS/MS to enable simultaneous genotyping and remote monitoring using dried blood/plasma collection devices.
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Affiliation(s)
- Irene van den Broek
- a Cedars-Sinai Medical Center, The Advanced Clinical Biosystems Research Institute , The Heart Institute , Los Angeles , CA , USA
| | - Kimia Sobhani
- b Department of Pathology and Laboratory Medicine , Cedars-Sinai Medical Center , Los Angeles , CA , USA
| | - Jennifer E Van Eyk
- a Cedars-Sinai Medical Center, The Advanced Clinical Biosystems Research Institute , The Heart Institute , Los Angeles , CA , USA
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29
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Absolute Quantification of Middle- to High-Abundant Plasma Proteins via Targeted Proteomics. Methods Mol Biol 2017. [PMID: 28674901 DOI: 10.1007/978-1-4939-7057-5_29] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The increasing number of peptide and protein biomarker candidates requires expeditious and reliable quantification strategies. The utilization of liquid chromatography coupled to quadrupole tandem mass spectrometry (LC-MS/MS) for the absolute quantitation of plasma proteins and peptides facilitates the multiplexed verification of tens to hundreds of biomarkers from smallest sample quantities. Targeted proteomics assays derived from bottom-up proteomics principles rely on the identification and analysis of proteotypic peptides formed in an enzymatic digestion of the target protein. This protocol proposes a procedure for the establishment of a targeted absolute quantitation method for middle- to high-abundant plasma proteins waiving depletion or enrichment steps. Essential topics as proteotypic peptide identification and LC-MS/MS method development as well as sample preparation and calibration strategies are described in detail.
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30
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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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31
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A workflow for absolute quantitation of large therapeutic proteins in biological samples at intact level using LC-HRMS. Bioanalysis 2016; 8:1679-91. [DOI: 10.4155/bio-2016-0096] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Aim: The commonly used LC–MS workflow to quantify protein therapeutics in biological samples is ‘bottom-up’ approach. In this study, the aim is to establish ‘top-down’ approach for absolute quantitation of therapeutic antibodies or proteins of similar sizes in biological samples at intact level. Materials & methods: Using a recombinant human monoclonal antibody as the model molecule, we present a workflow to measure large therapeutic proteins in plasma at intact level based on deconvoluted high-resolution MS (HRMS) peaks. A novel MultiQuant™ software function was developed to automatically deconvolute the peaks and process the data. Results & conclusion: The workflow showed satisfying performance. This is a proof of concept study demonstrating the feasibility of bioanalysis of large therapeutic proteins at intact level using LC-HRMS.
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32
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Hoofnagle AN, Whiteaker JR, Carr SA, Kuhn E, Liu T, Massoni SA, Thomas SN, Townsend RR, Zimmerman LJ, Boja E, Chen J, Crimmins DL, Davies SR, Gao Y, Hiltke TR, Ketchum KA, Kinsinger CR, Mesri M, Meyer MR, Qian WJ, Schoenherr RM, Scott MG, Shi T, Whiteley GR, Wrobel JA, Wu C, Ackermann BL, Aebersold R, Barnidge DR, Bunk DM, Clarke N, Fishman JB, Grant RP, Kusebauch U, Kushnir MM, Lowenthal MS, Moritz RL, Neubert H, Patterson SD, Rockwood AL, Rogers J, Singh RJ, Van Eyk JE, Wong SH, Zhang S, Chan DW, Chen X, Ellis MJ, Liebler DC, Rodland KD, Rodriguez H, Smith RD, Zhang Z, Zhang H, Paulovich AG. Recommendations for the Generation, Quantification, Storage, and Handling of Peptides Used for Mass Spectrometry-Based Assays. Clin Chem 2016; 62:48-69. [PMID: 26719571 DOI: 10.1373/clinchem.2015.250563] [Citation(s) in RCA: 151] [Impact Index Per Article: 18.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND For many years, basic and clinical researchers have taken advantage of the analytical sensitivity and specificity afforded by mass spectrometry in the measurement of proteins. Clinical laboratories are now beginning to deploy these work flows as well. For assays that use proteolysis to generate peptides for protein quantification and characterization, synthetic stable isotope-labeled internal standard peptides are of central importance. No general recommendations are currently available surrounding the use of peptides in protein mass spectrometric assays. CONTENT The Clinical Proteomic Tumor Analysis Consortium of the National Cancer Institute has collaborated with clinical laboratorians, peptide manufacturers, metrologists, representatives of the pharmaceutical industry, and other professionals to develop a consensus set of recommendations for peptide procurement, characterization, storage, and handling, as well as approaches to the interpretation of the data generated by mass spectrometric protein assays. Additionally, the importance of carefully characterized reference materials-in particular, peptide standards for the improved concordance of amino acid analysis methods across the industry-is highlighted. The alignment of practices around the use of peptides and the transparency of sample preparation protocols should allow for the harmonization of peptide and protein quantification in research and clinical care.
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Affiliation(s)
| | | | | | | | - Tao Liu
- Pacific Northwest National Laboratory, Richland, WA
| | | | | | | | | | | | - Jing Chen
- Johns Hopkins University, Baltimore, MD
| | | | | | - Yuqian Gao
- Pacific Northwest National Laboratory, Richland, WA
| | | | | | | | | | | | - Wei-Jun Qian
- Pacific Northwest National Laboratory, Richland, WA
| | | | | | - Tujin Shi
- Pacific Northwest National Laboratory, Richland, WA
| | | | - John A Wrobel
- University of North Carolina School of Medicine, Chapel Hill, NC
| | - Chaochao Wu
- Pacific Northwest National Laboratory, Richland, WA
| | | | - Ruedi Aebersold
- Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | | | | | | | - Russ P Grant
- Laboratory Corporation of America Holdings, Inc., Burlington, NC
| | | | - Mark M Kushnir
- University of Utah and ARUP Laboratories, Salt Lake City, UT
| | | | | | | | | | - Alan L Rockwood
- University of Utah and ARUP Laboratories, Salt Lake City, UT
| | | | | | | | | | | | | | - Xian Chen
- University of North Carolina School of Medicine, Chapel Hill, NC
| | | | | | | | | | | | | | - Hui Zhang
- Johns Hopkins University, Baltimore, MD
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33
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Schafer MJ, Atkinson EJ, Vanderboom PM, Kotajarvi B, White TA, Moore MM, Bruce CJ, Greason KL, Suri RM, Khosla S, Miller JD, Bergen HR, LeBrasseur NK. Quantification of GDF11 and Myostatin in Human Aging and Cardiovascular Disease. Cell Metab 2016; 23:1207-1215. [PMID: 27304512 PMCID: PMC4913514 DOI: 10.1016/j.cmet.2016.05.023] [Citation(s) in RCA: 162] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/15/2015] [Revised: 04/01/2016] [Accepted: 05/31/2016] [Indexed: 01/08/2023]
Abstract
Growth and differentiation factor 11 (GDF11) is a transforming growth factor β superfamily member with a controversial role in aging processes. We have developed a highly specific LC-MS/MS assay to quantify GDF11, resolved from its homolog, myostatin (MSTN), based on unique amino acid sequence features. Here, we demonstrate that MSTN, but not GDF11, declines in healthy men throughout aging. Neither GDF11 nor MSTN levels differ as a function of age in healthy women. In an independent cohort of older adults with severe aortic stenosis, we show that individuals with higher GDF11 were more likely to be frail and have diabetes or prior cardiac conditions. Following valve replacement surgery, higher GDF11 at surgical baseline was associated with rehospitalization and multiple adverse events. Cumulatively, our results show that GDF11 levels do not decline throughout aging but are associated with comorbidity, frailty, and greater operative risk in older adults with cardiovascular disease.
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Affiliation(s)
- Marissa J Schafer
- Robert and Arlene Kogod Center on Aging, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Department of Physical Medicine and Rehabilitation, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Elizabeth J Atkinson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Patrick M Vanderboom
- Medical Genome Facility-Proteomics Core, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Brian Kotajarvi
- Center for Clinical and Translational Sciences, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Thomas A White
- Robert and Arlene Kogod Center on Aging, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Matthew M Moore
- Center for Innovation, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Charles J Bruce
- Division of Cardiovascular Diseases, Department of Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Kevin L Greason
- Division of Cardiovascular Surgery, Department of Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Rakesh M Suri
- Division of Cardiovascular Surgery, Department of Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Sundeep Khosla
- Robert and Arlene Kogod Center on Aging, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Center for Clinical and Translational Sciences, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Division of Endocrinology, Department of Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Jordan D Miller
- Robert and Arlene Kogod Center on Aging, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Division of Cardiovascular Surgery, Department of Medicine, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - H Robert Bergen
- Medical Genome Facility-Proteomics Core, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Department of Biochemistry and Molecular Biology, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Nathan K LeBrasseur
- Robert and Arlene Kogod Center on Aging, Mayo Clinic College of Medicine, Rochester, MN 55905, USA; Department of Physical Medicine and Rehabilitation, Mayo Clinic College of Medicine, Rochester, MN 55905, USA.
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Kito K, Okada M, Ishibashi Y, Okada S, Ito T. A strategy for absolute proteome quantification with mass spectrometry by hierarchical use of peptide-concatenated standards. Proteomics 2016; 16:1457-73. [DOI: 10.1002/pmic.201500414] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2015] [Revised: 02/18/2016] [Accepted: 03/24/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Keiji Kito
- Department of Life Sciences, School of Agriculture; Meiji University; Kawasaki Japan
| | - Mitsuhiro Okada
- Department of Life Sciences, School of Agriculture; Meiji University; Kawasaki Japan
| | - Yuko Ishibashi
- Department of Life Sciences, School of Agriculture; Meiji University; Kawasaki Japan
| | - Satoshi Okada
- Department of Biochemistry; Kyushu University Graduate School of Medical Science; Fukuoka Japan
| | - Takashi Ito
- Department of Biochemistry; Kyushu University Graduate School of Medical Science; Fukuoka Japan
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35
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Henderson CM, Lutsey PL, Misialek JR, Laha TJ, Selvin E, Eckfeldt JH, Hoofnagle AN. Measurement by a Novel LC-MS/MS Methodology Reveals Similar Serum Concentrations of Vitamin D-Binding Protein in Blacks and Whites. Clin Chem 2016; 62:179-87. [PMID: 26453697 PMCID: PMC4698095 DOI: 10.1373/clinchem.2015.244541] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 08/28/2015] [Indexed: 12/20/2022]
Abstract
BACKGROUND Vitamin D deficiency is associated with poor bone health and other adverse health outcomes; however, the associations are greatly attenuated in black vs white individuals. One possible explanation for this attenuation is different concentrations of bioavailable vitamin D metabolites in plasma, which are estimated with equations that include the total concentration of vitamin D binding globulin (VDBG) and haplotype-specific dissociation constants. METHODS We developed a method to quantify VDBG with LC-MS/MS that could also identify the haplotypes/isoforms of VDBG present. We validated the method according to recent recommendations for publications of biomarker studies. We determined serum VDBG concentrations in samples from the Atherosclerosis Risk in Communities cohort and compared the results with a widely used monoclonal immunoassay. RESULTS With 10 μL of serum or plasma, the lower limit of quantification for the assay (<20% CV) was 71 μg/mL. The assay was linear from 62 to 434 μg/mL, with total imprecision of 7.3-9.0% CV at approximately 250 μg/mL. Significant hemolysis interfered with quantification. The identification of isoforms was 97% concordant with genotyping (κ coefficient). Method comparison with immunoassay revealed significant isoform-specific effects in the immunoassay. Mean concentrations (SD) of VDBG by mass spectrometry were similar in whites and blacks [262 (25) vs 266 (35) μg/mL, respectively; P = 0.43]. CONCLUSIONS Validated mass spectrometric methods for the quantification of proteins in human samples can provide additional information beyond immunoassay. Counter to prior observations by immunoassay, VDBG concentrations did not vary by race.
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Affiliation(s)
| | | | | | | | - Elizabeth Selvin
- Department of Epidemiology and the Welch Center for Prevention, Epidemiology and Clinical Research, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - John H Eckfeldt
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine and Department of Medicine, University of Washington, Seattle, WA;
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Fu Q, Grote E, Zhu J, Jelinek C, Köttgen A, Coresh J, Van Eyk JE. An Empirical Approach to Signature Peptide Choice for Selected Reaction Monitoring: Quantification of Uromodulin in Urine. Clin Chem 2015; 62:198-207. [PMID: 26589548 DOI: 10.1373/clinchem.2015.242495] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Accepted: 11/03/2015] [Indexed: 02/01/2023]
Abstract
BACKGROUND Many avenues have been proposed for a seamless transition between biomarker discovery data and selected reaction monitoring (SRM) assays for biomarker validation. Unfortunately, studies with the abundant urinary protein uromodulin have shown that these methods do not converge on a consistent set of surrogate peptides for targeted mass spectrometry. As an alternative, we present an empirical peptide selection work flow for robust protein quantification. METHODS We compared the relative SRM signal intensity of 12 uromodulin-derived peptides between tryptic digests of 9 urine samples. Pairwise CVs between the 12 peptides were 0.19-0.99. We used a correlation matrix to identify peptides that reproducibly tracked the amount of uromodulin protein and selected 4 peptides with robust and highly correlated SRM signals. Absolute quantification was performed with stable isotope-labeled versions of these peptides as internal standards and a standard curve prepared from a tryptic digest of purified uromodulin. RESULTS Absolute quantification of uromodulin in 40 clinical urine samples yielded interpeptide correlations of ≥0.984 and correlations of ≥0.912 with ELISA data. The SRM assays were linear over >3 orders of magnitude and had typical interdigest CVs of <10%, interinjection CVs of <7%, and intertransition CVs of <7%. CONCLUSIONS Comparing the apparent abundance of a plurality of peptides derived from the same target protein makes it possible to select signature peptides that are unaffected by the unpredictable confounding factors inevitably present in biological samples.
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Affiliation(s)
- Qin Fu
- Advanced Clinical Biosystems Research Institute, The Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA;
| | - Eric Grote
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Jie Zhu
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Christine Jelinek
- Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD
| | - Anna Köttgen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD; Renal Division, Medical Center, University of Freiburg, Freiburg, Germany
| | - Josef Coresh
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Jennifer E Van Eyk
- Advanced Clinical Biosystems Research Institute, The Heart Institute, Cedars Sinai Medical Center, Los Angeles, CA; Department of Medicine, School of Medicine, Johns Hopkins University, Baltimore, MD
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37
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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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38
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Looße C, Galozzi S, Debor L, Julsing MK, Bühler B, Schmid A, Barkovits K, Müller T, Marcus K. Direct infusion-SIM as fast and robust method for absolute protein quantification in complex samples. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
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39
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Absolute quantification of γH2AX using liquid chromatography–triple quadrupole tandem mass spectrometry. Anal Bioanal Chem 2015; 407:5521-7. [DOI: 10.1007/s00216-015-8725-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/16/2015] [Accepted: 04/17/2015] [Indexed: 01/13/2023]
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40
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Heikkinen AT, Lignet F, Cutler P, Parrott N. The role of quantitative ADME proteomics to support construction of physiologically based pharmacokinetic models for use in small molecule drug development. Proteomics Clin Appl 2015; 9:732-44. [DOI: 10.1002/prca.201400147] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2014] [Revised: 01/16/2015] [Accepted: 02/05/2015] [Indexed: 01/26/2023]
Affiliation(s)
- Aki T. Heikkinen
- School of Pharmacy; Faculty of Health Sciences; University of Eastern Finland; Kuopio Finland
| | - Floriane Lignet
- Pharmaceutical Sciences; Pharmaceutical Research & Early Development; Roche Innovation Center Basel; Basel Switzerland
| | - Paul Cutler
- Pharmaceutical Sciences; Pharmaceutical Research & Early Development; Roche Innovation Center Basel; Basel Switzerland
| | - Neil Parrott
- Pharmaceutical Sciences; Pharmaceutical Research & Early Development; Roche Innovation Center Basel; Basel Switzerland
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41
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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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42
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Abbatiello SE, Schilling B, Mani DR, Zimmerman LJ, Hall SC, MacLean B, Albertolle M, Allen S, Burgess M, Cusack MP, Gosh M, Hedrick V, Held JM, Inerowicz HD, Jackson A, Keshishian H, Kinsinger CR, Lyssand J, Makowski L, Mesri M, Rodriguez H, Rudnick P, Sadowski P, Sedransk N, Shaddox K, Skates SJ, Kuhn E, Smith D, Whiteaker JR, Whitwell C, Zhang S, Borchers CH, Fisher SJ, Gibson BW, Liebler DC, MacCoss MJ, Neubert TA, Paulovich AG, Regnier FE, Tempst P, Carr SA. Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma. Mol Cell Proteomics 2015; 14:2357-74. [PMID: 25693799 DOI: 10.1074/mcp.m114.047050] [Citation(s) in RCA: 141] [Impact Index Per Article: 15.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Indexed: 11/06/2022] Open
Abstract
There is an increasing need in biology and clinical medicine to robustly and reliably measure tens to hundreds of peptides and proteins in clinical and biological samples with high sensitivity, specificity, reproducibility, and repeatability. Previously, we demonstrated that LC-MRM-MS with isotope dilution has suitable performance for quantitative measurements of small numbers of relatively abundant proteins in human plasma and that the resulting assays can be transferred across laboratories while maintaining high reproducibility and quantitative precision. Here, we significantly extend that earlier work, demonstrating that 11 laboratories using 14 LC-MS systems can develop, determine analytical figures of merit, and apply highly multiplexed MRM-MS assays targeting 125 peptides derived from 27 cancer-relevant proteins and seven control proteins to precisely and reproducibly measure the analytes in human plasma. To ensure consistent generation of high quality data, we incorporated a system suitability protocol (SSP) into our experimental design. The SSP enabled real-time monitoring of LC-MRM-MS performance during assay development and implementation, facilitating early detection and correction of chromatographic and instrumental problems. Low to subnanogram/ml sensitivity for proteins in plasma was achieved by one-step immunoaffinity depletion of 14 abundant plasma proteins prior to analysis. Median intra- and interlaboratory reproducibility was <20%, sufficient for most biological studies and candidate protein biomarker verification. Digestion recovery of peptides was assessed and quantitative accuracy improved using heavy-isotope-labeled versions of the proteins as internal standards. Using the highly multiplexed assay, participating laboratories were able to precisely and reproducibly determine the levels of a series of analytes in blinded samples used to simulate an interlaboratory clinical study of patient samples. Our study further establishes that LC-MRM-MS using stable isotope dilution, with appropriate attention to analytical validation and appropriate quality control measures, enables sensitive, specific, reproducible, and quantitative measurements of proteins and peptides in complex biological matrices such as plasma.
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Affiliation(s)
- Susan E Abbatiello
- From the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | | | - D R Mani
- From the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Lisa J Zimmerman
- Department of Biochemistry, Vanderbilt University School of Medicine, and the Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232
| | - Steven C Hall
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California 94143
| | - Brendan MacLean
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Matthew Albertolle
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California 94143
| | - Simon Allen
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California 94143
| | - Michael Burgess
- From the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | | | - Mousumi Gosh
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065
| | | | - Jason M Held
- Buck Institute for Research on Aging, Novato, California 94945
| | | | - Angela Jackson
- University of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8 CAN
| | - Hasmik Keshishian
- From the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | | | - John Lyssand
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016
| | - Lee Makowski
- Argonne National Laboratory (currently at Northeastern University, Boston Massachusetts 02115
| | - Mehdi Mesri
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Henry Rodriguez
- National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Paul Rudnick
- National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Pawel Sadowski
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016
| | - Nell Sedransk
- National Institute of Statistical Sciences, Research Triangle Park, North Carolina 27709
| | - Kent Shaddox
- Department of Biochemistry, Vanderbilt University School of Medicine, and the Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232
| | - Stephen J Skates
- Biostatistics Center, Massachusetts General Hospital, Boston, Massachusetts 02114
| | - Eric Kuhn
- From the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142
| | - Derek Smith
- University of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8 CAN
| | | | - Corbin Whitwell
- Department of Biochemistry, Vanderbilt University School of Medicine, and the Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232
| | - Shucha Zhang
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109
| | - Christoph H Borchers
- University of Victoria-Genome BC Proteomics Centre, Victoria, British Columbia V8Z 7X8 CAN
| | - Susan J Fisher
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California, San Francisco, San Francisco, California 94143
| | | | - Daniel C Liebler
- Department of Biochemistry, Vanderbilt University School of Medicine, and the Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Nashville, Tennessee 37232
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195
| | - Thomas A Neubert
- Kimmel Center for Biology and Medicine at the Skirball Institute, New York University School of Medicine, New York, New York 10016
| | | | | | - Paul Tempst
- Memorial Sloan-Kettering Cancer Center, New York, New York 10065
| | - Steven A Carr
- From the Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142;
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43
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Wohlgemuth I, Lenz C, Urlaub H. Studying macromolecular complex stoichiometries by peptide-based mass spectrometry. Proteomics 2015; 15:862-79. [PMID: 25546807 PMCID: PMC5024058 DOI: 10.1002/pmic.201400466] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 11/24/2014] [Accepted: 12/22/2014] [Indexed: 11/11/2022]
Abstract
A majority of cellular functions are carried out by macromolecular complexes. A host of biochemical and spectroscopic methods exists to characterize especially protein/protein complexes, however there has been a lack of a universal method to determine protein stoichiometries. Peptide‐based MS, especially as a complementary method to the MS analysis of intact protein complexes, has now been developed to a point where it can be employed to assay protein stoichiometries in a routine manner. While the experimental demands are still significant, peptide‐based MS has been successfully applied to analyze stoichiometries for a variety of protein complexes from very different biological backgrounds. In this review, we discuss the requirements especially for targeted MS acquisition strategies to be used in this context, with a special focus on the interconnected experimental aspects of sample preparation, protein digestion, and peptide stability. In addition, different strategies for the introduction of quantitative peptide standards and their suitability for different scenarios are compared.
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Affiliation(s)
- Ingo Wohlgemuth
- Department of Physical Biochemistry, Max Planck Institute for Biophysical Chemistry, Goettingen, Germany
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44
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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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45
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Lebert D, Louwagie M, Goetze S, Picard G, Ossola R, Duquesne C, Basler K, Ferro M, Rinner O, Aebersold R, Garin J, Mouz N, Brunner E, Brun V. DIGESTIF: a universal quality standard for the control of bottom-up proteomics experiments. J Proteome Res 2014; 14:787-803. [PMID: 25495225 DOI: 10.1021/pr500834z] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
In bottom-up mass spectrometry-based proteomics analyses, variability at any step of the process, particularly during sample proteolysis, directly affects the sensitivity, accuracy, and precision of peptide detection and quantification. Currently, no generic internal standards are available to control the quality of sample processing steps. This makes it difficult to assess the comparability of MS proteomic data obtained under different experimental conditions. Here, we describe the design, synthesis, and validation of a universal protein standard, called DIGESTIF, that can be added to any biological sample. The DIGESTIF standard consists of a soluble recombinant protein scaffold to which a set of 11 artificial peptides (iRT peptides) with good ionization properties has been incorporated. In the protein scaffold, the amino acids flanking iRT peptide cleavage sites were selected either to favor or hinder protease cleavage. After sample processing, the retention time and relative intensity pattern of the released iRT peptides can be used to assess the quality of sample workup, the extent of digestion, and the performance of the LC-MS system. Thus, DIGESTIF can be used to standardize a broad spectrum of applications, ranging from simple replicate measurements to large-scale biomarker screening in biomedical applications.
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46
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Dittrich J, Becker S, Hecht M, Ceglarek U. Sample preparation strategies for targeted proteomics via proteotypic peptides in human blood using liquid chromatography tandem mass spectrometry. Proteomics Clin Appl 2014; 9:5-16. [PMID: 25418444 DOI: 10.1002/prca.201400121] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 10/29/2014] [Accepted: 11/18/2014] [Indexed: 11/07/2022]
Abstract
The simultaneous quantification of protein concentrations via proteotypic peptides in human blood by liquid chromatography coupled to quadrupole MS/MS is an important field of bioanalytical research with a high potential for routine diagnostic applications. This review summarizes currently available sample preparation procedures and trends for absolute protein quantification in blood using LC-MS/MS. It discusses approaches of transferring established qualitative protocols to a quantitative analysis regarding their reliability and reproducibility. Techniques used to enhance method sensitivity such as the depletion of high-abundant proteins or the immunoaffinity enrichment of proteins and peptides are described. Furthermore, workflows for (i) protein denaturation, (ii) disulfide bridge reduction and (iii) thiol alkylation as well as (iv) enzymatic digestion for absolute protein quantification are presented. The main focus is on the tryptic digestion as a bottleneck of protein quantification via proteotypic peptides. Conclusively, requirements for a high-throughput application are discussed.
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Affiliation(s)
- Julia Dittrich
- Institute of Laboratory Medicine, Clinical Chemistry and Molecular Diagnostics, University Hospital Leipzig, Leipzig, Germany; LIFE - Leipzig Research Center for Civilization Diseases, University Leipzig, Leipzig, Germany
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47
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Steiner C, Ducret A, Tille JC, Thomas M, McKee TA, Rubbia-Brandt L, Scherl A, Lescuyer P, Cutler P. Applications of mass spectrometry for quantitative protein analysis in formalin-fixed paraffin-embedded tissues. Proteomics 2014; 14:441-51. [PMID: 24339433 PMCID: PMC4265304 DOI: 10.1002/pmic.201300311] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 11/04/2013] [Accepted: 11/11/2013] [Indexed: 12/12/2022]
Abstract
Proteomic analysis of tissues has advanced in recent years as instruments and methodologies have evolved. The ability to retrieve peptides from formalin-fixed paraffin-embedded tissues followed by shotgun or targeted proteomic analysis is offering new opportunities in biomedical research. In particular, access to large collections of clinically annotated samples should enable the detailed analysis of pathologically relevant tissues in a manner previously considered unfeasible. In this paper, we review the current status of proteomic analysis of formalin-fixed paraffin-embedded tissues with a particular focus on targeted approaches and the potential for this technique to be used in clinical research and clinical diagnosis. We also discuss the limitations and perspectives of the technique, particularly with regard to application in clinical diagnosis and drug discovery.
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Affiliation(s)
- Carine Steiner
- Division of Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland; Human Protein Sciences Department, University of Geneva, Geneva, Switzerland; Translational Technologies and Bioinformatics, Pharma Research and Early Development, F. Hoffmann-La Roche AG, Basel, Switzerland
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48
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Heikkinen AT, Friedlein A, Matondo M, Hatley OJD, Petsalo A, Juvonen R, Galetin A, Rostami-Hodjegan A, Aebersold R, Lamerz J, Dunkley T, Cutler P, Parrott N. Quantitative ADME Proteomics – CYP and UGT Enzymes in the Beagle Dog Liver and Intestine. Pharm Res 2014; 32:74-90. [DOI: 10.1007/s11095-014-1446-8] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 07/02/2014] [Indexed: 12/16/2022]
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49
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Gallien S, Bourmaud A, Domon B. A simple protocol to routinely assess the uniformity of proteomics analyses. J Proteome Res 2014; 13:2688-95. [PMID: 24617767 DOI: 10.1021/pr4011712] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mass-spectrometry-based proteomic approaches are increasingly applied to biological and clinical studies. Initially used by specialized laboratories, the technology has matured and gained acceptance by the community, using various analytical processes and platforms. To facilitate data comparison and integration across laboratories, there is a need to harmonize analytical processes to ensure the generation of reliable proteomic data sets. This is especially critical in the context of large initiatives, such as the Human Proteome Project promoted by the Human Proteome Organization (HUPO). Quality control is a first step toward the harmonization of proteomics data sets. We have developed a procedure to routinely assess the uniformity of proteomics analyses. It relies on a simple protocol based on three proteins and two sets of isotopically labeled peptides, one being added prior to tryptic digestion and the second one prior to liquid chromatography-mass spectrometry (LC-MS) analysis. The proposed method evaluates in a single step both the sample preparation, by measuring the relative amounts of endogenous peptides and their isotopically labeled counterparts, and the LC-MS platform performance, by monitoring the main LC-MS attributes for reference peptides. The procedure is simple and easy to implement into routine workflows typically employed by the proteomics community.
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Affiliation(s)
- Sebastien Gallien
- Luxembourg Clinical Proteomics Center (LCP), CRP-Santé , L-1445 Strassen, Luxembourg
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50
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Carr SA, Abbatiello SE, Ackermann BL, Borchers C, Domon B, Deutsch EW, Grant RP, Hoofnagle AN, Hüttenhain R, Koomen JM, Liebler DC, Liu T, MacLean B, Mani DR, Mansfield E, Neubert H, Paulovich AG, Reiter L, Vitek O, Aebersold R, Anderson L, Bethem R, Blonder J, Boja E, Botelho J, Boyne M, Bradshaw RA, Burlingame AL, Chan D, Keshishian H, Kuhn E, Kinsinger C, Lee JS, Lee SW, Moritz R, Oses-Prieto J, Rifai N, Ritchie J, Rodriguez H, Srinivas PR, Townsend RR, Van Eyk J, Whiteley G, Wiita A, Weintraub S. Targeted peptide measurements in biology and medicine: best practices for mass spectrometry-based assay development using a fit-for-purpose approach. Mol Cell Proteomics 2014; 13:907-17. [PMID: 24443746 PMCID: PMC3945918 DOI: 10.1074/mcp.m113.036095] [Citation(s) in RCA: 419] [Impact Index Per Article: 41.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/14/2014] [Indexed: 12/25/2022] Open
Abstract
Adoption of targeted mass spectrometry (MS) approaches such as multiple reaction monitoring (MRM) to study biological and biomedical questions is well underway in the proteomics community. Successful application depends on the ability to generate reliable assays that uniquely and confidently identify target peptides in a sample. Unfortunately, there is a wide range of criteria being applied to say that an assay has been successfully developed. There is no consensus on what criteria are acceptable and little understanding of the impact of variable criteria on the quality of the results generated. Publications describing targeted MS assays for peptides frequently do not contain sufficient information for readers to establish confidence that the tests work as intended or to be able to apply the tests described in their own labs. Guidance must be developed so that targeted MS assays with established performance can be made widely distributed and applied by many labs worldwide. To begin to address the problems and their solutions, a workshop was held at the National Institutes of Health with representatives from the multiple communities developing and employing targeted MS assays. Participants discussed the analytical goals of their experiments and the experimental evidence needed to establish that the assays they develop work as intended and are achieving the required levels of performance. Using this "fit-for-purpose" approach, the group defined three tiers of assays distinguished by their performance and extent of analytical characterization. Computational and statistical tools useful for the analysis of targeted MS results were described. Participants also detailed the information that authors need to provide in their manuscripts to enable reviewers and readers to clearly understand what procedures were performed and to evaluate the reliability of the peptide or protein quantification measurements reported. This paper presents a summary of the meeting and recommendations.
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Affiliation(s)
- Steven A. Carr
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | - Bruno Domon
- ‖Luxembourg Clinical Proteomics Center, Luxembourg
| | | | | | | | - Ruth Hüttenhain
- ¶¶Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
- ‖‖University of California San Francisco, California
| | | | | | - Tao Liu
- Pacific Northwest National Laboratory, Richland, Washington
| | | | - DR Mani
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | | | | | | | | | - Ruedi Aebersold
- ¶¶Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | | | | | | | - Emily Boja
- National Cancer Institute, NIH Bethesda, Maryland
| | | | | | | | | | - Daniel Chan
- Johns Hopkins University, Baltimore, Maryland
| | - Hasmik Keshishian
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | - Eric Kuhn
- From the ‡Broad Institute of MIT and Harvard, Cambridge, Massachusetts
| | | | - Jerry S.H. Lee
- National Cancer Institute, NIH Bethesda, Maryland
- Johns Hopkins University, Baltimore, Maryland
| | | | - Robert Moritz
- **Institute for Systems Biology, Seattle, Washington
| | | | | | | | | | | | | | | | - Gordon Whiteley
- Liedos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research
| | - Arun Wiita
- ‖‖University of California San Francisco, California
| | - Susan Weintraub
- University of Texas Health Science Center, San Antonio, Texas
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