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Wang CR, McFarlane LO, Pukala TL. Exploring snake venoms beyond the primary sequence: From proteoforms to protein-protein interactions. Toxicon 2024; 247:107841. [PMID: 38950738 DOI: 10.1016/j.toxicon.2024.107841] [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: 04/22/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/03/2024]
Abstract
Snakebite envenomation has been a long-standing global issue that is difficult to treat, largely owing to the flawed nature of current immunoglobulin-based antivenom therapy and the complexity of snake venoms as sophisticated mixtures of bioactive proteins and peptides. Comprehensive characterisation of venom compositions is essential to better understanding snake venom toxicity and inform effective and rationally designed antivenoms. Additionally, a greater understanding of snake venom composition will likely unearth novel biologically active proteins and peptides that have promising therapeutic or biotechnological applications. While a bottom-up proteomic workflow has been the main approach for cataloguing snake venom compositions at the toxin family level, it is unable to capture snake venom heterogeneity in the form of protein isoforms and higher-order protein interactions that are important in driving venom toxicity but remain underexplored. This review aims to highlight the importance of understanding snake venom heterogeneity beyond the primary sequence, in the form of post-translational modifications that give rise to different proteoforms and the myriad of higher-order protein complexes in snake venoms. We focus on current top-down proteomic workflows to identify snake venom proteoforms and further discuss alternative or novel separation, instrumentation, and data processing strategies that may improve proteoform identification. The current higher-order structural characterisation techniques implemented for snake venom proteins are also discussed; we emphasise the need for complementary and higher resolution structural bioanalytical techniques such as mass spectrometry-based approaches, X-ray crystallography and cryogenic electron microscopy, to elucidate poorly characterised tertiary and quaternary protein structures. We envisage that the expansion of the snake venom characterisation "toolbox" with top-down proteomics and high-resolution protein structure determination techniques will be pivotal in advancing structural understanding of snake venoms towards the development of improved therapeutic and biotechnology applications.
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Affiliation(s)
- C Ruth Wang
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Lewis O McFarlane
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide, 5005, Australia.
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2
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Wang CR, Harlington AC, Snel MF, Pukala TL. Characterisation of the forest cobra (Naja melanoleuca) venom using a multifaceted mass spectrometric-based approach. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2024; 1872:140992. [PMID: 38158032 DOI: 10.1016/j.bbapap.2023.140992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 12/20/2023] [Accepted: 12/25/2023] [Indexed: 01/03/2024]
Abstract
Snake venoms consist of highly biologically active proteins and peptides that are responsible for the lethal physiological effects of snakebite envenomation. In order to guide the development of targeted antivenom strategies, comprehensive understanding of venom compositions and in-depth characterisation of various proteoforms, often not captured by traditional bottom-up proteomic workflows, is necessary. Here, we employ an integrated 'omics' and intact mass spectrometry (MS)-based approach to profile the heterogeneity within the venom of the forest cobra (Naja melanoleuca), adopting different analytical strategies to accommodate for the dynamic molecular mass range of venom proteins present. The venom proteome of N. melanoleuca was catalogued using a venom gland transcriptome-guided bottom-up proteomics approach, revealing a venom consisting of six toxin superfamilies. The subtle diversity present in the venom components was further explored using reversed phase-ultra performance liquid chromatography (RP-UPLC) coupled to intact MS. This approach showed a significant increase in the number of venom proteoforms within various toxin families that were not captured in previous studies. Furthermore, we probed at the higher-order structures of the larger venom proteins using a combination of native MS and mass photometry and revealed significant structural heterogeneity along with extensive post-translational modifications in the form of glycosylation in these larger toxins. Here, we show the diverse structural heterogeneity of snake venom proteins in the venom of N. melanoleuca using an integrated workflow that incorporates analytical strategies that profile snake venom at the proteoform level, complementing traditional venom characterisation approaches.
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Affiliation(s)
- C Ruth Wang
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Alix C Harlington
- Department of Molecular and Biomedical Science, School of Biological Sciences, The University of Adelaide, Adelaide 5005, Australia
| | - Marten F Snel
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide 5005, Australia; Proteomics, Metabolomics and MS-Imaging Core Facility, South Australian Health and Medical Research Institute, Adelaide 5005, Australia
| | - Tara L Pukala
- Discipline of Chemistry, School of Physics, Chemistry and Earth Sciences, The University of Adelaide, Adelaide 5005, Australia.
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3
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Wang CF, Li L. Instrument-type effects on chemical isotope labeling LC-MS metabolome analysis: Quadrupole time-of-flight MS vs. Orbitrap MS. Anal Chim Acta 2022; 1226:340255. [PMID: 36068057 DOI: 10.1016/j.aca.2022.340255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 08/04/2022] [Accepted: 08/09/2022] [Indexed: 12/30/2022]
Abstract
Chemical isotope labeling (CIL) LC-MS is a powerful tool for metabolome analysis with markedly improved metabolomic coverage and quantification accuracy over the conventional LC-MS technique. In addition, with differential isotope labeling, each labeled metabolite is detected as a peak pair in the mass spectra, offering the possibility of differentiating true metabolite peaks from the singlet noise or background peaks. In this study, we examined the effects of instrument type on the detectability of true metabolites with a focus on the comparison of quadrupole time-of-flight (QTOF) and Orbitrap mass spectrometers. Using the same ultra-high-performance liquid chromatography setup and optimized running conditions for QTOF and Orbitrap, we compared the total number of peak pairs detected and identified from the two instruments using human urine and serum as the test samples. Many common peak pairs were detected from the two instruments; however, there were a significant number of unique peak pairs detected in each type of instrument. By combining the datasets obtained using QTOF and Orbitrap, the total number of peak pairs detected could be significantly increased. We also examined the effect of mass resolving power on peak pair detection in Orbitrap (60,000 vs. 120,000 resolution). The observed differences in peak pair detectability were much less than those of QTOF vs. Orbitrap. However, the type of peak pairs detected using different resolutions could be somewhat different, offering the possibility of increasing the overall number of peak pairs by combining the two datasets obtained at two different resolutions. The results from this study clearly indicate that instrument type can have a profound effect on metabolite detection in CIL LC-MS. Therefore, comparison of metabolome data generated using different instruments needs to be carefully done. Moreover, future research (e.g., hardware modifications) is warranted to minimize the differences in order to generate more reproducible metabolome data from different types of instruments.
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Affiliation(s)
- Chu-Fan Wang
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada
| | - Liang Li
- Department of Chemistry, University of Alberta, Edmonton, Alberta, Canada.
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4
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N-Glycosylation of monoclonal antibody therapeutics: A comprehensive review on significance and characterization. Anal Chim Acta 2022; 1209:339828. [DOI: 10.1016/j.aca.2022.339828] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 04/06/2022] [Accepted: 04/09/2022] [Indexed: 01/02/2023]
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5
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Naumann L, Schlossbauer P, Klingler F, Hesse F, Otte K, Neusüß C. High throughput glycosylation analysis of intact monoclonal antibodies by mass spectrometry coupled with capillary electrophoresis and liquid chromatography. J Sep Sci 2022; 45:2034-2044. [PMID: 35044720 DOI: 10.1002/jssc.202100865] [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: 10/27/2021] [Revised: 01/05/2022] [Accepted: 01/08/2022] [Indexed: 11/07/2022]
Abstract
The analysis of monoclonal antibodies glycosylation is a crucial quality control attribute of biopharmaceutical drugs. High throughput screening approaches for antibody glycoform analysis are required in various stages of process optimization. Here, we present high throughput screening suitable mass spectrometry-based workflows for the analysis of intact antibody glycosylation out of cell supernatants. Capillary electrophoresis and liquid chromatography were coupled with quadrupole time-of-flight MS or Orbitrap MS. Both separation methods offer fast separation (10-15 min) and the capability to prevent the separated cell supernatant matrix to enter the MS by post-separation valving. Both MS instruments provide comparable results and both are sufficient to determine the glycosylation pattern of the five major glycoforms of the measured antibodies. However, the Orbitrap yields higher sensitivity of 25 μg/mL (CE-nanoCEasy-Orbitrap MS) and 5 μg/mL (LC-Orbitrap MS). Data processing was optimized for a faster processing and easier detection of low abundant glycoforms based on averaged charge-deconvoluted mass spectra. This approach combines a non-target glycoform analysis, while yielding the same glycosylation pattern as the traditional approach based on extracted ion traces. The presented methods enable the high throughput screening of the glycosylation pattern of antibodies down to low μg/mL-range out of cell supernatant without any sample preparation. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Lukas Naumann
- Department of Chemistry, Aalen University, Beethovenstraße 1, Aalen, 73430, Germany
| | - Patrick Schlossbauer
- Department of applied Biotechnology, Biberach University of Applied Sciences, Karlstraße 6-11, Biberach, 88400, Germany
| | - Florian Klingler
- Department of applied Biotechnology, Biberach University of Applied Sciences, Karlstraße 6-11, Biberach, 88400, Germany
| | - Friedemann Hesse
- Department of applied Biotechnology, Biberach University of Applied Sciences, Karlstraße 6-11, Biberach, 88400, Germany
| | - Kerstin Otte
- Department of applied Biotechnology, Biberach University of Applied Sciences, Karlstraße 6-11, Biberach, 88400, Germany
| | - Christian Neusüß
- Department of Chemistry, Aalen University, Beethovenstraße 1, Aalen, 73430, Germany
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6
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Eremin DB, Fokin VV. Dual Electrospray Ionization Enhancement of Proteins Enabled by DMSO Supercharging Reagent. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:203-206. [PMID: 34850625 DOI: 10.1021/jasms.1c00280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Supercharging reagents assist protein ionization by producing higher charge states and increasing signal intensities, thus improving sensitivity. Described here is an approach to employ a dual-spray ionization source with DMSO as a supercharging reagent to expand in-source supercharging. Under denaturing conditions, dual-source supercharging enhances ionization up to an order of magnitude for proteins of various properties and sizes, but the effect is not uniform. Efficient mixing of solutions from two nebulizing plumes was observed, which allowed sufficient transfer of supercharging molecules to a protein. The described method and proposed mechanism require at least 2.5% of DMSO to produce visible enhancement.
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Affiliation(s)
- Dmitry B Eremin
- Bridge Institute, University of Southern California, 1002 Childs Way, Los Angeles, California 90089-3502, United States
- Loker Hydrocarbon Research Institute and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1661, United States
| | - Valery V Fokin
- Bridge Institute, University of Southern California, 1002 Childs Way, Los Angeles, California 90089-3502, United States
- Loker Hydrocarbon Research Institute and Department of Chemistry, University of Southern California, Los Angeles, California 90089-1661, United States
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7
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The challenge of detecting modifications on proteins. Essays Biochem 2020; 64:135-153. [PMID: 31957791 DOI: 10.1042/ebc20190055] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Revised: 12/17/2019] [Accepted: 12/19/2019] [Indexed: 12/16/2022]
Abstract
Post-translational modifications (PTMs) are integral to the regulation of protein function, characterising their role in this process is vital to understanding how cells work in both healthy and diseased states. Mass spectrometry (MS) facilitates the mass determination and sequencing of peptides, and thereby also the detection of site-specific PTMs. However, numerous challenges in this field continue to persist. The diverse chemical properties, low abundance, labile nature and instability of many PTMs, in combination with the more practical issues of compatibility with MS and bioinformatics challenges, contribute to the arduous nature of their analysis. In this review, we present an overview of the established MS-based approaches for analysing PTMs and the common complications associated with their investigation, including examples of specific challenges focusing on phosphorylation, lysine acetylation and redox modifications.
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Scientific Best Practices for Primary Sequence Confirmation and Sequence Variant Analysis in the Development of Therapeutic Proteins. J Pharm Sci 2020; 110:619-626. [PMID: 33212163 DOI: 10.1016/j.xphs.2020.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Revised: 11/04/2020] [Accepted: 11/10/2020] [Indexed: 02/01/2023]
Abstract
In this commentary, we will provide a high-level introduction into LC-MS product characterization methodologies deployed throughout biopharmaceutical development. The ICH guidelines for early and late phase filings is broad so that it is applicable to diverse biotherapeutic products in the clinic and industry pipelines. This commentary is meant to address areas of protein primary sequence confirmation and sequence variant analysis where ambiguity exists in industry on the specific scope of work that is needed to fulfill the general guidance that is given in sections Q5b and Q6b. This commentary highlights the discussion and outcomes of two recent workshops centering on the application of LC-MS to primary structure confirmation and sequence variant analysis (SVA) that were held at the 2018 and 2019 CASSS Practical Applications of Mass Spectrometry in the Biotechnology Industry Symposia in San Francisco, CA and Chicago, IL, respectively. Recommendations from the conferences fall into two distinct but related areas; 1) consolidation of opinions amongst industry stakeholders on the specific definitions of peptide mapping and peptide sequencing for primary structure confirmation and the technologies used for both, as they relate to regulatory expectations and submissions and 2) development of fit-for-purpose strategy to define appropriate assay controls in SVA experiments.
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Nabeshima Y, Abe C, Kawauchi T, Hiroi T, Uto Y, Nabeshima YI. Simple method for large-scale production of macrophage activating factor GcMAF. Sci Rep 2020; 10:19122. [PMID: 33154460 PMCID: PMC7645693 DOI: 10.1038/s41598-020-75571-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Accepted: 10/16/2020] [Indexed: 11/29/2022] Open
Abstract
Human group-specific component protein (Gc protein) is a multifunctional serum protein which has three common allelic variants, Gc1F, Gc1S and Gc2 in humans. Gc1 contains an O-linked trisaccharide [sialic acid-galactose-N-acetylgalactosamine (GalNAc)] on the threonine420 (Thr420) residue and can be converted to a potent macrophage activating factor (GcMAF) by selective removal of sialic acid and galactose, leaving GalNAc at Thr420. In contrast, Gc2 is not glycosylated. GcMAF is considered a promising candidate for immunotherapy and antiangiogenic therapy of cancers and has attracted great interest, but it remains difficult to compare findings among research groups because different procedures have been used to prepare GcMAF. Here, we present a simple, practical method to prepare high-quality GcMAF by overexpressing Gc-protein in a serum-free suspension culture of ExpiCHO-S cells, without the need for a de-glycosylation step. We believe this protocol is suitable for large-scale production of GcMAF for functional analysis and clinical testing.
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Affiliation(s)
- Yoko Nabeshima
- Laboratory of Molecular Life Science, Center of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, 2-2 Minatojima-Minamimachi Chuo-ku, Kobe, 650-0047, Japan
| | - Chiaki Abe
- Laboratory of Molecular Life Science, Center of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, 2-2 Minatojima-Minamimachi Chuo-ku, Kobe, 650-0047, Japan
| | - Takeshi Kawauchi
- Laboratory of Molecular Life Science, Center of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, 2-2 Minatojima-Minamimachi Chuo-ku, Kobe, 650-0047, Japan
| | - Tomoko Hiroi
- Laboratory of Molecular Life Science, Center of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, 2-2 Minatojima-Minamimachi Chuo-ku, Kobe, 650-0047, Japan
| | - Yoshihiro Uto
- Graduate School of Technology, Industrial and Social Science, Tokushima University, Tokushima, 770-8506, Japan
| | - Yo-Ichi Nabeshima
- Laboratory of Molecular Life Science, Center of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, 2-2 Minatojima-Minamimachi Chuo-ku, Kobe, 650-0047, Japan.
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10
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Wolters C, Flandinet L, He C, Isa J, Orthous-Daunay FR, Thissen R, Hörst S, Vuitton V. Enhancing data acquisition for the analysis of complex organic matter in direct-infusion Orbitrap mass spectrometry using micro-scans. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2020; 34:e8818. [PMID: 32342561 DOI: 10.1002/rcm.8818] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Revised: 04/17/2020] [Accepted: 04/23/2020] [Indexed: 06/11/2023]
Abstract
RATIONALE Acquisition quality in analytical science is key to obtaining optimal data from a sample. In very high-resolution mass spectrometry, quality is driven by the optimization of multiple parameters, including the use of scans and micro-scans (or transients) for performing a Fourier transformation. METHODS Thirty-nine mass spectra of a single synthesized complex sample were acquired using various numbers of scans and micro-scans determined through a simple experimental design. An electrospray ionization source coupled with an LTQ Orbitrap XL™ mass spectrometer was used, and acquisition was performed using a single mass range. All the resulting spectra were treated in the same way to enable comparisons of assigned stoichiometric formulae between acquisitions. RESULTS Converting the number of scans into micro-scans enhances signal quality by lowering noise and reducing artifacts. This modification also increases the number of attributed stoichiometric formulae for an equivalent acquisition time, giving access to a larger molecular diversity for the analyzed complex sample. CONCLUSIONS For complex samples, the use of long acquisition times leads to optimal data quality, and the use of micro-scans instead of scans-only maximizes the number of attributed stoichiometric formulae.
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Affiliation(s)
- Cédric Wolters
- Univ. Grenoble Alpes, CNRS, IPAG, Grenoble, 38000, France
| | | | - Chao He
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, USA
| | - Junko Isa
- Univ. Grenoble Alpes, CNRS, IPAG, Grenoble, 38000, France
| | | | - Roland Thissen
- Université Paris-Saclay, CNRS, Institut de Chimie Physique UMR8000, Orsay, 91405, France
| | - Sarah Hörst
- Department of Earth and Planetary Sciences, Johns Hopkins University, Baltimore, MD, USA
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11
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Kourtchev I, Szeto P, O'Connor I, Popoola OAM, Maenhaut W, Wenger J, Kalberer M. Comparison of Heated Electrospray Ionization and Nanoelectrospray Ionization Sources Coupled to Ultra-High-Resolution Mass Spectrometry for Analysis of Highly Complex Atmospheric Aerosol Samples. Anal Chem 2020; 92:8396-8403. [PMID: 32394709 DOI: 10.1021/acs.analchem.0c00971] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Direct infusion analysis using soft ionization techniques coupled to ultra-high-resolution mass spectrometers (UHRMS) allows screening of thousands of organic species in complex samples. Despite the high analytical throughput of direct infusion, this technique is known to be prone to matrix effects caused by changes in the ionization efficiency of an analyte, ion suppression, or enhancement due to the presence of certain compounds and inorganic salts in the sample. In this study we compared two soft ionization sources, that is, heated electrospray ionization (HESI) and nano-ESI for the analysis of atmospheric aerosol samples in the negative ionization mode. In-source fragmentation tests were conducted and experiments involving sample desalting through solid-phase extraction (SPE) with a reversed phase functionalized polymeric sorbent and spiking samples with inorganic salt were performed. Both ionization sources showed specific advantages and disadvantages for the direct infusion analysis of atmospheric aerosol extracts. The mass spectra of aerosol samples analyzed using HESI contained a large number of high molecular weight homologues containing sulfur and nitrogen, suggesting that this source is prone to formation of salt adducts and noncovalent compounds in samples enriched with inorganic salts. Data from the same aerosol sample extracts analyzed using nanoelectrospray ionization (nano-ESI) show less adduct formation; however, a decrease in the number of homologues was observed, as well as loss of molecules at higher mass range, indicating that the nano-ESI source is more prone to ion suppression. Irrespective of ionization source, SPE pretreatment significantly improved ion recoveries for organic species with nonpolar and moderately polar functional groups, but lower recoveries were obtained for highly oxygenated molecules. Therefore, while SPE reduced in-source adduct formation, it also limited the range of compounds identified through a single analysis.
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Affiliation(s)
- I Kourtchev
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - P Szeto
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - I O'Connor
- School of Chemistry and Environmental Research Institute, University College Cork, College Road, Cork T12 K8AF, Ireland
| | - O A M Popoola
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - W Maenhaut
- Department of Chemistry, Ghent University, Krijgslaan 281, S12, Ghent 9000, Belgium
| | - J Wenger
- School of Chemistry and Environmental Research Institute, University College Cork, College Road, Cork T12 K8AF, Ireland
| | - M Kalberer
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K.,Department of Environmental Sciences, University of Basel, Klingelbergstrasse 27, Basel 4056, Switzerland
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12
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Zhu X, Huo S, Xue C, An B, Qu J. Current LC-MS-based strategies for characterization and quantification of antibody-drug conjugates. J Pharm Anal 2020; 10:209-220. [PMID: 32612867 PMCID: PMC7322744 DOI: 10.1016/j.jpha.2020.05.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 05/21/2020] [Accepted: 05/21/2020] [Indexed: 01/28/2023] Open
Abstract
The past few years have witnessed enormous progresses in the development of antibody-drug conjugates (ADCs). Consequently, comprehensive analysis of ADCs in biological systems is critical in supporting discovery, development and evaluation of these agents. Liquid chromatography-mass spectrometry (LC-MS) has emerged as a promising and versatile tool for ADC analysis across a wide range of scenarios, owing to its multiplexing ability, rapid method development, as well as the capability of analyzing a variety of targets ranging from small-molecule payloads to the intact protein with a high, molecular resolution. However, despite this tremendous potential, challenges persist due to the high complexity in both the ADC molecules and the related biological systems. This review summarizes the up-to-date LC-MS-based strategies in ADC analysis and discusses the challenges and opportunities in this rapidly-evolving field.
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Affiliation(s)
- Xiaoyu Zhu
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14214, USA.,New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, 14203, USA
| | - Shihan Huo
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14214, USA.,New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, 14203, USA
| | - Chao Xue
- New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, 14203, USA.,Department of Chemical and Biological Engineering, School of Engineering and Applied Science, University at Buffalo, State University of New York, Buffalo, NY, 14260, USA
| | - Bo An
- Exploratory Biomarker, In-vitro/In-vivo Translation, R&D Research, GlaxoSmithKline Pharmaceuticals, 1250 South Collegeville Rd, Collegeville, PA, 19426, USA
| | - Jun Qu
- Department of Pharmaceutical Sciences, School of Pharmacy & Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, NY, 14214, USA.,New York State Center of Excellence in Bioinformatics & Life Sciences, Buffalo, NY, 14203, USA
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13
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Affiliation(s)
| | | | - Jennifer S. Brodbelt
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, United States
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14
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Kilpatrick EL. An Improved Program for the Estimation of Protein Theoretical Relative Molecular Mass and Uncertainty. J Proteome Res 2019; 18:4072-4077. [PMID: 31584828 DOI: 10.1021/acs.jproteome.9b00554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Presented here is the National Institute of Standards and Technology (NIST) Mass Calculator, a software tool that provides both a relative molecular mass (Mr) value and an associated uncertainty value for a given protein sequence. The calculation of a protein Mr based on its amino acid residue sequence is performed by many software applications. Unfortunately, many of the results do not agree with each other. Reasons for this lack of consensus may include the use of rounded values, calculation errors, or alternative calculation methods, and it is often not possible to distinguish the source of the differences. Additionally, the result is provided without an estimate of precision. This would imply that the Mr is perfectly known when in fact it is not because the basis for the calculation, either the relative atomic masses or the standard atomic weights, are themselves provided as estimates. Until the release of the NIST Mass Calculator, there were no applications available to provide both an Mr value and an associated uncertainty value. Furthermore, the full disclosure of the computation methods and elemental values allows for independent verification of the results. The uncertainty is obtained via Monte Carlo simulation and is now a useful feature in light of the high resolution capability now available in the mass spectrometry of intact proteins.
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Affiliation(s)
- Eric L Kilpatrick
- Biomolecular Measurement Division, Material Measurement Laboratory , National Institute of Standards and Technology , 100 Bureau Drive , Gaithersburg , Maryland 20832 , United States
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15
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Camperi J, Pichon V, Delaunay N. Separation methods hyphenated to mass spectrometry for the characterization of the protein glycosylation at the intact level. J Pharm Biomed Anal 2019; 178:112921. [PMID: 31671335 DOI: 10.1016/j.jpba.2019.112921] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 10/07/2019] [Accepted: 10/09/2019] [Indexed: 01/26/2023]
Abstract
Glycosylation is one of the most common post-translational modifications of proteins that affects their biological activity, solubility, and half-life. Therefore, its characterization is of great interest in proteomic, particularly from a diagnostic and therapeutic point of view. However, the number and type of glycosylation sites, the degree of site occupancy and the different possible structures of glycans can lead to a very large number of isoforms for a given protein, called glycoforms. The identification of these glycoforms constitutes an important analytical challenge. Indeed, to attempt to characterize all of them, it is necessary to develop efficient separation methods associated with a sensitive and informative detection mode, such as mass spectrometry (MS). Most analytical methods are based on bottom-up proteomics, which consists in the analysis of the protein at the glycopeptides level after its digestion. Even if this approach provides essential information, including the localization and composition of glycans on the protein, it is also characterized by a loss of information on macro-heterogeneity, i.e. the nature of the glycans present on a given glycoform. The analysis of glycoforms at the intact level can overcome this disadvantage. The aim of this review is to detail the state-of-the art of separation methods that can be easily hyphenated with MS for the characterization of protein glycosylation at the intact level. The different electrophoretic and chromatographic approaches are discussed in detail. The miniaturization of these separation methods is also discussed with their potential applications. While the first studies focused on the development and optimization of the separation step to achieve high resolution between isoforms, the recent ones are much more application-oriented, such as clinical diagnosis, quality control, and glycoprotein monitoring in formulations or biological samples.
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Affiliation(s)
- Julien Camperi
- Laboratory of Analytical, Bioanalytical Sciences and Miniaturization, UMR CBI 8231 CNRS - ESPCI Paris, PSL University, Paris, France
| | - Valerie Pichon
- Laboratory of Analytical, Bioanalytical Sciences and Miniaturization, UMR CBI 8231 CNRS - ESPCI Paris, PSL University, Paris, France; Sorbonne Université, Paris, France
| | - Nathalie Delaunay
- Laboratory of Analytical, Bioanalytical Sciences and Miniaturization, UMR CBI 8231 CNRS - ESPCI Paris, PSL University, Paris, France.
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16
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Foreman DJ, Dziekonski ET, McLuckey SA. Maximizing Selective Cleavages at Aspartic Acid and Proline Residues for the Identification of Intact Proteins. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:34-44. [PMID: 29713964 PMCID: PMC6207472 DOI: 10.1007/s13361-018-1965-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Revised: 04/06/2018] [Accepted: 04/09/2018] [Indexed: 05/03/2023]
Abstract
A new approach for the identification of intact proteins has been developed that relies on the generation of relatively few abundant products from specific cleavage sites. This strategy is intended to complement standard approaches that seek to generate many fragments relatively non-selectively. Specifically, this strategy seeks to maximize selective cleavage at aspartic acid and proline residues via collisional activation of precursor ions formed via electrospray ionization (ESI) under denaturing conditions. A statistical analysis of the SWISS-PROT database was used to predict the number of arginine residues for a given intact protein mass and predict a m/z range where the protein carries a similar charge to the number of arginine residues thereby enhancing cleavage at aspartic acid residues by limiting proton mobility. Cleavage at aspartic acid residues is predicted to be most favorable in the m/z range of 1500-2500, a range higher than that normally generated by ESI at low pH. Gas-phase proton transfer ion/ion reactions are therefore used for precursor ion concentration from relatively high charge states followed by ion isolation and subsequent generation of precursor ions within the optimal m/z range via a second proton transfer reaction step. It is shown that the majority of product ion abundance is concentrated into cleavages C-terminal to aspartic acid residues and N-terminal to proline residues for ions generated by this process. Implementation of a scoring system that weights both ion fragment type and ion fragment area demonstrated identification of standard proteins, ranging in mass from 8.5 to 29.0 kDa. Graphical Abstract ᅟ.
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Affiliation(s)
- David J Foreman
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA
| | | | - Scott A McLuckey
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, IN, 47907-2084, USA.
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17
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Wang H, Leeming MG, Ho J, Donald WA. Origin and Prediction of Highly Specific Bond Cleavage Sites in the Thermal Activation of Intact Protein Ions. Chemistry 2018; 25:823-834. [DOI: 10.1002/chem.201804668] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2018] [Indexed: 11/09/2022]
Affiliation(s)
- Huixin Wang
- School of Chemistry University of New South Wales Sydney New South Wales Australia
| | - Michael G. Leeming
- School of Chemistry, Bio21 Institute of Molecular Science and Biotechnology The University of Melbourne Melbourne Victoria Australia
| | - Junming Ho
- School of Chemistry University of New South Wales Sydney New South Wales Australia
| | - William A. Donald
- School of Chemistry University of New South Wales Sydney New South Wales Australia
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18
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Affiliation(s)
- Bifan Chen
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Kyle A. Brown
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ziqing Lin
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
| | - Ying Ge
- Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Department of Cell and Regenerative Biology, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
- Human Proteomics Program, University of Wisconsin-Madison, Madison, Wisconsin 53706, United States
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19
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Kilpatrick LE, Phinney KW. Quantification of Total Vitamin-D-Binding Protein and the Glycosylated Isoforms by Liquid Chromatography–Isotope Dilution Mass Spectrometry. J Proteome Res 2017; 16:4185-4195. [DOI: 10.1021/acs.jproteome.7b00560] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Lisa E. Kilpatrick
- National Institute of Standards and Technology, Material Measurement
Laboratory, Biomolecular Measurement Division, 100 Bureau Drive, Stop 8314, Gaithersburg, Maryland 20899, United States
| | - Karen W. Phinney
- National Institute of Standards and Technology, Material Measurement
Laboratory, Biomolecular Measurement Division, 100 Bureau Drive, Stop 8314, Gaithersburg, Maryland 20899, United States
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