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Ai Y, Xu J, Gunawardena HP, Zare RN, Chen H. Investigation of Tryptic Protein Digestion in Microdroplets and in Bulk Solution. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1238-1249. [PMID: 35647885 PMCID: PMC10512443 DOI: 10.1021/jasms.2c00072] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent studies have shown that ultrafast enzymatic digestion of proteins can be achieved in microdroplet within 250 μs. Further investigation of peptides resulting from microdroplet digestion (MD) would be necessary to evaluate it as an alternative to the conventional bulk digestion for bottom-up and biotherapeutic protein characterization. Herein we examined and compared protein tryptic digestion in both MD and bulk solution. In the case of MD of β-lactoglobulin B, the preservation of long peptides was observed due to the short digestion time. In addition, MD is applicable to digest both high- and low-abundance proteins in mixture. In the case of digesting NIST 8671 mAb antibody containing a low level of commonly encountered host cell protein (HCP) PLBL2 (mAb:PLBL2 = 100:1 by weight), MD produced lower levels of digestion-induced chemical modifications of asparagine/glutamine deamidation, compared with overnight digestion. No significant difference between MD and bulk digestion was observed in terms of trypsin digestion specificity based on examination of semi- and unspecific-cleaved peptides. Our study suggests that MD, a fast digestion approach, could be adopted for bottom-up proteomics research and for peptide mapping of mAbs to characterize site-specific deamidation and glycosylation, for the purpose of development of biopharmaceuticals.
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Affiliation(s)
- Yongling Ai
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Jeffrey Xu
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
| | - Harsha P. Gunawardena
- Janssen Research & Development, The Janssen Pharmaceutical Companies of Johnson & Johnson, Spring House, Pennsylvania 19477, USA
| | - Richard N. Zare
- Department of Chemistry, Stanford University, Stanford, California 94305-5080, USA
| | - Hao Chen
- Department of Chemistry & Environmental Science, New Jersey Institute of Technology, Newark, New Jersey 07102, USA
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2
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Toole EN, Dufresne C, Ray S, Schwann A, Cook K, Ivanov AR. Rapid Highly-Efficient Digestion and Peptide Mapping of Adeno-Associated Viruses. Anal Chem 2021; 93:10403-10410. [PMID: 34291903 DOI: 10.1021/acs.analchem.1c02117] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Adeno-associated viruses (AAVs) comprise an area of rapidly growing interest due to their ability to act as a gene delivery vehicle in novel gene therapy strategies and vaccine development. Peptide mapping is a common technique in the biopharmaceutical industry to confirm the correct sequence, product purity, post-translational modifications (PTMs), and stability. However, conventional peptide mapping is time-consuming and has proven difficult to reproduce with viral capsids because of their high structural stability and the suboptimal localization of trypsin cleavage sites in the AAV protein sequences. In this study, we present an optimized peptide mapping-based workflow that provides thorough characterization within 1 day. This workflow is also highly reproducible due to its simplicity having very few steps and is easy to perform proteolytic digestion utilizing thermally stable pepsin, which is active at 70 °C in acidic conditions. The acidic conditions of the peptic digestions drive viral capsid denaturation and improve cleavage site accessibility. We characterized the efficiency and ease of digestion through peptide mapping of the AAV2 viral capsid protein. Using nanoflow liquid chromatography coupled with tandem mass spectrometry, we achieved 100% sequence coverage of the low-abundance VP1 capsid protein with a digestion process taking only 10 min to prepare and 45 min to complete the digestion.
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Affiliation(s)
- Estee Naggar Toole
- Thermo Fisher Scientific, West Palm Beach, Florida 33401, United States.,Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Craig Dufresne
- Thermo Fisher Scientific, West Palm Beach, Florida 33401, United States
| | - Somak Ray
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
| | - Alexander Schwann
- Thermo Fisher Scientific, Neuhofstrasse 11, 4153 Reinach, Switzerland
| | - Ken Cook
- Thermo Fisher Scientific, Stafford House, 1 Boundary Park, Hemel Hempstead HP2 7GE, United Kingdom
| | - Alexander R Ivanov
- Barnett Institute of Chemical and Biological Analysis, Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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Inter-laboratory study of an optimised peptide mapping workflow using automated trypsin digestion for monitoring monoclonal antibody product quality attributes. Anal Bioanal Chem 2020; 412:6833-6848. [PMID: 32710279 PMCID: PMC7496030 DOI: 10.1007/s00216-020-02809-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 06/09/2020] [Accepted: 07/07/2020] [Indexed: 11/27/2022]
Abstract
Peptide mapping analysis is a regulatory expectation to verify the primary structure of a recombinant product sequence and to monitor post-translational modifications (PTMs). Although proteolytic digestion has been used for decades, it remains a labour-intensive procedure that can be challenging to accurately reproduce. Here, we describe a fast and reproducible protocol for protease digestion that is automated using immobilised trypsin on magnetic beads, which has been incorporated into an optimised peptide mapping workflow to show method transferability across laboratories. The complete workflow has the potential for use within a multi-attribute method (MAM) approach in drug development, production and QC laboratories. The sample preparation workflow is simple, ideally suited to inexperienced operators and has been extensively studied to show global applicability and robustness for mAbs by performing sample digestion and LC-MS analysis at four independent sites in Europe. LC-MS/MS along with database searching was used to characterise the protein and determine relevant product quality attributes (PQAs) for further testing. A list of relevant critical quality attributes (CQAs) was then established by creating a peptide workbook containing the specific mass-to-charge (m/z) ratios of the modified and unmodified peptides of the selected CQAs, to be monitored in a subsequent test using LC-MS analysis. Data is provided that shows robust digestion efficiency and low levels of protocol induced PTMs. Graphical abstract ![]()
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Wang D, Nowak C, Mason B, Katiyar A, Liu H. Analytical artifacts in characterization of recombinant monoclonal antibody therapeutics. J Pharm Biomed Anal 2020; 183:113131. [DOI: 10.1016/j.jpba.2020.113131] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 01/12/2023]
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5
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Simpson JP, Fascione M, Bergström E, Wilson J, Collins MJ, Penkman KE, Thomas‐Oates J. Ionisation bias undermines the use of matrix-assisted laser desorption/ionisation for estimating peptide deamidation: Synthetic peptide studies demonstrate electrospray ionisation gives more reliable response ratios. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2019; 33:1049-1057. [PMID: 30908787 PMCID: PMC6594239 DOI: 10.1002/rcm.8441] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 03/11/2019] [Accepted: 03/17/2019] [Indexed: 06/09/2023]
Abstract
RATIONALE Although mass spectrometry (MS) is routinely used to determine deamination in peptide mixtures, the effects of the choice of ionisation source have not yet been investigated. In particular, matrix-assisted laser desorption/ionisation (MALDI) has become a popular tool with which to measure levels of glutamine deamidation in ancient proteins. Here we use model synthetic peptides to rigorously compare MALDI and electrospray ionisation (ESI). METHODS We used two synthetic peptides, with glutamine (Q) in one substituted for glutamic acid (E) in the other, to investigate the suitability of MALDI and ESI sources for the assessment of deamidation in peptides using MS. We also compared measurements of the same Q- and E-containing peptide mixtures using two different mass analysers (time-of-flight (TOF) and Fourier transform ion cyclotron resonance (FT-ICR)). RESULTS When standard mixtures of the Q- and E-containing peptides were analysed using MALDI, under-representation of the E-containing peptide was observed. This observation was consistent between analyses carried out using either TOF or FT-ICR-MS. When the same mixtures were analysed using ESI FT-ICR-MS, no ionisation bias was observed. CONCLUSIONS MALDI may not be a suitable ionisation method for the determination of deamidation in peptide mixtures. However, ESI was successfully used to determine the ratio in known mixtures of Q- and E-containing peptides. These preliminary observations warrant further investigation into ionisation bias when measuring deamidation in other peptide sequences.
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Affiliation(s)
| | | | - Ed Bergström
- Department of ChemistryUniversity of YorkYorkUK
- Centre of Excellence in Mass SpectrometryUniversity of YorkYorkUK
| | - Julie Wilson
- Department of ChemistryUniversity of YorkYorkUK
- Department of MathematicsUniversity of YorkYorkUK
| | | | | | - Jane Thomas‐Oates
- Department of ChemistryUniversity of YorkYorkUK
- Centre of Excellence in Mass SpectrometryUniversity of YorkYorkUK
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Háda V, Bagdi A, Bihari Z, Timári SB, Fizil Á, Szántay C. Recent advancements, challenges, and practical considerations in the mass spectrometry-based analytics of protein biotherapeutics: A viewpoint from the biosimilar industry. J Pharm Biomed Anal 2018; 161:214-238. [PMID: 30205300 DOI: 10.1016/j.jpba.2018.08.024] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2018] [Revised: 08/08/2018] [Accepted: 08/10/2018] [Indexed: 01/22/2023]
Abstract
The extensive analytical characterization of protein biotherapeutics, especially of biosimilars, is a critical part of the product development and registration. High-resolution mass spectrometry became the primary analytical tool used for the structural characterization of biotherapeutics. Its high instrumental sensitivity and methodological versatility made it possible to use this technique to characterize both the primary and higher-order structure of these proteins. However, even by using high-end instrumentation, analysts face several challenges with regard to how to cope with industrial and regulatory requirements, that is, how to obtain accurate and reliable analytical data in a time- and cost-efficient way. New sample preparation approaches, measurement techniques and data evaluation strategies are available to meet those requirements. The practical considerations of these methods are discussed in the present review article focusing on hot topics, such as reliable and efficient sequencing strategies, minimization of artefact formation during sample preparation, quantitative peptide mapping, the potential of multi-attribute methodology, the increasing role of mass spectrometry in higher-order structure characterization and the challenges of MS-based identification of host cell proteins. On the basis of the opportunities in new instrumental techniques, methodological advancements and software-driven data evaluation approaches, for the future one can envision an even wider application area for mass spectrometry in the biopharmaceutical industry.
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Affiliation(s)
- Viktor Háda
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary.
| | - Attila Bagdi
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | - Zsolt Bihari
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | | | - Ádám Fizil
- Analytical Department of Biotechnology, Gedeon Richter Plc, Hungary
| | - Csaba Szántay
- Spectroscopic Research Department, Gedeon Richter Plc, Hungary.
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7
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Hao P, Adav SS, Gallart-Palau X, Sze SK. Recent advances in mass spectrometric analysis of protein deamidation. MASS SPECTROMETRY REVIEWS 2017; 36:677-692. [PMID: 26763661 DOI: 10.1002/mas.21491] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2015] [Revised: 12/28/2015] [Accepted: 12/28/2015] [Indexed: 06/05/2023]
Abstract
Protein deamidation has been proposed to represent a "molecular clock" that progressively disrupts protein structure and function in human degenerative diseases and natural aging. Importantly, this spontaneous process can also modify therapeutic proteins by altering their purity, stability, bioactivity, and antigenicity during drug synthesis and storage. Deamidation occurs non-enzymatically in vivo, but can also take place spontaneously in vitro, hence artificial deamidation during proteomic sample preparation can hamper efforts to identify and quantify endogenous deamidation of complex proteomes. To overcome this, mass spectrometry (MS) can be used to conduct rigorous site-specific characterization of protein deamidation due to the high sensitivity, speed, and specificity offered by this technique. This article reviews recent progress in MS analysis of protein deamidation and discusses the strengths and limitations of common "top-down" and "bottom-up" approaches. Recent advances in sample preparation methods, chromatographic separation, MS technology, and data processing have for the first time enabled the accurate and reliable characterization of protein modifications in complex biological samples, yielding important new data on how deamidation occurs across the entire proteome of human cells and tissues. These technological advances will lead to a better understanding of how deamidation contributes to the pathology of biological aging and major degenerative diseases. © 2016 Wiley Periodicals, Inc. Mass Spec Rev 36:677-692, 2017.
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Affiliation(s)
- Piliang Hao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Sunil S Adav
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Xavier Gallart-Palau
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, 637551, Singapore
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8
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Yin S, Zhang C, Li Z, Wang Q, Shi H, Yu R, Liu Y, Su Z. Identification, characterization, and stabilization of the deamidation degradation of recombinant human tumor necrosis factor-α. Process Biochem 2017. [DOI: 10.1016/j.procbio.2016.11.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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9
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Kori Y, Patel R, Neill A, Liu H. A conventional procedure to reduce Asn deamidation artifacts during trypsin peptide mapping. J Chromatogr B Analyt Technol Biomed Life Sci 2016; 1009-1010:107-13. [DOI: 10.1016/j.jchromb.2015.12.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2015] [Revised: 12/04/2015] [Accepted: 12/07/2015] [Indexed: 12/12/2022]
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10
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Chen HJC, Chen YC, Hsiao CF, Chen PF. Mass Spectrometric Analysis of Glyoxal and Methylglyoxal-Induced Modifications in Human Hemoglobin from Poorly Controlled Type 2 Diabetes Mellitus Patients. Chem Res Toxicol 2015; 28:2377-89. [DOI: 10.1021/acs.chemrestox.5b00380] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hauh-Jyun Candy Chen
- Department
of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
| | - Yu-Chin Chen
- Department
of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
| | - Chiung-Fong Hsiao
- Department
of Chemistry and Biochemistry, National Chung Cheng University, 168 University Road, Ming-Hsiung, Chia-Yi 62142, Taiwan
| | - Pin-Fan Chen
- Buddhist Dalin Tzu Chi General Hospital, No.2, Minsheng Road, Dalin, Chia-Yi 622, Taiwan
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11
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Li W, Kerwin JL, Schiel J, Formolo T, Davis D, Mahan A, Benchaar SA. Structural Elucidation of Post-Translational Modifications in Monoclonal Antibodies. ACS SYMPOSIUM SERIES 2015. [DOI: 10.1021/bk-2015-1201.ch003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Wenzhou Li
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - James L. Kerwin
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - John Schiel
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Trina Formolo
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Darryl Davis
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Andrew Mahan
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
| | - Sabrina A. Benchaar
- Amgen Inc., Thousand Oaks, California 91320, United States
- Sanovas Inc., Sausalito, California 94965, United States
- Analytical Chemistry Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899, United States
- Janssen Research and Development, LLC, Spring House, Pennsylvania 19477, United States
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12
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Affiliation(s)
- Piliang Hao
- School of Biological Sciences, Nanyang Technological University Singapore
- Singapore Centre on Environmental Life Sciences Engineering, Nanyang Technological University Singapore
| | - Siu Kwan Sze
- School of Biological Sciences, Nanyang Technological University Singapore
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13
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Formolo T, Heckert A, Phinney KW. Analysis of deamidation artifacts induced by microwave-assisted tryptic digestion of a monoclonal antibody. Anal Bioanal Chem 2014; 406:6587-98. [PMID: 25080027 DOI: 10.1007/s00216-014-8043-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2014] [Revised: 07/08/2014] [Accepted: 07/16/2014] [Indexed: 12/17/2022]
Abstract
The thorough characterization of biopharmaceuticals is essential for ensuring their quality and safety since many potential variations can cause changes to the properties of a drug that may be detrimental to the patient such as decreased efficacy, shorter half-life or increased immunogenicity. Prior to approval and release, protein-based drugs are subject to a battery of analyses to assess the nature of those parameters that are considered critical quality attributes. In some cases the analytical method used may itself cause modifications that are impossible to distinguish from those induced by the intended test conditions (e.g. storage time/temperature, light exposure) which are used to assess drug stability. It is therefore important to develop and utilize analytical methods which impose as few artifactual modifications as possible. Asparagine deamidation is a common protein modification and it is known to be induced during tryptic digestion. Therefore we examined common tryptic digestion protocols and compared their propensities towards asparagine modification. Since microwave assisted hydrolysis techniques are often used to shorten digestion times and the effect on deamidation is unknown we sought to compare this method against alternate digestion protocols.
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Affiliation(s)
- Trina Formolo
- Material Measurement Laboratory, Biomolecular Measurement Division, National Institute of Standards and Technology, 100 Bureau Drive, Stop 8314, Gaithersburg, MD, 20899, USA,
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Mikkat S, Kischstein T, Kreutzer M, Glocker MO. Mass spectrometric peptide analysis of 2DE-separated mouse spinal cord and rat hippocampus proteins suggests an NGxG motif of importance for in vivo deamidation. Electrophoresis 2013; 34:1610-8. [DOI: 10.1002/elps.201200682] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2012] [Revised: 02/11/2013] [Accepted: 02/20/2013] [Indexed: 12/16/2022]
Affiliation(s)
| | - Timo Kischstein
- Oscar Langendorff Institute of Physiology; University Medicine Rostock; Rostock; Germany
| | - Michael Kreutzer
- Proteome Center Rostock; University Medicine Rostock; Rostock; Germany
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15
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Quantitation of asparagine deamidation by isotope labeling and liquid chromatography coupled with mass spectrometry analysis. Anal Biochem 2013; 432:16-22. [DOI: 10.1016/j.ab.2012.09.024] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2012] [Accepted: 09/17/2012] [Indexed: 12/20/2022]
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16
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Du Y, Wang F, May K, Xu W, Liu H. Determination of Deamidation Artifacts Introduced by Sample Preparation Using 18O-Labeling and Tandem Mass Spectrometry Analysis. Anal Chem 2012; 84:6355-60. [DOI: 10.1021/ac3013362] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Yi Du
- Merck Research Laboratory, 1011
Morris Avenue, Union, New Jersey 07083, United States
| | - Fengqiang Wang
- Merck Research Laboratory, 1011
Morris Avenue, Union, New Jersey 07083, United States
| | - Kimberly May
- Merck Research Laboratory, 1011
Morris Avenue, Union, New Jersey 07083, United States
| | - Wei Xu
- Merck Research Laboratory, 1011
Morris Avenue, Union, New Jersey 07083, United States
| | - Hongcheng Liu
- Merck Research Laboratory, 1011
Morris Avenue, Union, New Jersey 07083, United States
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18
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Stroop SD, Conca DM, Lundgard RP, Renz ME, Peabody LM, Leigh SD. Photosensitizers Form in Histidine Buffer and Mediate the Photodegradation of a Monoclonal Antibody. J Pharm Sci 2011; 100:5142-55. [DOI: 10.1002/jps.22714] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2011] [Revised: 06/29/2011] [Accepted: 07/01/2011] [Indexed: 11/09/2022]
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19
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Hao P, Ren Y, Alpert AJ, Sze SK. Detection, evaluation and minimization of nonenzymatic deamidation in proteomic sample preparation. Mol Cell Proteomics 2011; 10:O111.009381. [PMID: 21784994 DOI: 10.1074/mcp.o111.009381] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Identification of deamidated sites in proteins is commonly used for assignment of N-glycosylation sites. It is also important for assessing the role of deamidation in vivo. However, nonenzymatic deamidation occurs easily in peptides under conditions commonly used in treatment with trypsin and PNGase F. The impact on proteomic sample preparation has not yet been evaluated systematically. In addition, the (13)C peaks of amidated peptides can be misassigned as monoisotopic peaks of the corresponding deamidated ones in database searches. The 19.34 mDa mass difference between them is proposed as a means for eliminating the resulting false positive identifications in large-scale proteomic analysis. We evaluated five groups of proteomic data, obtained mainly through an electrostatic repulsion-hydrophilic interaction chromatography (ERLIC)-reverse phase (RP) chromatography sequence, and ascertained that nonenzymatic asparagine deamidation occurred to some extent on 4-9% of the peptides, resulting in the false positive identification of many N-glycosylation sites. A comprehensive investigation indicated that the chief causative factors were the mildly alkaline pH and prolonged incubations at 37 °C during proteomic sample preparation. An improved protocol is proposed featuring tryptic digestion at pH 6 and deglycosylation at pH 5, resulting in a significant decrease in nonenzymatic deamidation while conserving adequate digestion efficiency. The number of identified deamidation sites was improved significantly by increasing the sample loading amount in liquid chromatography-tandem MS. This permitted the identification of a significant number of glutamine deamidation sites, which featured sequence motifs largely different from those for asparagine deamidation: -Q-V-, -Q-L- and -Q-G- and, to a lesser extent, -Q-A- and -Q-E-.
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Affiliation(s)
- Piliang Hao
- School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore
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20
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Ren D, Pipes GD, Liu D, Shih LY, Nichols AC, Treuheit MJ, Brems DN, Bondarenko PV. An improved trypsin digestion method minimizes digestion-induced modifications on proteins. Anal Biochem 2009; 392:12-21. [DOI: 10.1016/j.ab.2009.05.018] [Citation(s) in RCA: 136] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2009] [Revised: 05/11/2009] [Accepted: 05/12/2009] [Indexed: 11/25/2022]
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21
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Suh MJ, Alami H, Clark DJ, Parmar PP, Robinson JM, Huang ST, Fleischmann RD, Peterson SN, Pieper R. Widespread Occurrence of Non-Enzymatic Deamidations of Asparagine Residues in Yersinia pestis Proteins Resulting from Alkaline pH Membrane Extraction Conditions. ACTA ACUST UNITED AC 2008; 1:106-115. [PMID: 20428468 DOI: 10.2174/1875039700801010106] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Extraction of crude membrane fractions with alkaline solutions, such as 100-200 mM Na(2)CO(3) (pH ~11), is often used to solubilize peripheral membrane proteins. Integral membrane proteins are largely retained in membrane pellets. We applied this method to the fractionation of membrane proteins of the plague bacterium Yersinia pestis. Extensive horizontal spot trains were observed in 2-DE gels. The pI values of the most basic spots part of such protein spot trains usually matched the computationally predicted pI values. Regular patterns of decreasing spot pI values and in silico analysis with the software ProMoST suggested ;n-1' deamidations of asparagine (N) and/or glutamine (Q) side chains for ;n' observed spots of a protein in a given spot train. MALDI-MS analysis confirmed the occurrence of deamidations, particularly in N side chains part of NG dipeptide motifs. In more than ten cases, tandem MS data for tryptic peptides provided strong evidence for deamidations, with y- and b-ion series increased by 1 Da following N-to-D substitutions. Horizontal spot trains in 2-DE gels were rare when alkaline extraction was omitted during membrane protein sample preparation. This study strongly supports the notion that exposure to alkaline pH solutions is a dominant cause of extensive N and Q side chain deamidations in proteins during sample preparation of membrane extracts. The modifications are of non-enzymatic nature and not physiologically relevant. Therefore, quantitative spot differences within spot trains in differential protein display experiments following the aforementioned sample preparation steps need to be interpreted cautiously.
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Affiliation(s)
- Moo-Jin Suh
- J. Craig Venter Institute, 9704 Medical Center Drive, Rockville, MD 20850, U.S.A
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Rivers J, McDonald L, Edwards IJ, Beynon RJ. Asparagine Deamidation and the Role of Higher Order Protein Structure. J Proteome Res 2008; 7:921-7. [DOI: 10.1021/pr070425l] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jenny Rivers
- Proteomics and Functional Genomics Group, Faculty of Veterinary Science, University of Liverpool, Crown Street, Liverpool L69 7ZJ, United Kingdom
| | - Lucy McDonald
- Proteomics and Functional Genomics Group, Faculty of Veterinary Science, University of Liverpool, Crown Street, Liverpool L69 7ZJ, United Kingdom
| | - Ian J. Edwards
- Proteomics and Functional Genomics Group, Faculty of Veterinary Science, University of Liverpool, Crown Street, Liverpool L69 7ZJ, United Kingdom
| | - Robert J. Beynon
- Proteomics and Functional Genomics Group, Faculty of Veterinary Science, University of Liverpool, Crown Street, Liverpool L69 7ZJ, United Kingdom
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23
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Yu LR, Zhu Z, Chan KC, Issaq HJ, Dimitrov DS, Veenstra TD. Improved Titanium Dioxide Enrichment of Phosphopeptides from HeLa Cells and High Confident Phosphopeptide Identification by Cross-Validation of MS/MS and MS/MS/MS Spectra. J Proteome Res 2007; 6:4150-62. [DOI: 10.1021/pr070152u] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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