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Miyagi M, Kiesel E, Neumbo K, Nakazawa T. Deuterium Labeling of Isoaspartic and Isoglutamic Acids for Mass Spectrometry Analysis. Anal Chem 2024; 96:3077-3086. [PMID: 38344941 PMCID: PMC10984558 DOI: 10.1021/acs.analchem.3c05194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/31/2024] [Accepted: 02/02/2024] [Indexed: 04/02/2024]
Abstract
Isoaspartic acid (isoAsp) is a common protein modification that spontaneously arises from asparagine or aspartic acid and has been linked to various diseases and health conditions. However, current methods for identifying isoAsp sites in proteins often suffer from ambiguity and have not gained widespread adoption. We developed a novel method that exclusively labels isoAsp with deuterium. This method capitalizes on the unique structural characteristics of isoAsp residues, which possess a free α-carboxyl group and can form an oxazolone ring. Once the oxazolone ring forms, it facilitates racemization at the Cα-position, incorporating a deuteron from a D2O solvent. The sites of deuterium-incorporated isoAsp in proteins can be unequivocally determined by comparing the precursor and product ion masses of the peptides from proteins reacted in H2O and D2O. The effectiveness of this method has been demonstrated through its application to model proteins lysozyme and rituximab. Furthermore, we have confirmed that the isoAsp deuterium-labeling reaction efficiently labels both l- and d-isoAsp without distinction, as well as isoglutamic acid (isoGlu), for which no effective detection methods currently exist.
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Affiliation(s)
- Masaru Miyagi
- Department
of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-4988, United States
| | - Evan Kiesel
- Department
of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-4988, United States
| | - Kelao Neumbo
- Department
of Pharmacology, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106-4988, United States
| | - Takashi Nakazawa
- Department
of Chemistry, Nara Women’s University, Nara 630-8506, Japan
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2
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Pomilio AB, Vitale AA, Lazarowski AJ. Neuroproteomics Chip-Based Mass Spectrometry and Other Techniques for Alzheimer´S Disease Biomarkers – Update. Curr Pharm Des 2022; 28:1124-1151. [DOI: 10.2174/1381612828666220413094918] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/25/2022] [Indexed: 11/22/2022]
Abstract
Background:
Alzheimer's disease (AD) is a progressive neurodegenerative disease of growing interest given that there is cognitive damage and symptom onset acceleration. Therefore, it is important to find AD biomarkers for early diagnosis, disease progression, and discrimination of AD and other diseases.
Objective:
To update the relevance of mass spectrometry for the identification of peptides and proteins involved in AD useful as discriminating biomarkers.
Methods:
Proteomics and peptidomics technologies that show the highest possible specificity and selectivity for AD biomarkers are analyzed, together with the biological fluids used. In addition to positron emission tomography and magnetic resonance imaging, MALDI-TOF mass spectrometry is widely used to identify proteins and peptides involved in AD. The use of protein chips in SELDI technology and electroblotting chips for peptides makes feasible small amounts (L) of samples for analysis.
Results:
Suitable biomarkers are related to AD pathology, such as intracellular neurofibrillary tangles; extraneuronal senile plaques; neuronal and axonal degeneration; inflammation and oxidative stress. Recently, peptides were added to the candidate list, which are not amyloid-b or tau fragments, but are related to coagulation, brain plasticity, and complement/neuroinflammation systems involving the neurovascular unit.
Conclusion:
The progress made in the application of mass spectrometry and recent chip techniques is promising for discriminating between AD, mild cognitive impairment, and matched healthy controls. The application of this technique to blood samples from patients with AD has shown to be less invasive and fast enough to determine the diagnosis, stage of the disease, prognosis, and follow-up of the therapeutic response.
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Affiliation(s)
- Alicia B. Pomilio
- Departamento de Bioquímica Clínica, Área Hematología, Hospital de Clínicas “José de San Martín”, Universidad de Buenos Aires, Av. Córdoba 2351, C1120AAF Buenos Aires, Argentina
| | - Arturo A. Vitale
- Departamento de Bioquímica Clínica, Área Hematología, Hospital de Clínicas “José de San Martín”, Universidad de Buenos Aires, Av. Córdoba 2351, C1120AAF Buenos Aires, Argentina
| | - Alberto J. Lazarowski
- Departamento de Bioquímica Clínica, Facultad de Farmacia y Bioquímica, Instituto de Fisiopatología y Bioquímica Clínica (INFIBIOC), Universidad de Buenos Aires, Córdoba 2351, C1120AAF Buenos Aires, Argentina
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Zakharova NV, Kononikhin AS, Indeykina MI, Bugrova AE, Strelnikova P, Pekov S, Kozin SA, Popov IA, Mitkevich V, Makarov AA, Nikolaev EN. Mass spectrometric studies of the variety of beta-amyloid proteoforms in Alzheimer's disease. MASS SPECTROMETRY REVIEWS 2022:e21775. [PMID: 35347731 DOI: 10.1002/mas.21775] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 03/03/2022] [Accepted: 03/12/2022] [Indexed: 06/14/2023]
Abstract
This review covers the results of the application of mass spectrometric (MS) techniques to study the diversity of beta-amyloid (Aβ) peptides in human samples. Since Aβ is an important hallmark of Alzheimer's disease (AD), which is a socially significant neurodegenerative disorder of the elderly worldwide, analysis of its endogenous variations is of particular importance for elucidating the pathogenesis of AD, predicting increased risks of the disease onset, and developing effective therapy. MS approaches have no alternative for the study of complex samples, including a wide variety of Aβ proteoforms, differing in length and modifications. Approaches based on matrix-assisted laser desorption/ionization time-of-flight and liquid chromatography with electrospray ionization tandem MS are most common in Aβ studies. However, Aβ forms with isomerized and/or racemized Asp and Ser residues require the use of special methods for separation and extra sensitive and selective methods for detection. Overall, this review summarizes current knowledge of Aβ species found in human brain, cerebrospinal fluid, and blood plasma; focuses on application of different MS approaches for Aβ studies; and considers the potential of MS techniques for further studies of Aβ-peptides.
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Affiliation(s)
- Natalia V Zakharova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Alexey S Kononikhin
- CMCB, Skolkovo Institute of Science and Technology, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Maria I Indeykina
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Anna E Bugrova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- CMCB, Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Polina Strelnikova
- Emanuel Institute of Biochemical Physics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Stanislav Pekov
- CMCB, Skolkovo Institute of Science and Technology, Moscow, Russia
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Igor A Popov
- Laboratory of ion and molecular physics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia
- N.N. Semenov Federal Center of Chemical Physics, V.L. Talrose Institute for Energy Problems of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Vladimir Mitkevich
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia
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The Dynamics of β-Amyloid Proteoforms Accumulation in the Brain of a 5xFAD Mouse Model of Alzheimer’s Disease. Int J Mol Sci 2021; 23:ijms23010027. [PMID: 35008451 PMCID: PMC8745018 DOI: 10.3390/ijms23010027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/16/2021] [Accepted: 12/19/2021] [Indexed: 12/15/2022] Open
Abstract
Alzheimer’s disease (AD) is the leading cause of dementia among the elderly. Neuropathologically, AD is characterized by the deposition of a 39- to 42-amino acid long β-amyloid (Aβ) peptide in the form of senile plaques. Several post-translational modifications (PTMs) in the N-terminal domain have been shown to increase the aggregation and cytotoxicity of Aβ, and specific Aβ proteoforms (e.g., Aβ with isomerized D7 (isoD7-Aβ)) are abundant in the senile plaques of AD patients. Animal models are indispensable tools for the study of disease pathogenesis, as well as preclinical testing. In the presented work, the accumulation dynamics of Aβ proteoforms in the brain of one of the most widely used amyloid-based mouse models (the 5xFAD line) was monitored. Mass spectrometry (MS) approaches, based on ion mobility separation and the characteristic fragment ion formation, were applied. The results indicated a gradual increase in the Aβ fraction of isoD7-Aβ, starting from approximately 8% at 7 months to approximately 30% by 23 months of age. Other specific PTMs, in particular, pyroglutamylation, deamidation, and oxidation, as well as phosphorylation, were also monitored. The results for mice of different ages demonstrated that the accumulation of Aβ proteoforms correlate with the formation of Aβ deposits. Although the mouse model cannot be a complete analogue of the processes occurring in the human brain in AD, and several of the observed parameters differ significantly from human values supposedly due to the limited lifespan of the model animals, this dynamic study provides evidence on at least one of the possible mechanisms that can trigger amyloidosis in AD, i.e., the hypothesis on the relationship between the accumulation of isoD7-Aβ and the progression of AD-like pathology.
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Matuszyk MM, Garwood CJ, Ferraiuolo L, Simpson JE, Staniforth RA, Wharton SB. Biological and methodological complexities of beta-amyloid peptide: Implications for Alzheimer's disease research. J Neurochem 2021; 160:434-453. [PMID: 34767256 DOI: 10.1111/jnc.15538] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 10/29/2021] [Accepted: 11/09/2021] [Indexed: 01/01/2023]
Abstract
Although controversial, the amyloid cascade hypothesis remains central to the Alzheimer's disease (AD) field and posits amyloid-beta (Aβ) as the central factor initiating disease onset. In recent years, there has been an increase in emphasis on studying the role of low molecular weight aggregates, such as oligomers, which are suggested to be more neurotoxic than fibrillary Aβ. Other Aβ isoforms, such as truncated Aβ, have also been implicated in disease. However, developing a clear understanding of AD pathogenesis has been hampered by the complexity of Aβ biochemistry in vitro and in vivo. This review explores factors contributing to the lack of consistency in experimental approaches taken to model Aβ aggregation and toxicity and provides an overview of the different techniques available to analyse Aβ, such as electron and atomic force microscopy, nuclear magnetic resonance spectroscopy, dye-based assays, size exclusion chromatography, mass spectrometry and SDS-PAGE. The review also explores how different types of Aβ can influence Aβ aggregation and toxicity, leading to variation in experimental outcomes, further highlighting the need for standardisation in Aβ preparations and methods used in current research.
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Affiliation(s)
- Martyna M Matuszyk
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Claire J Garwood
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Laura Ferraiuolo
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | - Julie E Simpson
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
| | | | - Stephen B Wharton
- Sheffield Institute for Translational Neuroscience, University of Sheffield, Sheffield, UK
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6
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Busch L, Vieten S, Brödel S, Endres K, Bufe B. Emerging contributions of formyl peptide receptors to neurodegenerative diseases. Biol Chem 2021; 403:27-41. [PMID: 34505459 DOI: 10.1515/hsz-2021-0258] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 08/23/2021] [Indexed: 12/28/2022]
Abstract
Inflammation is a central element of many neurodegenerative diseases. Formyl peptide receptors (FPRs) can trigger several receptor-dependent signal transduction pathways that play a key role in neuroinflammation and neurodegeneration. They are chemotactic receptors that help to regulate pro- and anti-inflammatory responses in most mammals. FPRs are primarily expressed in the immune and nervous systems where they interact with a complex pattern of pathogen-derived and host-endogenous molecules. Mounting evidence points towards a contribution of FPRs - via neuropathological ligands such as Amyloid beta, and neuroprotective ligands such as Humanin, Lipoxin A4, and Annexin A1 - to multiple pathological aspects of neurodegenerative diseases. In this review, we aim to summarize the interplay of FPRs with neuropathological and neuroprotective ligands. Next, we depict their capability to trigger a number of ligand-dependent cell signaling pathways and their potential to interact with additional intracellular cofactors. Moreover, we highlight first studies, demonstrating that a pharmacological inhibition of FPRs helps to ameliorate neuroinflammation, which may pave the way towards novel therapeutic strategies.
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Affiliation(s)
- Lukas Busch
- Department of Informatics and Microsystems Technology, University of Applied Sciences Kaiserslautern, D-66482 Zweibrücken, Germany
| | - Stefan Vieten
- Department of Informatics and Microsystems Technology, University of Applied Sciences Kaiserslautern, D-66482 Zweibrücken, Germany
| | - Susan Brödel
- Department of Informatics and Microsystems Technology, University of Applied Sciences Kaiserslautern, D-66482 Zweibrücken, Germany
| | - Kristina Endres
- Department of Psychiatry and Psychotherapy, University Medical Centre of the Johannes Gutenberg University, D-55131 Mainz, Germany
| | - Bernd Bufe
- Department of Informatics and Microsystems Technology, University of Applied Sciences Kaiserslautern, D-66482 Zweibrücken, Germany
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Hui JO, Flick T, Loo JA, Campuzano IDG. Unequivocal Identification of Aspartic Acid and isoAspartic Acid by MALDI-TOF/TOF: From Peptide Standards to a Therapeutic Antibody. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2021; 32:1901-1909. [PMID: 33390012 DOI: 10.1021/jasms.0c00370] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Aspartic acid (Asp) to isoaspartic acid (isoAsp) isomerization in therapeutic monoclonal antibodies (mAbs) and other biotherapeutics is a critical quality attribute (CQA) that requires careful control and monitoring during the drug discovery and production processes. The unwanted formation of isoAsp within biotherapeutics and resultant structural changes in the peptide backbone may negatively impact the efficacy, potency, and safety of the molecule or become immunogenic, especially if the isomerization occurs within the mAb complementarity determining region (CDR). Herein we describe a MALDI-TOF/TOF mass spectrometry method that affords unequivocal identification of the presence and the exact position of the isoAsp residue(s) in peptide standards ranging in size from a tripeptide to a docosapeptide (22 residues). In general, the peptide bond immediately N-terminal to the isoAsp residue is more susceptible to MALDI-TOF/TOF fragmentation than its unmodified counterpart. In some of the peptides evaluated in this study, fragmentation of the peptide bond C-terminal to the isoAsp residue (the aspartate effect) is also enhanced when compared to the control. Relative quantification by MALDI-TOF/TOF of this chemical modification is dependent upon a successful reversed-phase HPLC (rpHPLC) separation of the control and modified peptides. This method has also been validated on a therapeutic mAb that contains a well-documented isoAsp residue in the heavy chain CDR3 after forced degradation. Moreover, we also demonstrate that higher energy C-trap dissociation of only the singly charged species, and not the multiply charged form, of the isoAsp containing peptide, separated by rpHPLC, results in LC-MS/MS fragmentation that is highly consistent to that of MALDI-TOF/TOF.
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Affiliation(s)
- John O Hui
- Amgen Research, Discovery Attribute Sciences, Amgen, Inc., Thousand Oaks, California 91320, United States
| | - Tawnya Flick
- Attribute Sciences, Pivotal, Amgen, Inc., Thousand Oaks, California 91320, United States
| | - Joseph A Loo
- Department of Chemistry & Biochemistry, UCLA, Los Angeles, California 90095, United States
| | - Iain D G Campuzano
- Amgen Research, Discovery Attribute Sciences, Amgen, Inc., Thousand Oaks, California 91320, United States
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8
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Optical Characterization and Monitoring of Enzyme Catalyzed Short Chain Peptides in Cellular Environment. Catal Letters 2020. [DOI: 10.1007/s10562-020-03110-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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9
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Ivanov DG, Pekov SI, Bocharov KV, Bormotov DS, Spasskiy AI, Zhvansky ES, Sorokin AA, Eliferov VA, Zavorotnyuk DS, Tkachenko SI, Khaliullin IG, Kuksin AY, Shurkhay VA, Kononikhin AS, Nikolaev EN, Popov IA. Novel Mass Spectrometric Utilities for Assisting in Oncological Surgery. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY B 2020. [DOI: 10.1134/s1990793120030173] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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10
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Ivanov DG, Indeykina MI, Pekov SI, Bugrova AE, Kechko OI, Iusupov AE, Kononikhin AS, Makarov AA, Nikolaev EN, Popov IA. Relative Quantitation of Beta-Amyloid Peptide Isomers with Simultaneous Isomerization of Multiple Aspartic Acid Residues by Matrix Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:164-168. [PMID: 32881518 DOI: 10.1021/jasms.9b00025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Matrix assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry can be used for rapid quantitation of peptides with various post-translational modifications (PTM), even if they do not shift the mass of the native peptide. Previously, it was shown that MALDI-TOF MS can be used for quantitation of isoD7 beta-amyloid 1-42 peptide. On the basis of the differences in the collision-induced dissociation fragmentation pattern of native Aβ, isoD7 Aβ, isoD23 Aβ, and isoD7_23 peptide (a di-isomerized peptide with both isomerization of D7 and D23 residues), we developed a MALDI-TOF-based method for simultaneous quantitation of all of these isoforms. Using multivariate regression for analysis of fragment MS data, the method allows the determination of the molar fractions of all of these isoforms with up to 16% error for mixtures with 2 pmol total amount of the beta-amyloid peptide.
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Affiliation(s)
- Daniil G Ivanov
- Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Kosygina Street 4, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutskiy pr. 9, 141700 Dolgoprudny, Moscow Region, Russia
| | - Maria I Indeykina
- Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Kosygina Street 4, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutskiy pr. 9, 141700 Dolgoprudny, Moscow Region, Russia
| | - Stanislav I Pekov
- Moscow Institute of Physics and Technology, Institutskiy pr. 9, 141700 Dolgoprudny, Moscow Region, Russia
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Center of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
| | - Anna E Bugrova
- Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Kosygina Street 4, 119334 Moscow, Russia
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Akademika Oparina ul. 4, 117198 Moscow, Russia
| | - Olga I Kechko
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova ul. 32, 119991 Moscow, Russia
| | - Adel E Iusupov
- Emanuel Institute of Biochemical Physics Russian Academy of Sciences, Kosygina Street 4, 119334 Moscow, Russia
- Moscow Institute of Physics and Technology, Institutskiy pr. 9, 141700 Dolgoprudny, Moscow Region, Russia
| | - Alexey S Kononikhin
- Moscow Institute of Physics and Technology, Institutskiy pr. 9, 141700 Dolgoprudny, Moscow Region, Russia
- Skolkovo Institute of Science and Technology, Novaya Street 100, 143025 Skolkovo, Moscow Region, Russia
| | - Alexander A Makarov
- Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Vavilova ul. 32, 119991 Moscow, Russia
| | - Eugene N Nikolaev
- Skolkovo Institute of Science and Technology, Novaya Street 100, 143025 Skolkovo, Moscow Region, Russia
| | - Igor A Popov
- Moscow Institute of Physics and Technology, Institutskiy pr. 9, 141700 Dolgoprudny, Moscow Region, Russia
- V. L. Talrose Institute for Energy Problems of Chemical Physics, N. N. Semenov Federal Center of Chemical Physics, Russian Academy of Sciences, Moscow, Russia
- V. I. Kulakov Research Center for Obstetrics, Gynecology and Perinatology, Ministry of Healthcare of the Russian Federation, Akademika Oparina ul. 4, 117198 Moscow, Russia
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Probabilistic model applied to ion abundances in product-ion spectra: quantitative analysis of aspartic acid isomerization in peptides. Anal Bioanal Chem 2019; 411:7783-7789. [DOI: 10.1007/s00216-019-02174-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 09/05/2019] [Accepted: 09/25/2019] [Indexed: 12/29/2022]
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