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Comprehensive identification of protein disulfide bonds with pepsin/trypsin digestion, Orbitrap HCD and Spectrum Identification Machine. J Proteomics 2018; 198:78-86. [PMID: 30557666 DOI: 10.1016/j.jprot.2018.12.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Revised: 12/04/2018] [Accepted: 12/12/2018] [Indexed: 01/02/2023]
Abstract
Disulfide bonds (SS) are post-translational modifications important for the proper folding and stabilization of many cellular proteins with therapeutic uses, including antibodies and other biologics. With budding advances of biologics and biosimilars, there is a mounting need for a robust method for accurate identification of SS. Even though several mass spectrometry methods have emerged for this task, their practical use rests on the broad effectiveness of both sample preparation methods and bioinformatics tools. Here we present a new protocol tailored toward mapping SS; it uses readily available reagents, instruments, and software. For sample preparation, a 4-h pepsin digestion at pH 1.3 followed by an overnight trypsin digestion at pH 6.5 can maximize the release of SS-containing peptides from non-reduced proteins, while minimizing SS scrambling. For LC/MS/MS analysis, SS-containing peptides can be efficiently fragmented with HCD in a Q Exactive Orbitrap mass spectrometer, preserving SS for subsequent identification. Our bioinformatics protocol describes how we tailored our freely downloadable and easy-to-use software, Spectrum Identification Machine for Cross-Linked Peptides (SIM-XL), to minimize false identification and facilitate manual validation of SS-peptide mass spectra. To substantiate this optimized method, we've comprehensively identified 14 out of 17 known SS in BSA. SIGNIFICANCE: Comprehensive and accurate identification of SS in proteins is critical for elucidating protein structures and functions. Yet, it is far from routine to accomplish this task in many analytical or core laboratories. Numerous published methods require complex sample preparation methods, specialized mass spectrometers and cumbersome or proprietary software tools, thus cannot be easily implemented in unspecialized laboratories. Here, we describe a robust and rapid SS mapping approach that utilizes readily available reagents, instruments, and software; it can be easily implemented in any analytical core laboratories, and tested for its impact on the research community.
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Rogstad S, Faustino A, Ruth A, Keire D, Boyne M, Park J. A Retrospective Evaluation of the Use of Mass Spectrometry in FDA Biologics License Applications. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:786-794. [PMID: 27873217 DOI: 10.1007/s13361-016-1531-9] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/09/2016] [Revised: 10/12/2016] [Accepted: 10/13/2016] [Indexed: 05/12/2023]
Abstract
The characterization sections of biologics license applications (BLAs) approved by the United States Food and Drug Administration (FDA) between 2000 and 2015 were investigated to examine the extent of the use of mass spectrometry. Mass spectrometry was found to be integral to the characterization of these biotherapeutics. Of the 80 electronically submitted monoclonal antibody and protein biotherapeutic BLAs included in this study, 79 were found to use mass spectrometric workflows for protein or impurity characterization. To further examine how MS is being used in successful BLAs, the applications were filtered based on the type and number of quality attributes characterized, the mass spectrometric workflows used (peptide mapping, intact mass analysis, and cleaved glycan analysis), the methods used to introduce the proteins into the gas phase (ESI, MALDI, or LC-ESI), and the specific types of instrumentation used. Analyses were conducted over a time course based on the FDA BLA approval to determine if any trends in utilization could be observed over time. Additionally, the different classes of protein-based biotherapeutics among the approved BLAs were clustered to determine if any trends could be attributed to the specific type of biotherapeutic. Graphical Abstract ᅟ.
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Affiliation(s)
- Sarah Rogstad
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA.
| | - Anneliese Faustino
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | - Ashley Ruth
- Biotechlogic, Inc., Glenview, IL, 60025, USA
| | - David Keire
- Division of Pharmaceutical Analysis, Office of Testing and Research, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
| | | | - Jun Park
- Office of Biotechnology Products, Center for Drug Evaluation and Research, U.S. Food and Drug Administration, Silver Spring, MD, 20993, USA
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3
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Roberts AG, Johnston EV, Shieh JH, Sondey JP, Hendrickson RC, Moore MAS, Danishefsky SJ. Fully Synthetic Granulocyte Colony-Stimulating Factor Enabled by Isonitrile-Mediated Coupling of Large, Side-Chain-Unprotected Peptides. J Am Chem Soc 2015; 137:13167-75. [PMID: 26401918 PMCID: PMC4617663 DOI: 10.1021/jacs.5b08754] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Human granulocyte colony-stimulating factor (G-CSF) is an endogenous glycoprotein involved in hematopoiesis. Natively glycosylated and nonglycosylated recombinant forms, lenograstim and filgrastim, respectively, are used clinically to manage neutropenia in patients undergoing chemotherapeutic treatment. Despite their comparable therapeutic potential, the purpose of O-linked glycosylation at Thr133 remains a subject of controversy. In light of this, we have developed a synthetic platform to prepare G-CSF aglycone with the goal of enabling access to native and designed glycoforms with site-selectivity and glycan homogeneity. To address the synthesis of a relatively large, aggregation-prone sequence, we advanced an isonitrile-mediated ligation method. The chemoselective activation and coupling of C-terminal peptidyl Gly thioacids with the N-terminus of an unprotected peptide provide ligated peptides directly in a manner complementary to that with conventional native chemical ligation-desulfurization strategies. Herein, we describe the details and application of this method as it enabled the convergent total synthesis of G-CSF aglycone.
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Affiliation(s)
- Andrew G. Roberts
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
| | - Eric V. Johnston
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
| | - Jae-Hung Shieh
- Cell Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
| | - Joseph P. Sondey
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
| | - Ronald C. Hendrickson
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
| | - Malcolm A. S. Moore
- Cell Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
| | - Samuel J. Danishefsky
- Laboratory for Bio-Organic Chemistry, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
- Chemical Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
- Cell Biology Program, Sloan Kettering Institute (SKI) for Cancer Research, New York, New York 10065, United States
- Department of Chemistry, Columbia University, New York, New York 10027, United States
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4
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Levy MJ, Gucinski AC, Boyne MT. Primary Sequence Confirmation of a Protein Therapeutic Using Top Down MS/MS and MS3. Anal Chem 2015; 87:6995-9. [DOI: 10.1021/acs.analchem.5b01113] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Michaella J. Levy
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of
Testing and Research, Division of Pharmaceutical Analysis, 645 S. Newstead Ave., St. Louis, Missouri 63110, United States
| | - Ashley C. Gucinski
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of
Testing and Research, Division of Pharmaceutical Analysis, 645 S. Newstead Ave., St. Louis, Missouri 63110, United States
| | - Michael T. Boyne
- U.S. Food and Drug Administration, Center for Drug Evaluation and Research, Office of
Testing and Research, Division of Pharmaceutical Analysis, 645 S. Newstead Ave., St. Louis, Missouri 63110, United States
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Tanaka T, Kajiwara T, Torigoe T, Okamoto Y, Sato N, Tamura Y. Cancer-associated oxidoreductase ERO1-α drives the production of tumor-promoting myeloid-derived suppressor cells via oxidative protein folding. THE JOURNAL OF IMMUNOLOGY 2015; 194:2004-10. [PMID: 25595776 DOI: 10.4049/jimmunol.1402538] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Endoplasmic reticulum disulfide oxidase ERO1-α plays a role in the formation of disulfide bonds in collaboration with protein disulfide isomerase. Disulfide bond formation is required for the proper conformation and function of secreted and cell surface proteins. We found that ERO1-α was overexpressed in a variety of tumor types; therefore, we examined its role in tumor growth. In BALB/c mice, knockdown of ERO1-α within 4T1 mouse mammary gland cancer (KD) cells caused retardation of in vivo tumor growth compared with tumor growth of scrambled control (SCR) cells. In contrast, when ERO1-α-overexpressed 4T1 (OE) cells were compared with mock control cells, OE cells showed augmented tumor growth. However, differences in tumor growth were not observed among four groups of nude mice, suggesting that expression of ERO1-α diminished antitumor immunity. We observed dense peritumoral granulocytic infiltrates in tumors of wild-type 4T1 and SCR cells but not KD cells, and these cells were identified as polymorphonuclear myeloid-derived suppressor cells (MDSCs). In addition, production of G-CSF and CXCL1/2, which have intramolecular disulfide bonds, from KD cells was significantly decreased compared with that from SCR cells. In contrast, OE cells produced a larger amount of these molecules than did mock cells. These changes were regulated at the posttranscriptional level. These results suggest that overexpression of ERO1-α in the tumor inhibits the T cell response by recruiting polymorphonuclear MDSCs via regulation of MDSC-prone cytokines and chemokines.
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Affiliation(s)
- Tsutomu Tanaka
- Department of Pathology, Sapporo Medical University, Sapporo 060-8556, Japan; The United Graduate School of Veterinary Sciences, Yamaguchi University, Yamaguchi 753-8551, Japan
| | - Toshimitsu Kajiwara
- Department of Pathology, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Toshihiko Torigoe
- Department of Pathology, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Yoshiharu Okamoto
- Joint Department of Veterinary Medicine, Tottori University, Tottori 680-8553, Japan; and
| | - Noriyuki Sato
- Department of Pathology, Sapporo Medical University, Sapporo 060-8556, Japan
| | - Yasuaki Tamura
- Department of Molecular Therapeutics, Center for Food and Medical Innovation, Hokkaido University, Sapporo 001-0021, Japan
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Addepalli B. Detection of disulfide linkage by chemical derivatization and mass spectrometry. Methods Mol Biol 2015; 1255:117-126. [PMID: 25487208 DOI: 10.1007/978-1-4939-2175-1_10] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The location of disulfide linkage(s) or status of unpaired cysteines is a critical structural feature required for the characterization of three-dimensional structure of a protein and for the correlation of protein structure-function relationships. Cysteine, with its reactive thiol group, can undergo enzymatic or oxidative posttranslational modification in response to changing redox conditions to signal a cascade of downstream reactions. In such a situation, it becomes even more critical to obtain the information on the pair of cysteines involved in such a redox switch operation. Here, a method involving chemical derivatization and liquid chromatography-mass spectrometry (LC-MS) is described to determine the cysteine residues involved in disulfide bond formation for a protein containing multiple cysteines in its sequence.
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Affiliation(s)
- Balasubrahmanyam Addepalli
- Rieveschl Laboratories for Mass Spectrometry, Department of Chemistry, University of Cincinnati, 312 College Dr, Cincinnati, OH, 45221, USA,
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Borges CR, Sherma ND. Techniques for the analysis of cysteine sulfhydryls and oxidative protein folding. Antioxid Redox Signal 2014; 21:511-31. [PMID: 24383618 PMCID: PMC4076987 DOI: 10.1089/ars.2013.5559] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
SIGNIFICANCE Modification of cysteine thiols dramatically affects protein function and stability. Hence, the abilities to quantify specific protein sulfhydryl groups within complex biological samples and map disulfide bond structures are crucial to gaining greater insights into how proteins operate in human health and disease. RECENT ADVANCES Many different molecular probes are now commercially available to label and track cysteine residues at great sensitivity. Coupled with mass spectrometry, stable isotope-labeled sulfhydryl-specific reagents can provide previously unprecedented molecular insights into the dynamics of cysteine modification. Likewise, the combined application of modern mass spectrometers with improved sample preparation techniques and novel data mining algorithms is beginning to routinize the analysis of complex protein disulfide structures. CRITICAL ISSUES Proper application of these modern tools and techniques, however, still requires fundamental understanding of sulfhydryl chemistry as well as the assumptions that accompany sample preparation and underlie effective data interpretation. FUTURE DIRECTIONS The continued development of tools, technical approaches, and corresponding data processing algorithms will, undoubtedly, facilitate site-specific protein sulfhydryl quantification and disulfide structure analysis from within complex biological mixtures with ever-improving accuracy and sensitivity. Fully routinizing disulfide structure analysis will require an equal but balanced focus on sample preparation and corresponding mass spectral dataset reproducibility.
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Affiliation(s)
- Chad R Borges
- Center for Personalized Diagnostics, The Biodesign Institute at Arizona State University , Tempe, Arizona
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Liu F, van Breukelen B, Heck AJR. Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS. Mol Cell Proteomics 2014; 13:2776-86. [PMID: 24980484 DOI: 10.1074/mcp.o114.039057] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Disulfide bond identification is important for a detailed understanding of protein structures, which directly affect their biological functions. Here we describe an integrated workflow for the fast and accurate identification of authentic protein disulfide bridges. This novel workflow incorporates acidic proteolytic digestion using pepsin to eliminate undesirable disulfide reshuffling during sample preparation and a novel search engine, SlinkS, to directly identify disulfide-bridged peptides isolated via electron transfer higher energy dissociation (EThcD). In EThcD fragmentation of disulfide-bridged peptides, electron transfer dissociation preferentially leads to the cleavage of the S-S bonds, generating two intense disulfide-cleaved peptides as primary fragment ions. Subsequently, higher energy collision dissociation primarily targets unreacted and charge-reduced precursor ions, inducing peptide backbone fragmentation. SlinkS is able to provide the accurate monoisotopic precursor masses of the two disulfide-cleaved peptides and the sequence of each linked peptide by matching the remaining EThcD product ions against a linear peptide database. The workflow was validated using a protein mixture containing six proteins rich in natural disulfide bridges. Using this pepsin-based workflow, we were able to efficiently and confidently identify a total of 31 unique Cys-Cys bonds (out of 43 disulfide bridges present), with no disulfide reshuffling products detected. Pepsin digestion not only outperformed trypsin digestion in terms of the number of detected authentic Cys-Cys bonds, but, more important, prevented the formation of artificially reshuffled disulfide bridges due to protein digestion under neutral pH. Our new workflow therefore provides a precise and generic approach for disulfide bridge mapping, which can be used to study protein folding, structure, and stability.
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Affiliation(s)
- Fan Liu
- From the ‡Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands; §Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Bas van Breukelen
- From the ‡Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands; §Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
| | - Albert J R Heck
- From the ‡Biomolecular Mass Spectrometry and Proteomics Bijvoet Centre for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, University of Utrecht, Padualaan 8, 3584 CH, Utrecht, The Netherlands; §Netherlands Proteomics Center, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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