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Sadygov RG. Protein turnover models for LC-MS data of heavy water metabolic labeling. Brief Bioinform 2022; 23:bbab598. [PMID: 35062023 PMCID: PMC8921656 DOI: 10.1093/bib/bbab598] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 12/12/2021] [Accepted: 12/26/2021] [Indexed: 01/23/2023] Open
Abstract
Protein turnover is vital for cellular functioning and is often associated with the pathophysiology of a variety of diseases. Metabolic labeling with heavy water followed by liquid chromatography coupled to mass spectrometry is a powerful tool to study in vivo protein turnover in high throughput and large scale. Heavy water is a cost-effective and easy to use labeling agent. It labels all nonessential amino acids. Due to its toxicity in high concentrations (20% or higher), small enrichments (8% or smaller) of heavy water are used with most organisms. The low concentration results in incomplete labeling of peptides/proteins. Therefore, the data processing is more challenging and requires accurate quantification of labeled and unlabeled forms of a peptide from overlapping mass isotopomer distributions. The work describes the bioinformatics aspects of the analysis of heavy water labeled mass spectral data, available software tools and current challenges and opportunities.
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Affiliation(s)
- Rovshan G Sadygov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University of Blvd, Galveston, TX 77555, USA
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2
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Borzou A, Sadygov VR, Zhang W, Sadygov RG. Proteome Dynamics from Heavy Water Metabolic Labeling and Peptide Tandem Mass Spectrometry. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2019; 445:10.1016/j.ijms.2019.116194. [PMID: 32055233 PMCID: PMC7017751 DOI: 10.1016/j.ijms.2019.116194] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Protein homeostasis (proteostasis) is a result of a dynamic equilibrium between protein synthesis and degradation. It is important for healthy cell/organ functioning and is often associated with diseases such as neurodegenerative diseases and non-Alcoholic Fatty Liver disease. Heavy water metabolic labeling, combined with liquid-chromatography and mass spectrometry (LC-MS), is a powerful approach to study proteostasis in vivo in high throughput. Traditionally, intact peptide signals are used to estimate stable isotope incorporation in time-course experiments. The time-course of label incorporation is used to extract protein decay rate constant (DRC). Intact peptide signals, computed from integration in chromatographic time and mass-to-charge ratio (m/z) domains, usually, provide an accurate estimate of label incorporation. However, sample complexity (co-elution), limited dynamic range, and low signal-to-noise ratio (S/N) may adversely interfere with the peptide signals. These artifacts complicate the DRC estimations by distorting peak shape in chromatographic time and m/z domains. Fragment ions, on the other hand, are less prone to these artifacts and are potentially well suited in aiding DRC estimations. Here, we show that the label incorporation encoded into the isotope distributions of fragment ions reflect the isotope enrichment during the metabolic labeling with heavy water. We explore the label incorporation statistics for devising practical approaches for DRC estimations.
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Affiliation(s)
- Ahmad Borzou
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University of Blvd, Galveston, TX 77555
| | - Vugar R. Sadygov
- Clear Creek High School, 2305 E. Main St., League City, TX 77573
| | - William Zhang
- Clear Lake High School, 2929 Bay Area Blvd, Houston, TX, 77058
| | - Rovshan G. Sadygov
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, 301 University of Blvd, Galveston, TX 77555
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Perspectives on potentiating immunocapture-LC-MS for the bioanalysis of biotherapeutics and biomarkers. Bioanalysis 2018; 10:1679-1690. [PMID: 30371100 DOI: 10.4155/bio-2018-0205] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The integration of ligand-binding assay and LC-MS/MS (immunocapture-LC-MS) has unleashed the combined advantages of both powerful techniques for addressing the ever increasing bioanalytical challenges for biotherapeutics and biomarker assays. The highly specific, selective and sensitive characteristics of the immunocapture-LC-MS-based assays have enabled the determination of biotherapeutics and biomarkers in biomatrices with ease of method development, less requirements on key reagents as well as structural specificity for endogenous and engineered biomolecules. In addition, the versatile immunocapture-LC-MS technology has expanded into many challenging areas to enhance mechanistic studies of drug interactions with their targets. This paper intends to summarize our perspectives on enhancing the use of immunocapture-LC-MS in drug discovery and development for emerging new modalities.
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4
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Farrokhi V, Chen X, Neubert H. Protein Turnover Measurements in Human Serum by Serial Immunoaffinity LC-MS/MS. Clin Chem 2018; 64:279-288. [DOI: 10.1373/clinchem.2017.272922] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 08/17/2017] [Indexed: 12/15/2022]
Abstract
Abstract
BACKGROUND
The half-life of target proteins is frequently an important parameter in mechanistic pharmacokinetic and pharmacodynamic (PK/PD) modeling of biotherapeutics. Clinical studies for accurate measurement of physiologically relevant protein turnover can reduce the uncertainty in PK/PD model-based predictions, for example, of the therapeutic dose and dosing regimen in first-in-human clinical trials.
METHODS
We used a targeted mass spectrometry work flow based on serial immunoaffinity enrichment ofmultiple human serum proteins from a [5,5,5-2H3]-L-leucine tracer pulse-chase study in healthy volunteers. To confirm the reproducibility of turnover measurements from serial immunoaffinity enrichment, multiple aliquots from the same sample set were subjected to protein turnover analysis in varying order. Tracer incorporation was measured by multiple–reaction-monitoring mass spectrometry and target turnover was calculated using a four-compartment pharmacokinetic model.
RESULTS
Five proteins of clinical or therapeutic relevance including soluble tumor necrosis factor receptor superfamily member 12A, tissue factor pathway inhibitor, soluble interleukin 1 receptor like 1, soluble mucosal addressin cell adhesion molecule 1, and muscle-specific creatine kinase were sequentially subjected to turnover analysis from the same human serum sample. Calculated half-lives ranged from 5–15 h; however, no tracer incorporation was observed for mucosal addressin cell adhesion molecule 1.
CONCLUSIONS
The utility of clinical pulse-chase studies to investigate protein turnover can be extended by serial immunoaffinity enrichment of target proteins. Turnover analysis from serum and subsequently from remaining supernatants provided analytical sensitivity and reproducibility for multiple human target proteins in the same sample set, irrespective of the order of analysis.
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Affiliation(s)
- Vahid Farrokhi
- Biomedicine Design, Worldwide Research & Development, Pfizer, Inc., Andover, MA
| | - Xiaoying Chen
- Clinical Pharmacology, Worldwide Research & Development, Pfizer, Inc., La Jolla, CA
| | - Hendrik Neubert
- Biomedicine Design, Worldwide Research & Development, Pfizer, Inc., Andover, MA
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Holman SW, Hammond DE, Simpson DM, Waters J, Hurst JL, Beynon RJ. Protein turnover measurement using selected reaction monitoring-mass spectrometry (SRM-MS). PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2016; 374:rsta.2015.0362. [PMID: 27644981 PMCID: PMC5031629 DOI: 10.1098/rsta.2015.0362] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 06/23/2016] [Indexed: 05/28/2023]
Abstract
Protein turnover represents an important mechanism in the functioning of cells, with deregulated synthesis and degradation of proteins implicated in many diseased states. Therefore, proteomics strategies to measure turnover rates with high confidence are of vital importance to understanding many biological processes. In this study, the more widely used approach of non-targeted precursor ion signal intensity (MS1) quantification is compared with selected reaction monitoring (SRM), a data acquisition strategy that records data for specific peptides, to determine if improved quantitative data would be obtained using a targeted quantification approach. Using mouse liver as a model system, turnover measurement of four tricarboxylic acid cycle proteins was performed using both MS1 and SRM quantification strategies. SRM outperformed MS1 in terms of sensitivity and selectivity of measurement, allowing more confident determination of protein turnover rates. SRM data are acquired using cheaper and more widely available tandem quadrupole mass spectrometers, making the approach accessible to a larger number of researchers than MS1 quantification, which is best performed on high mass resolution instruments. SRM acquisition is ideally suited to focused studies where the turnover of tens of proteins is measured, making it applicable in determining the dynamics of proteins complexes and complete metabolic pathways.This article is part of the themed issue 'Quantitative mass spectrometry'.
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Affiliation(s)
- Stephen W Holman
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - Dean E Hammond
- Cellular and Molecular Physiology, Institute of Translational Medicine, University of Liverpool, Crown Street, Liverpool L69 3BX, UK
| | - Deborah M Simpson
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
| | - John Waters
- Mammalian Behaviour and Evolution Group, Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | - Jane L Hurst
- Mammalian Behaviour and Evolution Group, Department of Evolution, Ecology and Behaviour, Institute of Integrative Biology, University of Liverpool, Leahurst Campus, Neston CH64 7TE, UK
| | - Robert J Beynon
- Centre for Proteome Research, Department of Biochemistry, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK
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Nolte H, Hölper S, Selbach M, Braun T, Krüger M. Assessment of serum protein dynamics by native SILAC flooding (SILflood). Anal Chem 2014; 86:11033-7. [PMID: 25347402 DOI: 10.1021/ac502883p] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Turnover of blood serum proteins is a vital function in mammals, but technical challenges have thus far prevented comprehensive measurements of serum protein half-lives. Here, we injected native serum from heavy stable isotope labeled (SIL) mice into nonlabeled recipients to quantify turnover of more than 200 proteins using mass spectrometry with high reproducibility and accuracy. We found a median of 19.4 h and a total range of 6-70 h for calculated half-lives. Moreover, we observed similar half-lives for proteins with equal function. To demonstrate the value and effectiveness of SILflood, we investigated the impaired serum clearance in β2-microglobulin (B2M-/-) deficient mice. Notably, we found that serum albumin and IgG half-lives were clearly reduced in B2M deficient animals compared to control animals. Taken together, our results demonstrate that SILflood is a versatile tool to investigate serum half-lives under regular and pathological conditions in living animals.
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Affiliation(s)
- Hendrik Nolte
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne , Joseph-Stelzmann-Strasse 26, 50931 Cologne, Germany
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7
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Quantitation of human peptides and proteins via MS: review of analytically validated assays. Bioanalysis 2014; 6:1843-57. [DOI: 10.4155/bio.14.145] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Since the development of monoclonal antibodies in the 1970s, antibody-based assays have been used for the quantitation of proteins and peptides and, today, they are the most widely used technology in routine laboratory medicine and bioanalysis. However, in the last couple of decades, liquid chromatography-mass spectrometry/mass spectrometry (LC–MS/MS) techniques have been adopted in the quantitation of small molecules, and more recently have made significant contributions in the quantitation of proteins and peptides. In this article, we will review clinical MS-based assays for endogenous peptides, proteins, and therapeutic antibodies, for which validated methods exist. We will also cover the measurement of protein turnover and the unique solutions that MS can offer in this field.
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8
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Applications of low-flow LC–SRM for the analysis of large molecules in pharmaceutical R&D. Bioanalysis 2014; 6:1859-67. [DOI: 10.4155/bio.14.141] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Although ligand-binding assays are frequently employed to measure large molecules, the use of LC–SRM assays is increasingly popular due to the inherent selectivity advantage and the ability to operate without exquisitely selective antibodies. Until recently LC–SRM assays have been unable to compete with ligand-binding assays in terms of sensitivity. However, the use of low-flow chromatography prior to mass spectrometry has played a crucial role in increasing the sensitivity of LC–SRM platforms and enabling measurements of large molecules that had previously been unmeasurable. In this article, we highlight some technical advances, describe strategies for employing low-flow chromatography, and review recent literature that describes implementation of low-flow LC–SRM to support large-molecule analysis in pharmaceutical R&D.
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Lassman ME, McAvoy T, Lee AYH, Chappell D, Wong O, Zhou H, Reyes-Soffer G, Ginsberg HN, Millar JS, Rader DJ, Gutstein DE, Laterza O. Practical immunoaffinity-enrichment LC-MS for measuring protein kinetics of low-abundance proteins. Clin Chem 2014; 60:1217-24. [PMID: 24751376 DOI: 10.1373/clinchem.2014.222455] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
BACKGROUND For a more complete understanding of pharmacodynamic, metabolic, and pathophysiologic effects, protein kinetics, such as production rate and fractional catabolic rate, can offer substantially more information than protein concentration alone. Kinetic experiments with stable isotope tracers typically require laborious sample preparation and are most often used for studying abundant proteins. Here we describe a practical methodology for measuring isotope enrichment into low-abundance proteins that uses an automated procedure and immunoaffinity enrichment (IA) with LC-MS. Low-abundance plasma proteins cholesteryl ester transfer protein (CETP) and proprotein convertase subtilisin/kexin type 9 (PCSK9) were studied as examples. METHODS Human participants (n = 39) were infused with [(2)H(3)]leucine, and blood samples were collected at multiple time points. Sample preparation and analysis were automated and multiplexed to increase throughput. Proteins were concentrated from plasma by use of IA and digested with trypsin to yield proteotypic peptides that were analyzed by microflow chromatography-mass spectrometry to measure isotope enrichment. RESULTS The IA procedure was optimized to provide the greatest signal intensity. Use of a gel-free method increased throughput while increasing the signal. The intra- and interassay CVs were <15% at all isotope enrichment levels studied. More than 1400 samples were analyzed in <3 weeks without the need for instrument stoppages or user interventions. CONCLUSIONS The use of automated gel-free methods to multiplex the measurement of isotope enrichment was applied to the low-abundance proteins CETP and PCSK9.
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Affiliation(s)
| | | | | | | | | | | | | | - Henry N Ginsberg
- Molecular Biomarkers and Diagnostics, Molecular Biomarkers-PPDM, and Clinical Pharmacology, Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Whitehouse Station, NJ; Columbia University Medical Center, New York, NY; Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA
| | - John S Millar
- Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA
| | - Daniel J Rader
- Division of Translational Medicine and Human Genetics, University of Pennsylvania, Philadelphia, PA
| | - David E Gutstein
- Clinical Pharmacology, Merck Sharp & Dohme Corp., a subsidiary of Merck & Co., Inc., Whitehouse Station, NJ
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10
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Zhou H, Castro-Perez J, Lassman ME, Thomas T, Li W, McLaughlin T, Dan X, Jumes P, Wagner JA, Gutstein DE, Hubbard BK, Rader DJ, Millar JS, Ginsberg HN, Reyes-Soffer G, Cleary M, Previs SF, Roddy TP. Measurement of apo(a) kinetics in human subjects using a microfluidic device with tandem mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2013; 27:1294-302. [PMID: 23681806 PMCID: PMC4944116 DOI: 10.1002/rcm.6572] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2013] [Revised: 02/20/2013] [Accepted: 03/14/2013] [Indexed: 05/15/2023]
Abstract
RATIONALE Apolipoprotein(a) [apo(a)] is the defining protein component of lipoprotein(a) [Lp(a)], an independent risk factor for cardiovascular disease. The regulation of Lp(a) levels in blood is poorly understood in part due to technical challenges in measuring Lp(a) kinetics. Improvements in the ability to readily and reliably measure the kinetics of apo(a) using a stable isotope labeled tracer is expected to facilitate studies of the role of Lp(a) in cardiovascular disease. Since investigators typically determine the isotopic labeling of protein-bound amino acids following acid-catalyzed hydrolysis of a protein of interest [e.g., apo(a)], studies of protein synthesis require extensive protein purification which limits throughput and often requires large sample volumes. We aimed to develop a rapid and efficient method for studying apo(a) kinetics that is suitable for use in studies involving human subjects. METHODS Microfluidic device and tandem mass spectrometry were used to quantify the incorporation of [(2)H3]-leucine tracer into protein-derived peptides. RESULTS We demonstrated that it is feasible to quantify the incorporation of [(2)H3]-leucine tracer into a proteolytic peptide from the non-kringle repeat region of apo(a) in human subjects. Specific attention was directed toward optimizing the multiple reaction monitoring (MRM) transitions, mass spectrometer settings, and chromatography (i.e., critical parameters that affect the sensitivity and reproducibility of isotopic enrichment measurements). The results demonstrated significant advantages with the use of a microfluidic device technology for studying apo(a) kinetics, including enhanced sensitivity relative to conventional micro-flow chromatography, a virtually drift-free elution profile, and a stable and robust electrospray. CONCLUSIONS The technological advances described herein enabled the implementation of a novel method for studying the kinetics of apo(a) in human subjects infused with [(2)H3]-leucine.
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Affiliation(s)
- Haihong Zhou
- Molecular Biomarkers-PPDM, Merck Sharp & Dohme Corp., Whitehouse Station, NJ, USA
| | - Jose Castro-Perez
- Molecular Biomarkers-PPDM, Merck Sharp & Dohme Corp., Whitehouse Station, NJ, USA
| | - Michael E. Lassman
- Clinical Development Laboratory, Merck Sharp & Dohme Corp., Whitehouse Station, NJ, USA
| | | | - Wenyu Li
- Molecular Biomarkers-PPDM, Merck Sharp & Dohme Corp., Whitehouse Station, NJ, USA
| | - Theresa McLaughlin
- Molecular Biomarkers-PPDM, Merck Sharp & Dohme Corp., Whitehouse Station, NJ, USA
| | - Xie Dan
- Molecular Biomarkers-PPDM, Merck Sharp & Dohme Corp., Whitehouse Station, NJ, USA
| | - Patricia Jumes
- Clinical Pharmacology, Merck Sharp & Dohme Corp., Whitehouse Station, NJ, USA
| | - John A. Wagner
- Clinical Pharmacology, Merck Sharp & Dohme Corp., Whitehouse Station, NJ, USA
| | - David E. Gutstein
- Clinical Pharmacology, Merck Sharp & Dohme Corp., Whitehouse Station, NJ, USA
| | - Brian K. Hubbard
- Molecular Biomarkers-PPDM, Merck Sharp & Dohme Corp., Whitehouse Station, NJ, USA
| | - Daniel J. Rader
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John S. Millar
- Division of Translational Medicine and Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | | | | | - Michele Cleary
- Molecular Biomarkers-PPDM, Merck Sharp & Dohme Corp., Whitehouse Station, NJ, USA
| | - Stephen F. Previs
- Molecular Biomarkers-PPDM, Merck Sharp & Dohme Corp., Whitehouse Station, NJ, USA
- Correspondence to: S. F. Previs, Molecular Biomarkers, Merck Sharp & Dohme Corp., 2015 Galloping Hill Road, Kenilworth, NJ 07033, USA.
| | - Thomas P. Roddy
- Molecular Biomarkers-PPDM, Merck Sharp & Dohme Corp., Whitehouse Station, NJ, USA
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Zhang Y, Fonslow BR, Shan B, Baek MC, Yates JR. Protein analysis by shotgun/bottom-up proteomics. Chem Rev 2013; 113:2343-94. [PMID: 23438204 PMCID: PMC3751594 DOI: 10.1021/cr3003533] [Citation(s) in RCA: 986] [Impact Index Per Article: 89.6] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yaoyang Zhang
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bryan R. Fonslow
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Bing Shan
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Moon-Chang Baek
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
- Department of Molecular Medicine, Cell and Matrix Biology Research Institute, School of Medicine, Kyungpook National University, Daegu 700-422, Republic of Korea
| | - John R. Yates
- Department of Chemical Physiology, The Scripps Research Institute, La Jolla, CA 92037, USA
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Abstract
![]()
Quantitative
measurement of proteins is one of the most fundamental analytical
tasks in a biochemistry laboratory, but widely used immunochemical
methods often have limited specificity and high measurement variation.
In this review, we discuss applications of multiple-reaction monitoring
(MRM) mass spectrometry, which allows sensitive, precise quantitative
analyses of peptides and the proteins from which they are derived.
Systematic development of MRM assays is permitted by databases of
peptide mass spectra and sequences, software tools for analysis design
and data analysis, and rapid evolution of tandem mass spectrometer
technology. Key advantages of MRM assays are the ability to target
specific peptide sequences, including variants and modified forms,
and the capacity for multiplexing that allows analysis of dozens to
hundreds of peptides. Different quantitative standardization methods
provide options that balance precision, sensitivity, and assay cost.
Targeted protein quantitation by MRM and related mass spectrometry
methods can advance biochemistry by transforming approaches to protein
measurement.
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Affiliation(s)
- Daniel C Liebler
- Department of Biochemistry and Jim Ayers Institute for Precancer Detection and Diagnosis, Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, Tennessee 37232-6350, United States.
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Cilia M, Peter KA, Bereman MS, Howe K, Fish T, Smith D, Gildow F, MacCoss MJ, Thannhauser TW, Gray SM. Discovery and targeted LC-MS/MS of purified polerovirus reveals differences in the virus-host interactome associated with altered aphid transmission. PLoS One 2012; 7:e48177. [PMID: 23118947 PMCID: PMC3484124 DOI: 10.1371/journal.pone.0048177] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2012] [Accepted: 09/21/2012] [Indexed: 11/19/2022] Open
Abstract
Circulative transmission of viruses in the Luteoviridae, such as cereal yellow dwarf virus (CYDV), requires a series of precisely orchestrated interactions between virus, plant, and aphid proteins. Natural selection has favored these viruses to be retained in the phloem to facilitate acquisition and transmission by aphids. We show that treatment of infected oat tissue homogenate with sodium sulfite reduces transmission of the purified virus by aphids. Transmission electron microscopy data indicated no gross change in virion morphology due to treatments. However, treated virions were not acquired by aphids through the hindgut epithelial cells and were not transmitted when injected directly into the hemocoel. Analysis of virus preparations using nanoflow liquid chromatography coupled to tandem mass spectrometry revealed a number of host plant proteins co-purifying with viruses, some of which were lost following sodium sulfite treatment. Using targeted mass spectrometry, we show data suggesting that several of the virus-associated host plant proteins accumulated to higher levels in aphids that were fed on CYDV-infected plants compared to healthy plants. We propose two hypotheses to explain these observations, and these are not mutually exclusive: (a) that sodium sulfite treatment disrupts critical virion-host protein interactions required for aphid transmission, or (b) that host infection with CYDV modulates phloem protein expression in a way that is favorable for virus uptake by aphids. Importantly, the genes coding for the plant proteins associated with virus may be examined as targets in breeding cereal crops for new modes of virus resistance that disrupt phloem-virus or aphid-virus interactions.
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Affiliation(s)
- Michelle Cilia
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail: (MC); (SMG)
| | - Kari A. Peter
- Department of Plant Pathology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Michael S. Bereman
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Kevin Howe
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America
| | - Tara Fish
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America
| | - Dawn Smith
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
| | - Fredrick Gildow
- Department of Plant Pathology, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Theodore W. Thannhauser
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America
| | - Stewart M. Gray
- Robert W. Holley Center for Agriculture and Health, United States Department of Agriculture-Agricultural Research Service, Ithaca, New York, United States of America
- Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, New York, United States of America
- * E-mail: (MC); (SMG)
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14
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Bereman MS, MacLean B, Tomazela DM, Liebler DC, MacCoss MJ. The development of selected reaction monitoring methods for targeted proteomics via empirical refinement. Proteomics 2012; 12:1134-41. [PMID: 22577014 DOI: 10.1002/pmic.201200042] [Citation(s) in RCA: 85] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Software advancements in the last several years have had a significant impact on proteomics from method development to data analysis. Herein, we detail a method, which uses our in-house developed software tool termed Skyline, for empirical refinement of candidate peptides from targeted proteins. The method consists of four main steps from generation of a testable hypothesis, method development, peptide refinement, to peptide validation. The ultimate goal is to identify the best performing peptide in terms of ionization efficiency, reproducibility, specificity, and chromatographic characteristics to monitor as a proxy for protein abundance. It is important to emphasize that this method allows the user to perform this refinement procedure in the sample matrix and organism of interest with the instrumentation available. Finally, the method is demonstrated in a case study to determine the best peptide to monitor the abundance of surfactant protein B in lung aspirates.
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Affiliation(s)
- Michael S Bereman
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
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15
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Bereman MS, Tomazela DM, Heins HS, Simonato M, Cogo PE, Hamvas A, Patterson BW, Cole FS, MacCoss MJ. A method to determine the kinetics of multiple proteins in human infants with respiratory distress syndrome. Anal Bioanal Chem 2012; 403:2397-402. [PMID: 22526637 PMCID: PMC3694176 DOI: 10.1007/s00216-012-5953-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2012] [Revised: 03/02/2012] [Accepted: 03/14/2012] [Indexed: 12/18/2022]
Abstract
We report a method to measure in vivo turnover of four proteins from sequential tracheal aspirates obtained from human newborn infants with respiratory distress syndrome using targeted proteomics. We detected enrichment for all targeted proteins approximately 3 h from the start of infusion of [5,5,5-(2)H(3)] leucine, secretion times that varied from 1.2 to 2.5 h, and half lives that ranged between 10 and 21 h. Complement factor B, a component of the alternative pathway of complement activation, had an approximately twofold-longer half-life than the other three proteins. In addition, the kinetics of mature and carboxy-terminal tryptic peptides from the same protein (surfactant protein B) were not statistically different (p = 0.49).
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Affiliation(s)
- Michael S Bereman
- Department of Genome Sciences, University of Washington, Seattle, WA 98195-5502, USA.
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Genetics coupled to quantitative intact proteomics links heritable aphid and endosymbiont protein expression to circulative polerovirus transmission. J Virol 2010; 85:2148-66. [PMID: 21159868 DOI: 10.1128/jvi.01504-10] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Yellow dwarf viruses in the family Luteoviridae, which are the causal agents of yellow dwarf disease in cereal crops, are each transmitted most efficiently by different species of aphids in a circulative manner that requires the virus to interact with a multitude of aphid proteins. Aphid proteins differentially expressed in F2 Schizaphis graminum genotypes segregating for the ability to transmit Cereal yellow dwarf virus-RPV (CYDV-RPV) were identified using two-dimensional difference gel electrophoresis (DIGE) coupled to either matrix-assisted laser desorption ionization-tandem mass spectrometry or online nanoscale liquid chromatography coupled to electrospray tandem mass spectrometry. A total of 50 protein spots, containing aphid proteins and proteins from the aphid's obligate and maternally inherited bacterial endosymbiont, Buchnera, were identified as differentially expressed between transmission-competent and refractive aphids. Surprisingly, in virus transmission-competent F2 genotypes, the isoelectric points of the Buchnera proteins did not match those in the maternal Buchnera proteome as expected, but instead they aligned with the Buchnera proteome of the transmission-competent paternal parent. Among the aphid proteins identified, many were involved in energy metabolism, membrane trafficking, lipid signaling, and the cytoskeleton. At least eight aphid proteins were expressed as heritable, isoelectric point isoform pairs, one derived from each parental lineage. In the F2 genotypes, the expression of aphid protein isoforms derived from the competent parental lineage aligned with the virus transmission phenotype with high precision. Thus, these isoforms are candidate biomarkers for CYDV-RPV transmission in S. graminum. Our combined genetic and DIGE approach also made it possible to predict where several of the proteins may be expressed in refractive aphids with different barriers to transmission. Twelve proteins were predicted to act in the hindgut of the aphid, while six proteins were predicted to be associated with the accessory salivary glands or hemolymph. Knowledge of the proteins that regulate virus transmission and their predicted locations will aid in understanding the biochemical mechanisms regulating circulative virus transmission in aphids, as well as in identifying new targets to block transmission.
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