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High-throughput proteomic sample preparation using pressure cycling technology. Nat Protoc 2022; 17:2307-2325. [PMID: 35931778 PMCID: PMC9362583 DOI: 10.1038/s41596-022-00727-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 05/24/2022] [Indexed: 11/09/2022]
Abstract
High-throughput lysis and proteolytic digestion of biopsy-level tissue specimens is a major bottleneck for clinical proteomics. Here we describe a detailed protocol of pressure cycling technology (PCT)-assisted sample preparation for proteomic analysis of biopsy tissues. A piece of fresh frozen or formalin-fixed paraffin-embedded tissue weighing ~0.1–2 mg is placed in a 150 μL pressure-resistant tube called a PCT-MicroTube with proper lysis buffer. After closing with a PCT-MicroPestle, a batch of 16 PCT-MicroTubes are placed in a Barocycler, which imposes oscillating pressure to the samples from one atmosphere to up to ~3,000 times atmospheric pressure. The pressure cycling schemes are optimized for tissue lysis and protein digestion, and can be programmed in the Barocycler to allow reproducible, robust and efficient protein extraction and proteolysis digestion for mass spectrometry-based proteomics. This method allows effective preparation of not only fresh frozen and formalin-fixed paraffin-embedded tissue, but also cells, feces and tear strips. It takes ~3 h to process 16 samples in one batch. The resulting peptides can be analyzed by various mass spectrometry-based proteomics methods. We demonstrate the applications of this protocol with mouse kidney tissue and eight types of human tumors. High-throughput lysis and proteolytic digestion of biopsy-level tissue specimens is a major bottleneck for clinical proteomics. This protocol describes pressure cycling technology (PCT)-assisted sample preparation of biopsy tissues.
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2
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Nupur N, Rathore AS. Elucidating chemical and disulfide heterogeneities in rituximab using reduced and non-reduced peptide mapping. J Sep Sci 2022; 45:2887-2900. [PMID: 35670633 DOI: 10.1002/jssc.202200290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 06/03/2022] [Accepted: 06/03/2022] [Indexed: 11/07/2022]
Abstract
Peptide mapping by liquid chromatography-mass spectrometry is the gold standard to characterize post-translational modifications and disulfide bonds. The structural integrity, heterogeneity, and quality of biotherapeutic proteins are evaluated via reduced and non-reduced peptide mapping methods. However, non-enzymatic artifacts are often induced during sample preparation when alkaline pH conditions are used. To minimize these artifacts, methods using various acidic pH conditions have been developed by multiple researchers. However, these may lead to missed and non-specific cleavages during the analysis. In this study, improved reduced and non-reduced peptide mapping method has been proposed to characterize endogenous chemical modifications and native disulfide bonds of monoclonal antibody -based products. Solubilization has been carried out at acidic pH conditions under high temperature, followed by the addition of tris (2-carboxyethyl) phosphine as a reducing agent and a low alkylating agent. It was observed that the non-enzymatic post-translational modifications and non-native disulfide scrambled peptides significantly reduced under trypsin plus Lys-C digestion conditions at acidic pH as compared to the traditional methods. The results demonstrate that the proposed peptide mapping method using trypsin plus Lys-C could identify and quantify various chemical and disulfide heterogeneities with minimal artifacts. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Neh Nupur
- Department of Chemical Engineering, IIT Delhi, Hauz Khas, New Delhi, 110016, India.,DBT Center of Excellence for Biopharmaceutical Technology, IIT Delhi, Hauz Khas, New Delhi, 110016, India
| | - Anurag S Rathore
- Department of Chemical Engineering, IIT Delhi, Hauz Khas, New Delhi, 110016, India.,DBT Center of Excellence for Biopharmaceutical Technology, IIT Delhi, Hauz Khas, New Delhi, 110016, India
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3
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Nie S, Greer T, Huang X, Zheng X, Li N. Development of a simple non-reduced peptide mapping method that prevents disulfide scrambling of mAbs without affecting tryptic enzyme activity. J Pharm Biomed Anal 2021; 209:114541. [PMID: 34954467 DOI: 10.1016/j.jpba.2021.114541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 11/27/2022]
Abstract
Non-reduced peptide mapping by liquid chromatography-mass spectrometry (LC-MS) analysis is a commonly used method for disulfide linkage characterization to assess structural integrity and quality of therapeutic monoclonal antibodies (mAbs). However, disulfide scrambling artifacts induced during sample preparation are often observed when basic pH and high temperatures are used during denaturation and digestion. To minimize disulfide scrambling artifacts, methods using various acidic pH conditions have been developed by multiple groups. However, lower pH conditions increase missed and non-specific cleavages, which complicates disulfide bond analysis because the majority of enzymes used in protein characterization are most efficient at alkaline pH. Here, we developed a non-reduced peptide mapping method for mAb characterization that minimizes disulfide scrambling at basic pH by adding an oxidizing agent, cystamine, and a low concentration of iodoacetamide (IAA) alkylating agent. Two human IgG1 mAbs, one with kappa light chain and another one with lambda light chain, were used as model proteins to develop and optimize the method. Using this novel method, disulfide scrambled peptides related to light chain-heavy chain (LC-HC) inter-disulfide disruption were significantly reduced with high reproducibility compared to conventional methods. Results demonstrated that the cystamine-added method is robust and minimizes disulfide scrambling artifacts produced during sample preparation.
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Affiliation(s)
- Song Nie
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591-6707, United States
| | - Tyler Greer
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591-6707, United States
| | - Xiaoxiao Huang
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591-6707, United States
| | - Xiaojing Zheng
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591-6707, United States.
| | - Ning Li
- Analytical Chemistry, Regeneron Pharmaceuticals Inc., 777 Old Saw Mill River Road, Tarrytown, NY 10591-6707, United States
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4
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Smith JW, O'Meally RN, Ng DK, Chen JG, Kensler TW, Cole RN, Groopman JD. Biomonitoring of Ambient Outdoor Air Pollutant Exposure in Humans Using Targeted Serum Albumin Adductomics. Chem Res Toxicol 2021; 34:1183-1196. [PMID: 33793228 DOI: 10.1021/acs.chemrestox.1c00055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Outdoor air pollution, a spatially and temporally complex mixture, is a human carcinogen. However, ambient measurements may not reflect subject-level exposures, personal monitors do not assess internal dose, and spot assessments of urinary biomarkers may not recapitulate chronic exposures. Nucleophilic sites in serum albumin-particularly the free thiol at Cys34-form adducts with electrophiles. Due to the 4-week lifetime of albumin in circulation, accumulating adducts can serve as intermediate- to long-residence biomarkers of chronic exposure and implicate potential biological effects. Employing nanoflow liquid chromatography-high-resolution mass spectrometry (nLC-HRMS) and parallel reaction monitoring (PRM), we have developed and validated a novel targeted albumin adductomics platform capable of simultaneously monitoring dozens of Cys34 adducts per sample in only 2.5 μL of serum, with on-column limits of detection in the low-femtomolar range. Using this platform, we characterized the magnitude and impact of ambient outdoor air pollution exposures with three repeated measurements over 84 days in n = 26 nonsmoking women (n = 78 total samples) from Qidong, China, an area with a rising burden of lung cancer incidence. In concordance with seasonally rising ambient concentrations of NO2, SO2, and PM10 measured at stationary monitors, we observed elevations in concentrations of Cys34 adducts of benzoquinone (p < 0.05), benzene diol epoxide (BDE; p < 0.05), crotonaldehyde (p < 0.01), and oxidation (p < 0.001). Regression analysis revealed significant elevations in oxidation and BDE adduct concentrations of 300% to nearly 700% per doubling of ambient airborne pollutant levels (p < 0.05). Notably, the ratio of irreversibly oxidized to reduced Cys34 rose more than 3-fold during the 84-day period, revealing a dramatic perturbation of serum redox balance and potentially serving as a portent of increased pollution-related mortality risk. Our targeted albumin adductomics assay represents a novel and flexible approach for sensitive and multiplexed internal dosimetry of environmental exposures, providing a new strategy for personalized biomonitoring and prevention.
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Affiliation(s)
- Joshua W Smith
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Robert N O'Meally
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - Derek K Ng
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland 21205, United States
| | - Jian-Guo Chen
- Qidong Liver Cancer Institute, Qidong, Jiangsu 226200, China
| | - Thomas W Kensler
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States.,Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
| | - Robert N Cole
- Department of Biological Chemistry, School of Medicine, Johns Hopkins University, Baltimore, Maryland 21205, United States
| | - John D Groopman
- Department of Environmental Health and Engineering, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, Maryland 21205, United States
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5
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Park HM, Winton VJ, Drader JJ, Manalili Wheeler S, Lazar GA, Kelleher NL, Liu Y, Tran JC, Compton PD. Novel Interface for High-Throughput Analysis of Biotherapeutics by Electrospray Mass Spectrometry. Anal Chem 2020; 92:2186-2193. [PMID: 31880920 PMCID: PMC7008517 DOI: 10.1021/acs.analchem.9b04826] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
With the rapid rise of therapeutic antibodies and antibody-drug conjugates, significant investments have been made in developing workflows that utilize mass spectrometry to detect these intact molecules, the large fragments generated by their selective digestion, and the peptides generated by traditional proteomics workflows. The resultant data is used to gain insight into a wide range of parameters, including primary sequence, disulfide bonding, glycosylation patterns, biotransformation, and more. However, many of the technologies utilized to couple these workflows to mass spectrometers have significant limitations that force nonoptimal modifications to upstream sample preparation steps, limit the throughput of high-volume workflows, and prevent the harmonization of diverse experiments onto a single hardware platform. Here, we describe a new analytical platform that enables direct and high-throughput coupling to electrospray ionization mass spectrometry. The SampleStream platform is compatible with both native and denaturing electrospray, operates with a throughput of up to 15 s/sample, provides extensive concentration of dilute samples, and affords similar sensitivity to comparable liquid chromatographic methods.
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Affiliation(s)
- Hae-Min Park
- Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Valerie J. Winton
- Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208, United States
| | - Jared J. Drader
- Integrated Protein Technologies, Inc., 2170 Campus Drive, Evanston, IL 60208, United States
| | - Sheri Manalili Wheeler
- Integrated Protein Technologies, Inc., 2170 Campus Drive, Evanston, IL 60208, United States
| | - Greg A. Lazar
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Neil L. Kelleher
- Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208, United States
- Integrated Protein Technologies, Inc., 2170 Campus Drive, Evanston, IL 60208, United States
| | - Yichin Liu
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - John C. Tran
- Genentech, Inc., 1 DNA Way, South San Francisco, California 94080, United States
| | - Philip D. Compton
- Proteomics Center of Excellence, Northwestern University, 2170 Campus Drive, Evanston, Illinois 60208, United States
- Integrated Protein Technologies, Inc., 2170 Campus Drive, Evanston, IL 60208, United States
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Development of an efficient LC-MS peptide mapping method using accelerated sample preparation for monoclonal antibodies. J Chromatogr B Analyt Technol Biomed Life Sci 2020; 1137:121895. [DOI: 10.1016/j.jchromb.2019.121895] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 07/24/2019] [Accepted: 11/18/2019] [Indexed: 11/30/2022]
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Liu-Shin LPY, Fung A, Malhotra A, Ratnaswamy G. Evidence of disulfide bond scrambling during production of an antibody-drug conjugate. MAbs 2018; 10:1190-1199. [PMID: 30339473 DOI: 10.1080/19420862.2018.1521128] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Antibody-drug conjugates (ADCs) that are formed using thiol-maleimide chemistry are commonly produced by reactions that occur at or above neutral pHs. Alkaline environments can promote disulfide bond scrambling, and may result in the reconfiguration of interchain disulfide bonds in IgG antibodies, particularly in the IgG2 and IgG4 subclasses. IgG2-A and IgG2-B antibodies generated under basic conditions yielded ADCs with comparable average drug-to-antibody ratios and conjugate distributions. In contrast, the antibody disulfide configuration affected the distribution of ADCs generated under acidic conditions. The similarities of the ADCs derived from alkaline reactions were attributed to the scrambling of interchain disulfide bonds during the partial reduction step, where conversion of the IgG2-A isoform to the IgG2-B isoform was favored.
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Affiliation(s)
- Lily Pei-Yao Liu-Shin
- a Analytical and Formulation Development , Agensys, Inc., an affiliate of Astellas, Inc , Santa Monica , CA , USA.,b Department of Biochemistry and Molecular Biology , University of Miami Miller School of Medicine , Miami , FL , USA
| | - Adam Fung
- a Analytical and Formulation Development , Agensys, Inc., an affiliate of Astellas, Inc , Santa Monica , CA , USA
| | - Arun Malhotra
- b Department of Biochemistry and Molecular Biology , University of Miami Miller School of Medicine , Miami , FL , USA
| | - Gayathri Ratnaswamy
- a Analytical and Formulation Development , Agensys, Inc., an affiliate of Astellas, Inc , Santa Monica , CA , USA
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Cramer CN, Kelstrup CD, Olsen JV, Haselmann KF, Nielsen PK. Generic Workflow for Mapping of Complex Disulfide Bonds Using In-Source Reduction and Extracted Ion Chromatograms from Data-Dependent Mass Spectrometry. Anal Chem 2018; 90:8202-8210. [DOI: 10.1021/acs.analchem.8b01603] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Christian N. Cramer
- Protein Engineering, Global Research, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
- Proteomics Program, Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Christian D. Kelstrup
- Proteomics Program, Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Jesper V. Olsen
- Proteomics Program, Faculty of Health and Medical Sciences, The Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Kim F. Haselmann
- Protein Engineering, Global Research, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
| | - Peter Kresten Nielsen
- Protein Engineering, Global Research, Novo Nordisk A/S, Novo Nordisk Park, 2760 Måløv, Denmark
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