1
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Asakawa D, Iwamoto S, Tanaka K. Discrimination of Aspartic and Isoaspartic Acid Residues in Peptides by Tandem Mass Spectrometry with Hydrogen Attachment Dissociation. Anal Chem 2024; 96:8552-8559. [PMID: 38741470 DOI: 10.1021/acs.analchem.4c00561] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Long-lived proteins undergo chemical modifications that can cause age-related diseases. Among these chemical modifications, isomerization is the most difficult to identify. Isomerization often occurs at the aspartic acid (Asp) residues. In this study, we used tandem mass spectrometry equipped with a newly developed ion activation method, hydrogen attachment dissociation (HAD), to analyze peptides containing Asp isomers. Although HAD preferentially produces [cn + 2H]+ and [zm + 2H]+ via N-Cα bond cleavage, [cn + 58 + 2H]+ and [zm - 58 + 2H]+ originate from the fragmentation of the isoAsp residue. Notably, [cn + 58 + 2H]+ and [zm - 58 + 2H]+ could be used as diagnostic fragment ions for the isoAsp residue because these fragment ions did not originate from the Asp residue. The detailed fragmentation mechanism was investigated by computational analysis using density functional theory. According to the results, hydrogen attachment to the carbonyl oxygen in the isoAsp residue results in the Cα-Cβ bond cleavage. The experimental and theoretical joint study indicates that the present method allows us to discriminate Asp and isoAsp residues, including site identification of the isoAsp residue. Moreover, we demonstrated that the molar ratio of peptide isomers in the mixture could be estimated from their fragment ion abundance. Therefore, tandem mass spectrometry with HAD is a useful method for the rapid discrimination and semiquantitative analysis of peptides containing isoAsp residues.
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Affiliation(s)
- Daiki Asakawa
- National Institute of Advanced Industrial Science and Technology (AIST), National Metrology Institute of Japan (NMIJ), Tsukuba 305-8568, Japan
| | - Shinich Iwamoto
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
| | - Koichi Tanaka
- Koichi Tanaka Mass Spectrometry Research Laboratory, Shimadzu Corporation, 1 Nishinokyo-Kuwabaracho, Nakagyo-ku, Kyoto 604-8511, Japan
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2
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Hubbard EE, Heil LR, Merrihew GE, Chhatwal JP, Farlow MR, McLean CA, Ghetti B, Newell KL, Frosch MP, Bateman RJ, Larson EB, Keene CD, Perrin RJ, Montine TJ, MacCoss MJ, Julian RR. Does Data-Independent Acquisition Data Contain Hidden Gems? A Case Study Related to Alzheimer's Disease. J Proteome Res 2022; 21:118-131. [PMID: 34818016 PMCID: PMC8741752 DOI: 10.1021/acs.jproteome.1c00558] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
One of the potential benefits of using data-independent acquisition (DIA) proteomics protocols is that information not originally targeted by the study may be present and discovered by subsequent analysis. Herein, we reanalyzed DIA data originally recorded for global proteomic analysis to look for isomerized peptides, which occur as a result of spontaneous chemical modifications to long-lived proteins. Examination of a large set of human brain samples revealed a striking relationship between Alzheimer's disease (AD) status and isomerization of aspartic acid in a peptide from tau. Relative to controls, a surprising increase in isomer abundance was found in both autosomal dominant and sporadic AD samples. To explore potential mechanisms that might account for these observations, quantitative analysis of proteins related to isomerization repair and autophagy was performed. Differences consistent with reduced autophagic flux in AD-related samples relative to controls were found for numerous proteins, including most notably p62, a recognized indicator of autophagic inhibition. These results suggest, but do not conclusively demonstrate, that lower autophagic flux may be strongly associated with loss of function in AD brains. This study illustrates that DIA data may contain unforeseen results of interest and may be particularly useful for pilot studies investigating new research directions. In this case, a promising target for future investigations into the therapy and prevention of AD has been identified.
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Affiliation(s)
- Evan E. Hubbard
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Lilian R. Heil
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, United States
| | - Gennifer E. Merrihew
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, United States
| | - Jasmeer P. Chhatwal
- Harvard Medical School, Massachusetts General Hospital, Department of Neurology, 15 Parkman St, Suite 835, Boston MA 02114
| | - Martin R. Farlow
- Department of Neurology, Indiana University School of Medicine, Indianapolis, Indiana, 46202
| | | | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Kathy L. Newell
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, IN, 46202
| | - Matthew P. Frosch
- C.S. Kubik Laboratory for Neuropathology, and Massachusetts Alzheimer Disease Research Center, Massachusetts General Hospital, Boston, MA 02114
| | - Randall J. Bateman
- Department of Neurology, Washington University School of Medicine, 660 South Euclid Avenue, Box 8111, St. Louis, 63110, Missouri, USA
| | - Eric B. Larson
- Kaiser Permanente Washington Health Research Institute and Department of Medicine, University of Washington, Seattle WA
| | - C. Dirk Keene
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, 98195, United States
| | - Richard J. Perrin
- Department of Pathology and Immunology, Department of Neurology, Washington University School of Medicine, Saint Louis, Missouri 63110, United States
| | - Thomas J. Montine
- Department of Pathology, Stanford University, Stanford, CA, 94305, United States
| | - Michael J. MacCoss
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States,corresponding author:
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3
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Lobas AA, Solovyeva EM, Saparbaev E, Gorshkov MV, Boyarkin OV. Accelerating photofragmentation UV Spectroscopy-Mass spectrometry fingerprinting for quantification of isomeric peptides. Talanta 2021; 232:122412. [PMID: 34074402 DOI: 10.1016/j.talanta.2021.122412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 02/07/2023]
Abstract
Identification of isomeric biomolecules remains a challenging analytical problem. A recently developed spectroscopic method that combines UV photofragmentation and mass spectrometry for fingerprinting of cold ions (2D UV-MS), has already demonstrated its high performance in the library-based identification and quantification of different types of biomolecular isomers. The practical use of the method has been hindered by a slow rate of data acquisition, which makes the fingerprinting incompatible with high-throughput analysis and online liquid chromatography (LC) separation. Herein we demonstrate how the use of a few pre-selected wavelengths can accelerate the method by two orders of magnitude without a significant loss of accuracy. As a proof of principle, 2D UV-MS fingerprinting was coupled to online LC separation and tested for quantification of isomeric peptides containing either Asp or isoAsp residues. The relative concentrations of the peptides mixed in solution have been determined, on average, with better than 4% and 6% accuracy for resolving and non-resolving gradients of LC separation, respectively.
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Affiliation(s)
- Anna A Lobas
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland; V.L. Talrose Institute for Energy Problems of Chemical Physics, Federal Research Center of Chemical Physics, RAS, Moscow, Russia
| | - Elizaveta M Solovyeva
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland; V.L. Talrose Institute for Energy Problems of Chemical Physics, Federal Research Center of Chemical Physics, RAS, Moscow, Russia; Moscow Institute of Physics and Technology (National Research University), Dolgoprudny, Russia
| | - Erik Saparbaev
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland
| | - Mikhail V Gorshkov
- V.L. Talrose Institute for Energy Problems of Chemical Physics, Federal Research Center of Chemical Physics, RAS, Moscow, Russia
| | - Oleg V Boyarkin
- Laboratoire de Chimie Physique Moléculaire, École Polytechnique Fédérale de Lausanne, CH-1015, Lausanne, Switzerland.
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4
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Riggs DL, Silzel JW, Lyon YA, Kang AS, Julian RR. Analysis of Glutamine Deamidation: Products, Pathways, and Kinetics. Anal Chem 2019; 91:13032-13038. [PMID: 31498611 PMCID: PMC8805438 DOI: 10.1021/acs.analchem.9b03127] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Spontaneous chemical modifications play an important role in human disease and aging at the molecular level. Deamidation and isomerization are known to be among the most prevalent chemical modifications in long-lived human proteins and are implicated in a growing list of human pathologies, but the relatively minor chemical change associated with these processes has presented a long standing analytical challenge. Although the adoption of high-resolution mass spectrometry has greatly aided the identification of deamidation sites in proteomic studies, isomerization (and the isomeric products of deamidation) remain exceptionally challenging to characterize. Herein, we present a liquid chromatography/mass spectrometry-based approach for rapidly characterizing the isomeric products of Gln deamidation using diagnostic fragments that are abundantly produced and capable of unambiguously identifying both Glu and isoGlu. Importantly, the informative fragment ions are produced through orthogonal fragmentation pathways, thereby enabling the simultaneous detection of both isomeric forms while retaining compatibility with shotgun proteomics. Furthermore, the diagnostic fragments associated with isoGlu pinpoint the location of the modified residue. The utility of this technique is demonstrated by characterizing the isomeric products generated during in vitro aging of a series of glutamine-containing peptides. Sequence-dependent product profiles are obtained, and the abundance of deamidation-linked racemization is examined. Finally, comparisons are made between Gln deamidation, which is relatively poorly understood, and asparagine deamidation, which has been more thoroughly studied.
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Affiliation(s)
- Dylan L. Riggs
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Jacob W. Silzel
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Yana A. Lyon
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Amrik S. Kang
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States
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5
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Pekov SI, Ivanov DG, Bugrova AE, Indeykina MI, Zakharova NV, Popov IA, Kononikhin AS, Kozin SA, Makarov AA, Nikolaev EN. Evaluation of MALDI-TOF/TOF Mass Spectrometry Approach for Quantitative Determination of Aspartate Residue Isomerization in the Amyloid-β Peptide. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2019; 30:1325-1329. [PMID: 31073890 DOI: 10.1007/s13361-019-02199-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2018] [Revised: 03/11/2019] [Accepted: 03/29/2019] [Indexed: 06/09/2023]
Abstract
Immunoprecipitation (IP) combined with MALDI-TOF mass spectrometry is a powerful instrument for peptide and protein identification in biological samples. In this study, the analytical capabilities of MALDI-TOF/TOF mass spectrometry for relative quantitation of isoAsp7 in Aβ(1-42) and Aβ(1-16) were investigated. The possibility of quantitative determination of isoAsp7 in Aβ(1-42) with the detection limit as low as 2 pmol has been demonstrated. The same approach was applied for a shorter peptide Aβ(1-16) and resulted in enhanced accuracy (± 3.2%), and lower detection limit (50 fmol). Pilot experiments with artificial cerebrospinal fluid and mouse brain tissue were performed and showed that the proposed IP-MALDI-TOF/TOF approach could be applied for measuring isoAβ content in biological fluids and tissues. Additionally, it was shown that 6E10 anti-amyloid antibodies might affect the accuracy of the amyloid-β quantitation in the presence of the isomerized peptide.
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Affiliation(s)
- Stanislav I Pekov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
- V.L. Talrose Institute for Energy Problems of Chemical Physics RAS, Moscow, Russia
| | - Daniil G Ivanov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - Anna E Bugrova
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - Maria I Indeykina
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - Natalia V Zakharova
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia
- Emanuel Institute of Biochemical Physics RAS, Moscow, Russia
| | - Igor A Popov
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia.
| | - Alexey S Kononikhin
- Moscow Institute of Physics and Technology, Dolgoprudny, Moscow region, Russia.
- V.L. Talrose Institute for Energy Problems of Chemical Physics RAS, Moscow, Russia.
| | - Sergey A Kozin
- Engelhardt Institute of Molecular Biology RAS, Moscow, Russia
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6
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Riggs DL, Gomez SV, Julian RR. Sequence and Solution Effects on the Prevalence of d-Isomers Produced by Deamidation. ACS Chem Biol 2017; 12:2875-2882. [PMID: 28984444 PMCID: PMC5696650 DOI: 10.1021/acschembio.7b00686] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Deamidation of asparagine is a spontaneous and irreversible post-translational modification associated with a growing list of human diseases. While pervasive, deamidation is often overlooked because it represents a relatively minor chemical change. Structural and functional characterization of this modification is complicated because deamidation of asparagine yields four isomeric forms of Asp. Herein, radical directed dissociation (RDD), in conjunction with mass spectrometry, is used to identify and quantify all four isomers in a series of model peptides that were subjected to various deamidation conditions. Although primary sequence significantly influences the rate of deamidation, it has little impact on the relative proportions of the product isomers. Furthermore, the addition of ammonia can be used to increase the rate of deamidation without significantly perturbing isomer populations. Conversely, external factors such as buffer conditions and temperature alter product distributions but exhibit less dramatic effects on the deamidation rate. Strikingly, the common laboratory and biologically significant bicarbonate buffer is found to strongly promote racemization, yielding increased amounts of d-Asp and d-isoAsp. These outcomes following deamidation have broad implications in human aging and should be considered during the development of protein-based therapeutics.
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Affiliation(s)
- Dylan L. Riggs
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Sonia V. Gomez
- Department of Chemistry, University of California, Riverside, California 92521, United States
| | - Ryan R. Julian
- Department of Chemistry, University of California, Riverside, California 92521, United States
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7
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Müller MM. Post-Translational Modifications of Protein Backbones: Unique Functions, Mechanisms, and Challenges. Biochemistry 2017; 57:177-185. [PMID: 29064683 PMCID: PMC5770884 DOI: 10.1021/acs.biochem.7b00861] [Citation(s) in RCA: 107] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
![]()
Post-translational
modifications (PTMs) dramatically enhance the
capabilities of proteins. They introduce new functionalities and dynamically
control protein activity by modulating intra- and intermolecular interactions.
Traditionally, PTMs have been considered as reversible attachments
to nucleophilic functional groups on amino acid side chains, whereas
the polypeptide backbone is often thought to be inert. This paradigm
is shifting as chemically and functionally diverse alterations of
the protein backbone are discovered. Importantly, backbone PTMs can
control protein structure and function just as side chain modifications
do and operate through unique mechanisms to achieve these features.
In this Perspective, I outline the various types of protein backbone
modifications discovered so far and highlight their contributions
to biology as well as the challenges in studying this versatile yet
poorly characterized class of PTMs.
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Affiliation(s)
- Manuel M Müller
- Department of Chemistry, King's College London , 7 Trinity Street, London SE1 1DB, United Kingdom
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8
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Roher AE, Kokjohn TA, Clarke SG, Sierks MR, Maarouf CL, Serrano GE, Sabbagh MS, Beach TG. APP/Aβ structural diversity and Alzheimer's disease pathogenesis. Neurochem Int 2017; 110:1-13. [PMID: 28811267 PMCID: PMC5688956 DOI: 10.1016/j.neuint.2017.08.007] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 07/25/2017] [Accepted: 08/11/2017] [Indexed: 02/01/2023]
Abstract
The amyloid cascade hypothesis of Alzheimer's disease (AD) proposes amyloid- β (Aβ) is a chief pathological element of dementia. AD therapies have targeted monomeric and oligomeric Aβ 1-40 and 1-42 peptides. However, alternative APP proteolytic processing produces a complex roster of Aβ species. In addition, Aβ peptides are subject to extensive posttranslational modification (PTM). We propose that amplified production of some APP/Aβ species, perhaps exacerbated by differential gene expression and reduced peptide degradation, creates a diverse spectrum of modified species which disrupt brain homeostasis and accelerate AD neurodegeneration. We surveyed the literature to catalog Aβ PTM including species with isoAsp at positions 7 and 23 which may phenocopy the Tottori and Iowa Aβ mutations that result in early onset AD. We speculate that accumulation of these alterations induce changes in secondary and tertiary structure of Aβ that favor increased toxicity, and seeding and propagation in sporadic AD. Additionally, amyloid-β peptides with a pyroglutamate modification at position 3 and oxidation of Met35 make up a substantial portion of sporadic AD amyloid deposits. The intrinsic physical properties of these species, including resistance to degradation, an enhanced aggregation rate, increased neurotoxicity, and association with behavioral deficits, suggest their emergence is linked to dementia. The generation of specific 3D-molecular conformations of Aβ impart unique biophysical properties and a capacity to seed the prion-like global transmission of amyloid through the brain. The accumulation of rogue Aβ ultimately contributes to the destruction of vascular walls, neurons and glial cells culminating in dementia. A systematic examination of Aβ PTM and the analysis of the toxicity that they induced may help create essential biomarkers to more precisely stage AD pathology, design countermeasures and gauge the impacts of interventions.
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Affiliation(s)
- Alex E Roher
- Division of Neurobiology, Barrow Neurological Institute, Phoenix, AZ 85013, USA; Division of Clinical Education, Midwestern University, Glendale, AZ 85308, USA.
| | - Tyler A Kokjohn
- Department of Microbiology, Midwestern University, Glendale, AZ 85308, USA
| | - Steven G Clarke
- Department of Chemistry and Biochemistry and the Molecular Biology Institute, University of California, Los Angeles, Los Angeles CA 90095-1569, USA
| | - Michael R Sierks
- Department of Chemical Engineering, Arizona State University, Tempe, AZ 85287-6106, USA
| | - Chera L Maarouf
- Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Geidy E Serrano
- Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
| | - Marwan S Sabbagh
- Alzheimer's and Memory Disorders Division, Barrow Neurological Institute, Phoenix, AZ 85013, USA
| | - Thomas G Beach
- Laboratory of Neuropathology, Banner Sun Health Research Institute, Sun City, AZ 85351, USA
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9
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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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10
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Jansson ET. Strategies for analysis of isomeric peptides. J Sep Sci 2017; 41:385-397. [PMID: 28922569 DOI: 10.1002/jssc.201700852] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2017] [Revised: 09/06/2017] [Accepted: 09/06/2017] [Indexed: 01/09/2023]
Abstract
This review presents an overview and recent progress of strategies for detecting isomerism in peptides, with focus on d/l epimerization and the various isomers that the presence of an aspartic acid residue may yield in a protein or peptide. While mass spectrometry has become a majorly used method of choice within proteomics, isomerism is inherently difficult to analyze because it is a modification that does not yield any change in mass of the analyte. Here, several techniques used for analysis of peptide isomerism are discussed, including enzymatic assays, liquid chromatography, and capillary electrophoresis. Recent progress in method development using mass spectrometry is also discussed, including labeling strategies, fragmentation techniques, and ion-mobility spectrometry.
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Affiliation(s)
- Erik T Jansson
- Department of Chemistry-BMC, Uppsala University, Uppsala, Sweden
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11
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Faserl K, Sarg B, Maurer V, Lindner HH. Exploiting charge differences for the analysis of challenging post-translational modifications by capillary electrophoresis-mass spectrometry. J Chromatogr A 2017; 1498:215-223. [DOI: 10.1016/j.chroma.2017.01.086] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2016] [Revised: 01/25/2017] [Accepted: 01/29/2017] [Indexed: 12/27/2022]
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12
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Young C, Podtelejnikov AV, Nielsen ML. Improved Reversed Phase Chromatography of Hydrophilic Peptides from Spatial and Temporal Changes in Column Temperature. J Proteome Res 2017; 16:2307-2317. [DOI: 10.1021/acs.jproteome.6b01055] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Clifford Young
- The
Novo Nordisk Foundation Center for Protein Research, Proteomics Program,
Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
| | | | - Michael L. Nielsen
- The
Novo Nordisk Foundation Center for Protein Research, Proteomics Program,
Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen, Denmark
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13
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Yu X, Sargaeva NP, Thompson CJ, Costello CE, Lin C. In-Source Decay Characterization of Isoaspartate and β-Peptides. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2015; 390:101-109. [PMID: 26644780 PMCID: PMC4669973 DOI: 10.1016/j.ijms.2015.07.013] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Deamidation and the subsequent formation of isoaspartic acid (isoAsp) are common modifications of asparagine (Asn) residues in proteins. Differentiation of isoAsp and Asp residues is a challenging task owing to their similar chemical properties and identical molecular mass. Recent studies showed that they can be differentiated using electron capture dissociation (ECD) which generates diagnostic fragments c'+57 and z•-57 specific to the isoAsp residue. However, the ECD approach is only applicable towards multiply charged precursor ions and generally does not work for β-amino acids other than isoAsp. In this study, the potential of in-source decay (ISD) in characterization of isoAsp and other β-amino acids was explored. For isoAsp-containing peptides, ISD with a conventional hydrogen-donating matrix produced ECD-like, c'+57 and z•-57 diagnostic ions, even for singly charged precursor ions. For other β-amino acids, a hydrogen-accepting matrix was used to induce formation of site-specific a-14 ions from a synthetic β-analogue of substance P. These results indicated that ISD can be broadly applied for β-peptide characterization.
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Affiliation(s)
- Xiang Yu
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
| | - Nadezda P. Sargaeva
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
| | | | - Catherine E. Costello
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, Suite 504, Boston, MA 02118
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14
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Faserl K, Kremser L, Müller M, Teis D, Lindner HH. Quantitative proteomics using ultralow flow capillary electrophoresis-mass spectrometry. Anal Chem 2015; 87:4633-40. [PMID: 25839223 PMCID: PMC4423236 DOI: 10.1021/acs.analchem.5b00312] [Citation(s) in RCA: 43] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
![]()
In this work, we evaluate the incorporation
of an ultralow flow
interface for coupling capillary electrophoresis (CE) and mass spectrometry
(MS), in combination with reversed-phase high-pressure liquid chromatography
(HPLC) fractionation as an alternate workflow for quantitative proteomics.
Proteins, extracted from a SILAC (stable isotope labeling by amino
acids in cell culture) labeled and an unlabeled yeast strain were
mixed and digested enzymatically in solution. The resulting peptides
were fractionated using RP-HPLC and analyzed by CE–MS yielding
a total of 28 538 quantified peptides that correspond to 3 272
quantified proteins. CE–MS analysis was performed using a neutral
capillary coating, providing the highest separation efficiency at
ultralow flow conditions (<10 nL/min). Moreover, we were able to
demonstrate that CE–MS is a powerful method for the identification
of low-abundance modified peptides within the same sample. Without
any further enrichment strategies, we succeeded in quantifying 1 371
phosphopeptides present in the CE–MS data set and found 49
phosphopeptides to be differentially regulated in the two yeast strains.
Including acetylation, phosphorylation, deamidation, and oxidized
forms, a total of 8 106 modified peptides could be identified
in addition to 33 854 unique peptide sequences found. The work
presented here shows the first quantitative proteomics approach that
combines SILAC labeling with CE–MS analysis.
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Affiliation(s)
- Klaus Faserl
- †Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Leopold Kremser
- †Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Martin Müller
- ‡Division of Cell Biology, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - David Teis
- ‡Division of Cell Biology, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
| | - Herbert H Lindner
- †Division of Clinical Biochemistry, Biocenter, Innsbruck Medical University, Innrain 80-82, A-6020 Innsbruck, Austria
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15
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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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16
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Srzentić K, Fornelli L, Laskay ÜA, Monod M, Beck A, Ayoub D, Tsybin YO. Advantages of Extended Bottom-Up Proteomics Using Sap9 for Analysis of Monoclonal Antibodies. Anal Chem 2014; 86:9945-53. [DOI: 10.1021/ac502766n] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Kristina Srzentić
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Luca Fornelli
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Ünige A. Laskay
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Michel Monod
- Department
of Dermatology, Centre Hospitalier Universitaire Vaudois, 1011 Lausanne, Switzerland
| | - Alain Beck
- Centre d’Immunologie Pierre Fabre, 74160 St. Julien-en-Genevois, France
| | - Daniel Ayoub
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Yury O. Tsybin
- Biomolecular
Mass Spectrometry Laboratory, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
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17
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Tao Y, Julian RR. Identification of amino acid epimerization and isomerization in crystallin proteins by tandem LC-MS. Anal Chem 2014; 86:9733-41. [PMID: 25188914 PMCID: PMC4188265 DOI: 10.1021/ac502296c] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Post-translational modifications that do not result in a change in mass are particularly difficult to detect by mass spectrometry. For example, isomerization of aspartic acid or epimerization of any chiral residue within a peptide do not lead to mass shifts but can be identified by examination of independently acquired tandem mass spectra or by combination with another technique. For analysis of a biological sample, this means that liquid chromatography or some other type of separation must be used to first separate the isomers from one another. Furthermore, each specific m/z of interest must be sampled repeatedly to allow for comparison of the tandem mass spectra from each separated isomer, which contrasts with the traditional approach in proteomics where the goal is typically to avoid resampling the same m/z. We illustrate that isomerization and epimerization of peptides can be identified in this fashion by examination of long-lived crystallin proteins extracted from a sheep eye lens. Tandem mass spectrometry relying on a combination of radical directed dissociation (RDD) and collision induced dissociation (CID) following separation by liquid chromatography was used to identify modified peptides. Numerous sites of isomerization and epimerization, including several that have not been previously identified, were determined with peptide specificity. It is demonstrated that the specific sites of amino acid isomerization within each peptide can be identified by comparison with synthetic peptides. For α-crystallin proteins, the sites that undergo the greatest degree of isomerization correspond to disordered regions, which may have important implications on chaperone functionality within the context of aging.
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Affiliation(s)
- Yuanqi Tao
- Department of Chemistry, University of California , Riverside, California 92521, United States
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18
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Yang H, Lowenson JD, Clarke S, Zubarev RA. Brain proteomics supports the role of glutamate metabolism and suggests other metabolic alterations in protein l-isoaspartyl methyltransferase (PIMT)-knockout mice. J Proteome Res 2013; 12:4566-76. [PMID: 23947766 DOI: 10.1021/pr400688r] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Protein l-isoaspartyl methyltransferase (PIMT) repairs the isoaspartyl residues (isoAsp) that originate from asparagine deamidation and aspartic acid (Asp) isomerization to Asp residues. Deletion of the gene encoding PIMT in mice (Pcmt1) leads to isoAsp accumulation in all tissues measured, especially in the brain. These PIMT-knockout (PIMT-KO) mice have perturbed glutamate metabolism and die prematurely of epileptic seizures. To elucidate the role of PIMT further, brain proteomes of PIMT-KO mice and controls were analyzed. The isoAsp levels from two of the detected 67 isoAsp sites (residue 98 from calmodulin and 68 from glyceraldehyde-3-phosphate dehydrogenase) were quantified and found to be significantly increased in PIMT-KO mice (p < 0.01). Additionally, the abundance of at least 151 out of the 1017 quantified proteins was found to be altered in PIMT-KO mouse brains. Gene ontology analysis revealed that many down-regulated proteins are involved in cellular amino acid biosynthesis. For example, the serine synthesis pathway was suppressed, possibly leading to reduced serine production in PIMT-KO mice. Additionally, the abundances of enzymes in the glutamate-glutamine cycle were altered toward the accumulation of glutamate. These findings support the involvement of PIMT in glutamate metabolism and suggest that the absence of PIMT also affects other processes involving amino acid synthesis and metabolism.
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Affiliation(s)
- Hongqian Yang
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet , Scheeles väg 2, SE-17 177 Stockholm, Sweden
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19
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Wang S, Kaltashov IA. An 18O-labeling assisted LC/MS method for assignment of aspartyl/isoaspartyl products from Asn deamidation and Asp isomerization in proteins. Anal Chem 2013; 85:6446-52. [PMID: 23713887 DOI: 10.1021/ac400984r] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
An (18)O-labeling assisted LC/MS method was designed for unambiguous assignment of aspartyl/isoaspartyl products produced by Asn deamidation and Asp isomerization. By preparing the acid- and base-catalyzed deamidation standards in H2(18)O, isomer-specific mass tags were introduced to aspartyl- and isoaspartyl-containing peptides, which could be easily distinguished by mass spectrometry (MS). In contrast to the traditional ways of assigning the isomers on the basis of their elution order in reverse phase HPLC, the new method is more reliable and universal. Furthermore, the new method can be applied to the entire protein digest, and is therefore more time- and cost-effective compared with existing methods that use synthetic aspartyl- and isoaspartyl-containing peptide standards. Finally, since the identification of isomers in the new method only relies on LC/MS analysis, it can be easily implemented using the most basic and inexpensive MS instrumentation, thus providing an attractive alternative to tandem MS based approaches. The feasibility of this new method is demonstrated using a model peptide as well as the entire digest of human serum transferrin.
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Affiliation(s)
- Shunhai Wang
- Department of Chemistry, University of Massachusetts Amherst, Amherst, Massachusetts 01003, USA
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20
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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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21
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Dai S, Ni W, Patananan AN, Clarke SG, Karger BL, Zhou ZS. Integrated proteomic analysis of major isoaspartyl-containing proteins in the urine of wild type and protein L-isoaspartate O-methyltransferase-deficient mice. Anal Chem 2013; 85:2423-30. [PMID: 23327623 DOI: 10.1021/ac303428h] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
The formation of isoaspartyl residues (isoAsp or isoD) via either aspartyl isomerization or asparaginyl deamidation alters protein structure and potentially biological function. This is a spontaneous and nonenzymatic process, ubiquitous both in vivo and in nonbiological systems, such as in protein pharmaceuticals. In almost all organisms, protein L-isoaspartate O-methyltransferase (PIMT, EC2.1.1.77) recognizes and initiates the conversion of isoAsp back to aspartic acid. Additionally, alternative proteolytic and excretion pathways to metabolize isoaspartyl-containing proteins have been proposed but not fully explored, largely due to the analytical challenges for detecting isoAsp. We report here the relative quantitation and site profiling of isoAsp in urinary proteins from wild type and PIMT-deficient mice, representing products from excretion pathways. First, using a biochemical approach, we found that the total isoaspartyl level of proteins in urine of PIMT-deficient male mice was elevated. Subsequently, the major isoaspartyl protein species in urine from these mice were identified as major urinary proteins (MUPs) by shotgun proteomics. To enhance the sensitivity of isoAsp detection, a targeted proteomic approach using electron transfer dissociation-selected reaction monitoring (ETD-SRM) was developed to investigate isoAsp sites in MUPs. A total of 38 putative isoAsp modification sites in MUPs were investigated, with five derived from the deamidation of asparagine that were confirmed to contribute to the elevated isoAsp levels. Our findings lend experimental evidence for the hypothesized excretion pathway for isoAsp proteins. Additionally, the developed method opens up the possibility to explore processing mechanisms of isoaspartyl proteins at the molecular level, such as the fate of protein pharmaceuticals in circulation.
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Affiliation(s)
- Shujia Dai
- Barnett Institute of Chemical and Biological Analysis, Northeastern University, Boston Massachusetts 02115, United States
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22
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Kumar M, Chatterjee A, Khedkar AP, Kusumanchi M, Adhikary L. Mass spectrometric distinction of in-source and in-solution pyroglutamate and succinimide in proteins: a case study on rhG-CSF. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2013; 24:202-212. [PMID: 23283728 DOI: 10.1007/s13361-012-0531-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2012] [Revised: 10/17/2012] [Accepted: 10/29/2012] [Indexed: 06/01/2023]
Abstract
Formation of cyclic intermediates involving water or ammonia loss is a common occurrence in any reaction involving terminal amines or hydroxyl group containing species. Proteins that have both these functional groups in abundance are no exception, and presence of amino acids such as asparagine, glutamines, aspartic acids, and glutamic acids aid in formation of such intermediates. In the biopharma scenario, such intermediates lead to product- or process-related impurities that might be immunogenic. Mass spectroscopy is a powerful technique that is used to decipher the presence and physicochemical characteristics of such impurities. However, such intermediates can also form in situ during mass spectrometric analysis. We present here the detection of in-source and in-solution formation of succinimide and pyroglutamate in the protein granulocyte colony stimulating factor. We also propose an approach for quick differentiation of such in-situ species from the tangible impurities. We believe that this will not only reduce the time spent in unambiguous identification of succinimide- and/or pyroglutamate-related impurity in bio-pharmaceutics but also provide a platform for similar studies on other impurities that may form due to stabilized intermediates.
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Affiliation(s)
- Mukesh Kumar
- Molecular Characterization Laboratory, Biocon Research Ltd., Bangalore, Karnataka, India
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23
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Hurtado PP, O'Connor PB. Differentiation of isomeric amino acid residues in proteins and peptides using mass spectrometry. MASS SPECTROMETRY REVIEWS 2012; 31:609-25. [PMID: 22322410 DOI: 10.1002/mas.20357] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Characterization and differentiation of isomers in biological macromolecules using mass spectrometry is one of the most significant challenges facing scientists in the field. The capability of high-resolution MS instruments along with the development of new fragmentation methods now provides the ability to indirectly differentiate between some isomers. This ability has enabled mass spectrometry to evolve into a multidisciplinary technique incorporating areas such as pharmaceutical research, proteomics, polymer science, medicine, environmental chemistry, and recently archeology. This article aims to review recent developments in mass spectrometry methodologies in the identification of structural and spatial isomers in biological macromolecules, such as aspartic acid and isoaspartic acid (Asp/IsoAsp), leucine and isoleucine (Leu/Ile), glutamic acid and γ-glutamic acid, and D/L enantiomers.
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24
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Abstract
Although differentiation of the isomeric Asn deamidation products (Asp and isoAsp) at the peptide level by electron capture dissociation (ECD) has been well-established, isoAsp identification at the intact protein level remains a challenging task. Here, a comprehensive top-down deamidation study is presented using the protein beta2-microglobulin (β(2)M) as the model system. Of the three deamidation sites identified in the aged β(2)M, isoAsp formation was detected at only one site by the top-down ECD analysis. The absence of diagnostic ions likely resulted from an increased number of competing fragmentation channels and a decreased likelihood of product ion separation in ECD of proteins. To overcome this difficulty, an MS(3) approach was applied where a protein ion was first fragmented by collisionally activated dissociation (CAD) and the resulting product ion was isolated and further analyzed by ECD. IsoAsp formation at all three deamidation sites was successfully identified by this CAD-ECD approach. Furthermore, the abundance of the isoAsp diagnostic ion was found to increase linearly with the extent of deamidation. These results demonstrated the potential of ECD in the detection and quantitative analysis of isoAsp formation using the top-down approach.
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Affiliation(s)
- Xiaojuan Li
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine
| | - Xiang Yu
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine
| | - Catherine E. Costello
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine
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25
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Berkowitz SA, Engen JR, Mazzeo JR, Jones GB. Analytical tools for characterizing biopharmaceuticals and the implications for biosimilars. Nat Rev Drug Discov 2012; 11:527-40. [PMID: 22743980 DOI: 10.1038/nrd3746] [Citation(s) in RCA: 376] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Biologics such as monoclonal antibodies are much more complex than small-molecule drugs, which raises challenging questions for the development and regulatory evaluation of follow-on versions of such biopharmaceutical products (also known as biosimilars) and their clinical use once patent protection for the pioneering biologic has expired. With the recent introduction of regulatory pathways for follow-on versions of complex biologics, the role of analytical technologies in comparing biosimilars with the corresponding reference product is attracting substantial interest in establishing the development requirements for biosimilars. Here, we discuss the current state of the art in analytical technologies to assess three characteristics of protein biopharmaceuticals that regulatory authorities have identified as being important in development strategies for biosimilars: post-translational modifications, three-dimensional structures and protein aggregation.
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Affiliation(s)
- Steven A Berkowitz
- Analytical Development, Biogen Idec, 14 Cambridge Center, Cambridge, Massachusetts 02142, USA
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26
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Hao P, Qian J, Dutta B, Cheow ESH, Sim KH, Meng W, Adav SS, Alpert A, Sze SK. Enhanced separation and characterization of deamidated peptides with RP-ERLIC-based multidimensional chromatography coupled with tandem mass spectrometry. J Proteome Res 2012; 11:1804-11. [PMID: 22239700 DOI: 10.1021/pr201048c] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Deamidation of asparaginyl residues in proteins produces a mixture of asparaginyl, n-aspartyl, and isoaspartyl residues, which affects the proteins' structure, function, and stability. Thus, it is important to identify and quantify the products to evaluate the effects in biological systems. It is still a challenging task to distinguish between the n-Asp and isoAsp deamidation products in a proteome-wide analysis because of their similar physicochemical properties. The quantification of the isomeric deamidated peptides is also rather difficult because of their coelution/poor separation in reverse-phase liquid chromatography (RPLC). We here propose a RP-ERLIC-MS/MS approach for separating and quantifying on a proteome-wide scale the three products related to deamidation of the same peptide. The key to the method is the use of RPLC in the first dimensional separation and ERLIC (electrostatic repulsion-hydrophilic interaction chromatography) in the second, with direct online coupling to tandem MS. The coelution of the three deamidation-related peptides in RPLC is then an asset, as they are collected in the same fraction. They are then separated and identified in the second dimension with ERLIC, which separates peptides on the basis of both pI and GRAVY values. The coelution of the three products in RPLC and their efficient separation in ERLIC were validated using synthetic peptides, and the performance of ERLIC-MS/MS was tested using peptide mixtures from two proteins. Applying this sequence to rat liver tissue, we identified 302 unique N-deamidated peptides, of which 20 were identified via all three deamidation-related products and 70 of which were identified via two of them.
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Affiliation(s)
- Piliang Hao
- School of Biological Sciences, Nanyang Technological University , 60 Nanyang Drive, 637551, Singapore
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27
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Kim MS, Pandey A. Electron transfer dissociation mass spectrometry in proteomics. Proteomics 2012; 12:530-42. [PMID: 22246976 DOI: 10.1002/pmic.201100517] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 10/25/2011] [Accepted: 11/02/2011] [Indexed: 01/30/2023]
Abstract
Mass spectrometry has rapidly evolved to become the platform of choice for proteomic analysis. While CID remains the major fragmentation method for peptide sequencing, electron transfer dissociation (ETD) is emerging as a complementary method for the characterization of peptides and post-translational modifications (PTMs). Here, we review the evolution of ETD and some of its newer applications including characterization of PTMs, non-tryptic peptides and intact proteins. We will also discuss some of the unique features of ETD such as its complementarity with CID and the use of alternating CID/ETD along with issues pertaining to analysis of ETD data. The potential of ETD for applications such as multiple reaction monitoring and proteogenomics in the future will also be discussed.
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Affiliation(s)
- Min-Sik Kim
- Department of Biological Chemistry, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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28
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Sargaeva NP, Lin C, O’Connor PB. Differentiating N-terminal aspartic and isoaspartic acid residues in peptides. Anal Chem 2011; 83:6675-82. [PMID: 21736361 PMCID: PMC3165085 DOI: 10.1021/ac201223d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Formation of isoaspartic acid (isoAsp) is a common modification of aspartic acid (Asp) or asparagine (Asn) residue in proteins. Differentiation of isoAsp and Asp residues is a challenging task owing to their similar properties and identical molecular mass. It was recently shown that they can be differentiated using ion-electron or ion-ion interaction fragmentation methods (ExD) because these methods provide diagnostic fragments c + 57 and z(•) - 57 specific to the isoAsp residue. To date, however, the presence of such fragments has not been explored on peptides with an N-terminal isoAsp residue. To address this question, several N-terminal isoAsp-containing peptides were analyzed using ExD methods alone or combined with chromatography. A diagnostic fragment [M + 2H - 74](+•) was observed for the doubly charged precursor ions with N-terminal isoAsp residues. For some peptides, identification of the N-terminal isoAsp residue was challenging because of the low diagnostic ion peak intensity and the presence of interfering peaks. Supplemental activation was used to improve diagnostic ion detection. Further, N-terminal acetylation was offered as a means to overcome the interference problem by shifting the diagnostic fragment peak to [M + 2H - 116](+•).
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Affiliation(s)
- Nadezda P. Sargaeva
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
| | - Peter B. O’Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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29
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New proteomic developments to analyze protein isomerization and their biological significance in plants. J Proteomics 2011; 74:1475-82. [DOI: 10.1016/j.jprot.2011.04.026] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Revised: 04/01/2011] [Accepted: 04/28/2011] [Indexed: 11/30/2022]
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30
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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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31
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Sargaeva NP, Goloborodko AA, O'Connor PB, Moskovets E, Gorshkov MV. Sequence-specific predictive chromatography to assist mass spectrometric analysis of asparagine deamidation and aspartate isomerization in peptides. Electrophoresis 2011; 32:1962-9. [DOI: 10.1002/elps.201000507] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Revised: 12/21/2010] [Accepted: 12/30/2010] [Indexed: 11/08/2022]
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32
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Jung HJ, Purvine SO, Kim H, Petyuk VA, Hyung SW, Monroe ME, Mun DG, Kim KC, Park JM, Kim SJ, Tolic N, Slysz GW, Moore RJ, Zhao R, Adkins JN, Anderson GA, Lee H, Camp DG, Yu MH, Smith RD, Lee SW. Integrated post-experiment monoisotopic mass refinement: an integrated approach to accurately assign monoisotopic precursor masses to tandem mass spectrometric data. Anal Chem 2011; 82:8510-8. [PMID: 20863060 DOI: 10.1021/ac101388b] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Accurate assignment of monoisotopic precursor masses to tandem mass spectrometric (MS/MS) data is a fundamental and critically important step for successful peptide identifications in mass spectrometry based proteomics. Here we describe an integrated approach that combines three previously reported methods of treating MS/MS data for precursor mass refinement. This combined method, "integrated post-experiment monoisotopic mass refinement" (iPE-MMR), integrates steps (1) generation of refined MS/MS data by DeconMSn; (2) additional refinement of the resultant MS/MS data by a modified version of PE-MMR; and (3) elimination of systematic errors of precursor masses using DtaRefinery. iPE-MMR is the first method that utilizes all MS information from multiple MS scans of a precursor ion including multiple charge states, in an MS scan, to determine precursor mass. With the combination of these methods, iPE-MMR increases sensitivity in peptide identification and provides increased accuracy when applied to complex high-throughput proteomics data.
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Affiliation(s)
- Hee-Jung Jung
- Department of Chemistry, Korea University, 1, 5-ka, Anam-dong, Seongbuk-gu, Seoul 136-701, Republic of Korea
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33
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Indeykina MI, Popov IA, Kozin SA, Kononikhin AS, Kharybin ON, Tsvetkov PO, Makarov AA, Nikolaev EN. Capabilities of MS for Analytical Quantitative Determination of the Ratio of α- and βAsp7 Isoforms of the Amyloid-β Peptide in Binary Mixtures. Anal Chem 2011; 83:3205-10. [DOI: 10.1021/ac103213j] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Maria I. Indeykina
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
| | - Igor A. Popov
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
| | - Sergey A. Kozin
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Pogodinskaya Street 10, Moscow, Russia, 119121
| | - Alexey S. Kononikhin
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
| | - Oleg N. Kharybin
- Orekhovich Institute of Biomedical Chemistry of the Russian Academy of Medical Sciences, Pogodinskaya Street 10, Moscow, Russia, 119121
| | - Philippe O. Tsvetkov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
| | - Alexander A. Makarov
- Engelhardt Institute of Molecular Biology of the Russian Academy of Sciences, Vavilova Street 32, Moscow, Russia, 119991
| | - Evgenij N. Nikolaev
- Emanuel Institute of Biochemical Physics of the Russian Academy of Sciences, Kosygina Street 4, Moscow, Russia, 119334
- Institute for Energy Problems of Chemical Physics of the Russian Academy of Sciences, Leninsky Prospekt 38 Bldg 2, Moscow, Russia, 119334
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Sargaeva NP, Lin C, O’Connor PB. Unusual fragmentation of β-linked peptides by ExD tandem mass spectrometry. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2011; 22:480-91. [PMID: 21472566 PMCID: PMC4361814 DOI: 10.1007/s13361-010-0049-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Revised: 11/18/2010] [Accepted: 11/18/2010] [Indexed: 05/11/2023]
Abstract
Ion-electron reaction based fragmentation methods (ExD) in tandem mass spectrometry (MS), such as electron capture dissociation (ECD) and electron transfer dissociation (ETD) represent a powerful tool for biological analysis. ExD methods have been used to differentiate the presence of the isoaspartate (isoAsp) from the aspartate (Asp) in peptides and proteins. IsoAsp is a β(3)-type amino acid that has an additional methylene group in the backbone, forming a C(α)-C(β) bond within the polypeptide chain. Cleavage of this bond provides specific fragments that allow differentiation of the isomers. The presence of a C(α)-C(β) bond within the backbone is unique to β-amino acids, suggesting a similar application of ExD toward the analysis of peptides containing other β-type amino acids. In the current study, ECD and ETD analysis of several β-amino acid containing peptides was performed. It was found that N-C(β) and C(α)-C(β) bond cleavages were rare, providing few c and z• type fragments, which was attributed to the instability of the C(β) radical. Instead, the electron capture resulted primarily in the formation of a• and y fragments, representing an alternative fragmentation pathway, likely initiated by the electron capture at a backbone amide nitrogen protonation site within the β amino acid residues.
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Affiliation(s)
- Nadezda P. Sargaeva
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
| | - Cheng Lin
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
| | - Peter B. O’Connor
- Mass Spectrometry Resource, Department of Biochemistry, Boston University School of Medicine, 670 Albany Street, R504, Boston, Massachusetts 02118
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
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Ni W, Dai S, Karger BL, Zhou ZS. Analysis of isoaspartic Acid by selective proteolysis with Asp-N and electron transfer dissociation mass spectrometry. Anal Chem 2011; 82:7485-91. [PMID: 20712325 DOI: 10.1021/ac101806e] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
A ubiquitous yet underappreciated protein post-translational modification, isoaspartic acid (isoAsp, isoD, or beta-Asp), generated via the deamidation of asparagine or isomerization of aspartic acid in proteins, plays a diverse and crucial role in aging, as well as autoimmune, cancer, neurodegeneration, and other diseases. In addition, formation of isoAsp is a major concern in protein pharmaceuticals, as it may lead to aggregation or activity loss. The scope and significance of isoAsp have, up to now, not been fully explored, as an unbiased screening of isoAsp at low abundance remains challenging. This difficulty is due to the subtle difference in the physicochemical properties between isoAsp and Asp, e.g., identical mass. In contrast, endoprotease Asp-N (EC 3.4.24.33) selectively cleaves aspartyl peptides but not the isoaspartyl counterparts. As a consequence, isoaspartyl peptides can be differentiated from those containing Asp and also enriched by Asp-N digestion. Subsequently, the existence and site of isoaspartate can be confirmed by electron transfer dissociation (ETD) mass spectrometry. As little as 0.5% of isoAsp was detected in synthetic beta-amyloid and cytochrome c peptides, even though both were initially assumed to be free of isoAsp. Taken together, our approach should expedite the unbiased discovery of isoAsp.
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Affiliation(s)
- Wenqin Ni
- Barnett Institute of Chemical and Biological Analysis and Department of Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, USA
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Yang H, Zubarev RA. Mass spectrometric analysis of asparagine deamidation and aspartate isomerization in polypeptides. Electrophoresis 2010; 31:1764-72. [PMID: 20446295 PMCID: PMC3104603 DOI: 10.1002/elps.201000027] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
One of the most frequent modifications in proteins and peptides is the deamidation of asparagine, a spontaneous non-enzymatic reaction leading to a mixture of L,D-succinimidyl, L,D-aspartyl, and L,D-isoaspartyl forms, with L-isoaspartyl dominating. Spontaneous isomerization of L-Asp yields the same products. In vivo, these unusual forms of aspartate are repaired by the protein L-isoaspartyl O-methyltransferase enzyme, with the balance between isomerization and repair affecting the organism physiology. Mass spectrometric analysis of this balance involves isomer separation, iso-Asp/Asp quantification, and iso-Asp site identification. This review highlights the issues associated with these steps and discusses the prospects of high-throughput iso-Asp analysis.
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Affiliation(s)
- Hongqian Yang
- Division of Molecular Biometry, Department of Medicinal Biochemistry and Biophysics, Karolinska Institute, Stockholm, Sweden
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Mukherjee R, Adhikary L, Khedkar A, Iyer H. Probing deamidation in therapeutic immunoglobulin gamma (IgG1) by 'bottom-up' mass spectrometry with electron transfer dissociation. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2010; 24:879-884. [PMID: 20196189 DOI: 10.1002/rcm.4464] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Aspartic acid formed by nonenzymatic deamidation of asparagine often isomerizes to isoaspartic acid through a succinimide intermediate. Accumulation of isoaspartic acid initiates aggregation and degradation in proteins. Deamidation at the antigen-binding region reduces the efficacy and also upregulates immunogenicity of monoclonal antibodies. We report an improved 'bottom-up' tandem mass spectrometric method to detect and decipher the position of isoaspartate formation in therapeutic immunoglobulin gamma in a single chromatographic run. Differentiation between aspartate and isoaspartate residues through collision-induced tandem mass spectrometry is formidable due to their identical mass. Signature backbone cleavage ions, c(n) + 57 and z(l-n) - 57, produced upon radical-mediated fragmentation, were used to delineate the site of isomerization. It is more conclusive than monitoring the relative peak intensity and the decrease in hydrophobicity of the isoaspartate-containing peptide in a chromatographic elution. Collectively, this methodology provides a useful tool to monitor deamidation and isomerization in biopharmaceuticals during their production, downstream processing and storage.
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Affiliation(s)
- Raju Mukherjee
- Research and Development, Biocon Limited, 20th KM, Hosur Road, Bangalore-560100, India.
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