17 results on '"Daniel G. Delafield"'
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2. Proteome-wide and matrisome-specific alterations during human pancreas development and maturation
- Author
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Zihui Li, Daniel M. Tremmel, Fengfei Ma, Qinying Yu, Min Ma, Daniel G. Delafield, Yatao Shi, Bin Wang, Samantha A. Mitchell, Austin K. Feeney, Vansh S. Jain, Sara Dutton Sackett, Jon S. Odorico, and Lingjun Li
- Subjects
Science - Abstract
The pancreatic extracellular matrix (ECM) is known to differ between species, age groups and physiological states, but its compositional changes throughout human life are not well understood. Here, the authors study how the proteome of pancreatic ECM changes during human development and maturation.
- Published
- 2021
- Full Text
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3. Mass spectrometry imaging: the rise of spatially resolved single-cell omics
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Hua Zhang, Daniel G. Delafield, and Lingjun Li
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Cell Biology ,Molecular Biology ,Biochemistry ,Biotechnology - Published
- 2023
4. Enabling Global Analysis of Protein Citrullination via Biotin Thiol Tag-Assisted Mass Spectrometry
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Yatao Shi, Zihui Li, Bin Wang, Xudong Shi, Hui Ye, Daniel G. Delafield, Langlang Lv, Zhengqing Ye, Zhengwei Chen, Fengfei Ma, and Lingjun Li
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Article ,Analytical Chemistry - Abstract
Citrullination is a key post-translational modification (PTM) that affects protein structures and functions. Although it has been linked to various biological processes and disease pathogenesis, the underlying mechanism remains poorly understood due to a lack of effective tools to enrich, detect, and localize this PTM. Herein, we report the design and development of a biotin thiol tag that enables derivatization, enrichment, and confident identification of citrullination via mass spectrometry. We perform global mapping of the citrullination proteome of mouse tissues. In total, we identify 691 citrullination sites from 432 proteins which represents the largest data set to date. We discover novel distribution and functions of this PTM. This study depicts a landscape of protein citrullination and lays the foundation for further deciphering their physiological and pathological roles.
- Published
- 2022
5. Site-specific chirality-conferred structural compaction differentially mediates the cytotoxicity of Aβ42
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Gongyu Li, Chae Kyung Jeon, Min Ma, Yifei Jia, Zhen Zheng, Daniel G. Delafield, Gaoyuan Lu, Elena V. Romanova, Jonathan V. Sweedler, Brandon T. Ruotolo, and Lingjun Li
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General Chemistry - Abstract
Analytical and technological advancements in multidimensional ion mobility-mass spectrometry and molecular dynamic simulations catalyze the birth of a new precise strategy for fine-tuning Aβ42 structure and cytotoxicity.
- Published
- 2023
6. Higher Temperature Porous Graphitic Carbon Separations Differentially Impact Distinct Glycopeptide Classes
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Daniel G. Delafield, Hannah N. Miles, William A. Ricke, and Lingjun Li
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Chromatography, Reverse-Phase ,Structural Biology ,Glycopeptides ,Temperature ,Animals ,Humans ,Cattle ,Graphite ,Porosity ,Spectroscopy ,Article ,Carbon - Abstract
Mass spectrometry-based discovery glycoproteomics is highly dependent on the use of chromatography paradigms amenable to analyte retention and separation. When compared against established stationary phases such as reversed-phase and hydrophilic interaction liquid chromatography, reports utilizing porous graphitic carbon have detailed its numerous advantages. Recent efforts have highlighted the utility in porous graphitic carbon in high-throughput glycoproteomics, principally through enhanced profiling depth and liquid-phase resolution at higher column temperatures. However, increasing column temperature has been shown to impart disparaging effects in glycopeptide identification. Herein we further elucidate this trend, describing qualitative and semiquantitative effects of increased column temperature on glycopeptide identification rates, signal intensity, resolution, and spectral count linear response. Through analysis of enriched bovine and human glycopeptides, species with high mannose and sialylated glycans were shown to most significantly benefit and suffer from high column temperatures, respectively. These results provide insight as to how porous graphitic carbon separations may be appropriately leveraged for glycopeptide identification while raising concerns over quantitative and semiquantitative label-free comparisons as the temperature changes. RAW MS glycoproteomic data are available via ProteomeXchange with identifier PXD034354.
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- 2022
7. Recent developments and applications of quantitative proteomics strategies for high-throughput biomolecular analyses in cancer research
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Lingjun Li, Hannah N. Miles, and Daniel G. Delafield
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0301 basic medicine ,business.industry ,Systems biology ,Quantitative proteomics ,Health technology ,Cancer ,Early detection ,Computational biology ,medicine.disease ,Biochemistry, Genetics and Molecular Biology (miscellaneous) ,Biochemistry ,03 medical and health sciences ,Chemistry ,030104 developmental biology ,0302 clinical medicine ,Chemistry (miscellaneous) ,030220 oncology & carcinogenesis ,Pancreatic cancer ,medicine ,Biomarker discovery ,business ,Molecular Biology ,Throughput (business) - Abstract
Innovations in medical technology and dedicated focus from the scientific community have inspired numerous treatment strategies for benign and invasive cancers. While these improvements often lend themselves to more positive prognoses and greater patient longevity, means for early detection and severity stratification have failed to keep pace. Detection and validation of cancer-specific biomarkers hinges on the ability to identify subtype-specific phenotypic and proteomic alterations and the systematic screening of diverse patient groups. For this reason, clinical and scientific research settings rely on high throughput and high sensitivity mass spectrometry methods to discover and quantify unique molecular perturbations in cancer patients. Discussed within is an overview of quantitative proteomics strategies and a summary of recent applications that enable revealing potential biomarkers and treatment targets in prostate, ovarian, breast, and pancreatic cancer in a high throughput manner., Various quantitative strategies can be utilized in mass spectrometry (MS)-based proteomic investigations. Here we explore recent applications of quantitative MS-based strategies and the resulting advances in the areas of prostate, pancreatic, breast and ovarian cancer research.
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- 2021
8. Enabling global analysis of protein citrullination and homocitrullination via biotin thiol tag-assisted mass spectrometry
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Daniel G. Delafield, Hui Ye, Zhengwei Chen, Xudong Shi, Fengfei Ma, Bin Wang, Zihui Li, Langlang Lv, Yatao Shi, Zhengqing Ye, and Lingjun Li
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chemistry.chemical_classification ,chemistry.chemical_compound ,Biochemistry ,Biotin ,Chemistry ,Thiol ,Mass spectrometry ,Protein citrullination - Abstract
Citrullination and homocitrullination are key post-translational modifications (PTMs) that affect protein structures and functions. Although they have been linked to various biological processes and disease pathogenesis, the underlying mechanism remains poorly understood due to a lack of effective tools to enrich, detect, and localize these PTMs. Herein, we report the design and development of a biotin thiol tag that enables derivatization, enrichment, and confident identification of these two PTMs simultaneously via mass spectrometry. We perform global mapping of the citrullination and homocitrullination proteomes of mouse tissues. In total, we identify 691 citrullination sites and 81 homocitrullination sites from 432 and 63 proteins, respectively, representing the largest datasets to date. We discover novel distribution and functions of these two PTMs. We also perform multiplexing quantitative analysis via isotopic labeling techniques. This study depicts a landscape of protein citrullination and homocitrullination and lays the foundation for further deciphering their physiological and pathological roles.
- Published
- 2022
9. Complementary proteome and glycoproteome access revealed through comparative analysis of reversed phase and porous graphitic carbon chromatography
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Daniel G. Delafield, Hannah N. Miles, Yuan Liu, William A. Ricke, and Lingjun Li
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Male ,Proteomics ,Chromatography, Reverse-Phase ,Proteome ,Glycopeptides ,Humans ,Graphite ,Biochemistry ,Porosity ,Carbon ,Article ,Analytical Chemistry - Abstract
Continual development in instrumental and analytical techniques have aided in establishing rigorous connections between protein glycosylation and human illness. These illnesses, such as various forms of cancer, are often associated with poor prognoses, prompting the need for more comprehensive characterization of the glycoproteome. While innovative instrumental and computational strategies have largely benefited glycoproteomic analyses, less attention is given to benefits gained through alternative, optimized chromatographic techniques. Porous graphitic carbon (PGC) chromatography has gained considerable interest in glycomics research due to its mobile phase flexibility, increased retention of polar analytes and improved structural elucidation at higher temperatures. PGC has yet to be systematically compared against or in tandem with standard reversed phase liquid chromatography (RPLC) in high-throughput bottom-up glycoproteomics experiments, leaving the potential benefits unexplored. Performing comparative analysis of single and biphasic separation regimes at a range of column temperatures illustrates complementary advantages for each method. PGC separation is shown to selectively retain shorter, more hydrophilic glycopeptide species, imparting higher average charge, and exhibiting greater microheterogeneity coverage for identified glycosites. Additionally, we demonstrate that liquid-phase separation of glycopeptide isomers may be achieved through both single and biphasic PGC separations, providing a means towards facile, multidimensional glycopeptide characterization. Beyond this, we demonstrate how utilization of multiple separation regimes and column temperatures can aid in profiling the glycoproteome in tumorigenic and aggressive prostate cancer cells. RAW MS proteomics and glycoproteomics datasets have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD024196 (10.6019/PXD024196) and PXD024195, respectively.
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- 2021
10. On-tissue spatial proteomics integrating MALDI-MS imaging with shotgun proteomics reveals soy consumption-induced biomarkers in a fragile X syndrome mouse model
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Qinying Yu, Daniel G. Delafield, Wenxin Wu, Yusi Cui, Min Ma, Lingjun Li, Cara J. Westmark, Pamela R. Westmark, Zihui Li, Meng Xu, Xudong Shi, and Alejandra Gutierrez
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Synapse ,Fragile X syndrome ,Maldi ms ,Spatially resolved ,medicine ,Hippocampus ,Computational biology ,Biology ,medicine.disease ,Proteomics ,Shotgun proteomics ,Mass spectrometry imaging - Abstract
Soy-based diets are associated with increased seizures and autism. Thus, there is an acute need for unbiased protein biomarker identification in Fragile X syndrome (FXS) in response to soy consumption. Herein, we present a spatial proteomics approach integrating mass spectrometry imaging (MSI) with label-free proteomics in a mouse model of FXS to map the spatial distribution and quantify the levels of proteins in the hippocampus and hypothalamus brain regions. In total, 1,004 unique peptides were spatially resolved, demonstrating the diverse array of peptidomes present in the tissue slices and the broad coverage of the strategy. A group of proteins that are known to be involved in the GABAergic system, synaptic transmission, and co-expression network analysis indicated that protein in soy group was significantly associated with metabolism and synapse modules in the Fmr1KO brain. Ultimately, this spatial proteomics work laid the ground for identifying novel therapeutic targets and biomarkers for FXS.
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- 2021
11. High-end ion mobility mass spectrometry: A current review of analytical capacity in omics applications and structural investigations
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Daniel G. Delafield, Gaoyuan Lu, Cameron J. Kaminsky, and Lingjun Li
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Spectroscopy ,Analytical Chemistry - Published
- 2022
12. Cyclic immonium ion of lactyllysine reveals widespread lactylation in the human proteome
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Ning Wan, Nian Wang, Siqin Yu, Hanqing Zhang, Shuo Tang, Dexiang Wang, Wenjie Lu, Huanhuan Li, Daniel G. Delafield, Ying Kong, Xinmiao Wang, Chang Shao, Langlang Lv, Guangji Wang, Renxiang Tan, Nanxi Wang, Haiping Hao, and Hui Ye
- Subjects
Histones ,Proteome ,Tandem Mass Spectrometry ,Humans ,Cell Biology ,Oxidoreductases ,Molecular Biology ,Biochemistry ,Glycolysis ,Biotechnology - Abstract
Lactylation was initially discovered on human histones. Given its nascence, its occurrence on nonhistone proteins and downstream functional consequences remain elusive. Here we report a cyclic immonium ion of lactyllysine formed during tandem mass spectrometry that enables confident protein lactylation assignment. We validated the sensitivity and specificity of this ion for lactylation through affinity-enriched lactylproteome analysis and large-scale informatic assessment of nonlactylated spectral libraries. With this diagnostic ion-based strategy, we confidently determined new lactylation, unveiling a wide landscape beyond histones from not only the enriched lactylproteome but also existing unenriched human proteome resources. Specifically, by mining the public human Meltome Atlas, we found that lactylation is common on glycolytic enzymes and conserved on ALDOA. We also discovered prevalent lactylation on DHRS7 in the draft of the human tissue proteome. We partially demonstrated the functional importance of lactylation: site-specific engineering of lactylation into ALDOA caused enzyme inhibition, suggesting a lactylation-dependent feedback loop in glycolysis.
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- 2021
13. Proteome-wide and matrisome-specific alterations during human pancreas development and maturation
- Author
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Bin Wang, Vansh S. Jain, Qinying Yu, Austin K. Feeney, Yatao Shi, Zihui Li, Jon S. Odorico, Daniel M. Tremmel, Sara Dutton Sackett, Lingjun Li, Min Ma, Daniel G. Delafield, Fengfei Ma, and Samantha A. Mitchell
- Subjects
0301 basic medicine ,Proteomics ,Male ,Proteome ,Cellular differentiation ,Organogenesis ,General Physics and Astronomy ,Fluorescent Antibody Technique ,Extracellular matrix ,0302 clinical medicine ,Tandem Mass Spectrometry ,skin and connective tissue diseases ,Child ,Regulation of gene expression ,Extracellular Matrix Proteins ,Multidisciplinary ,geography.geographical_feature_category ,Gene Expression Regulation, Developmental ,Middle Aged ,Islet ,Cell biology ,medicine.anatomical_structure ,030220 oncology & carcinogenesis ,Child, Preschool ,Female ,Pancreas ,Adult ,Adolescent ,Science ,Quantitative proteomics ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,Fetus ,medicine ,Humans ,geography ,Molecular Sequence Annotation ,General Chemistry ,Ageing ,030104 developmental biology ,Gene Ontology ,sense organs ,Chromatography, Liquid - Abstract
The extracellular matrix (ECM) is unique to each tissue and capable of guiding cell differentiation, migration, morphology, and function. The ECM proteome of different developmental stages has not been systematically studied in the human pancreas. In this study, we apply mass spectrometry-based quantitative proteomics strategies using N,N-dimethyl leucine isobaric tags to delineate proteome-wide and ECM-specific alterations in four age groups: fetal (18-20 weeks gestation), juvenile (5-16 years old), young adults (21-29 years old) and older adults (50-61 years old). We identify 3,523 proteins including 185 ECM proteins and quantify 117 of them. We detect previously unknown proteome and matrisome features during pancreas development and maturation. We also visualize specific ECM proteins of interest using immunofluorescent staining and investigate changes in ECM localization within islet or acinar compartments. This comprehensive proteomics analysis contributes to an improved understanding of the critical roles that ECM plays throughout human pancreas development and maturation., The pancreatic extracellular matrix (ECM) is known to differ between species, age groups and physiological states, but its compositional changes throughout human life are not well understood. Here, the authors study how the proteome of pancreatic ECM changes during human development and maturation.
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- 2021
14. Recent Advances in Analytical Approaches for Glycan and Glycopeptide Quantitation
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Lingjun Li and Daniel G. Delafield
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ESI, Electrospray Ionization ,Special Issue: Glycoproteomics ,Computer science ,Review ,Biochemistry ,Analytical Chemistry ,HCD, Higher-energy Collisional Dissociation ,Stable isotope labeling by amino acids in cell culture ,Data-independent acquisition ,ETciD, Electron Transfer/Collisional-Induced Dissociation ,iTRAQ, Isotopic Tags for Relative and Absolute Quantitation ,Glycomics ,mass spectrometry ,ETD, Electron Transfer Dissociation ,0303 health sciences ,glycan ,biology ,SCE, Stepped Collision Energy ,030302 biochemistry & molecular biology ,Glycopeptides ,CHO, Chinese Hamster Ovary ,EThcD, Electron Transfer/Higher-Energy Dissociation ,Glycopeptide ,Glycoproteomics ,chemical labeling ,Isobaric labeling ,glycopeptide ,PGC, Porous Graphitic Carbon ,isobaric labeling ,Chemical labeling ,MRM, Multiple Reaction Monitoring ,Glycan ,glycosylation ,DIA, Data-Independent Acquisition ,Computational biology ,03 medical and health sciences ,PRM, Parallel Reaction Monitoring ,Polysaccharides ,Animals ,Humans ,metabolic labeling ,Molecular Biology ,isotopic labeling ,SRM, Selected Reaction Monitoring ,030304 developmental biology ,FDR, False Discovery Rate ,posttranslational modification ,quantitation ,MALDI, Matrix-Assisted Laser Desorption/Ionization ,CID, Collisional-Induced Dissociation ,SILAC, Stable Isotopic Labeling of Amino Acids in Cell Culture ,biology.protein ,DDA, Data-Dependent Acquisition - Abstract
Growing implications of glycosylation in physiological occurrences and human disease have prompted intensive focus on revealing glycomic perturbations through absolute and relative quantification. Empowered by seminal methodologies and increasing capacity for detection, identification, and characterization, the past decade has provided a significant increase in the number of suitable strategies for glycan and glycopeptide quantification. Mass-spectrometry-based strategies for glycomic quantitation have grown to include metabolic incorporation of stable isotopes, deposition of mass difference and mass defect isotopic labels, and isobaric chemical labeling, providing researchers with ample tools for accurate and robust quantitation. Beyond this, workflows have been designed to harness instrument capability for label-free quantification, and numerous software packages have been developed to facilitate reliable spectrum scoring. In this review, we present and highlight the most recent advances in chemical labeling and associated techniques for glycan and glycopeptide quantification., Graphical Abstract, Highlights • Novel glycomic applications of label-free, metabolic, isotopic, and isobaric labeling quantitation • Informatic tools for investigative quantitative glycomics • Critical considerations for entry or expansion of quantitative glycomics • Introduction of synthetically facile, cost-effective labeling technology, In Brief Recent years have seen an explosion in novel strategies for quantitative glycomics and glycoproteomics. Whether through metabolic incorporation of stable isotopes, deposition of custom isotopic labels, or high-throughput isobaric chemical tags, these numerous novel strategies provide ease of access to glycomic and glycoproteomic investigation. This review highlights the recent innovations in labeling methods, label-free strategies, acquisition modes, and bioinformatic tools for glycan and glycopeptide quantitation, while providing critical evaluations and technical considerations to enable effective analysis.
- Published
- 2020
15. Finding Biomass Degrading Enzymes Through an Activity-Correlated Quantitative Proteomics Platform (ACPP)
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Daniel G. Delafield, Hongyan Ma, Si Wu, Zhe Wang, and Jianlan You
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Proteomics ,0301 basic medicine ,Quantitative proteomics ,Biomass ,Cellulase ,010402 general chemistry ,01 natural sciences ,Article ,Fungal Proteins ,03 medical and health sciences ,Structural Biology ,Cellulose ,Spectroscopy ,chemistry.chemical_classification ,biology ,Chemistry ,Elution ,Hydrolysis ,Aspergillus niger ,alpha-Glucosidases ,biology.organism_classification ,Enzyme assay ,0104 chemical sciences ,030104 developmental biology ,Enzyme ,Biochemistry ,biology.protein - Abstract
The microbial secretome, known as a pool of biomass (i.e., plant-based materials) degrading enzymes, can be utilized to discover industrial enzyme candidates for biofuel production. Proteomics approaches have been applied to discover novel enzyme candidates through comparing protein expression profiles with enzyme activity of the whole secretome under different growth conditions. However, the activity measurement of each enzyme candidate is needed for confident "active" enzyme assignments, which remains to be elucidated. To address this challenge, we have developed an Activity-Correlated Quantitative Proteomics Platform (ACPP) that systematically correlates protein-level enzymatic activity patterns and protein elution profiles using a label-free quantitative proteomics approach. The ACPP optimized a high performance anion exchange separation for efficiently fractionating complex protein samples while preserving enzymatic activities. The detected enzymatic activity patterns in sequential fractions using microplate-based assays were cross-correlated with protein elution profiles using a customized pattern-matching algorithm with a correlation R-score. The ACPP has been successfully applied to the identification of two types of "active" biomass-degrading enzymes (i.e., starch hydrolysis enzymes and cellulose hydrolysis enzymes) from Aspergillus niger secretome in a multiplexed fashion. By determining protein elution profiles of 156 proteins in A. niger secretome, we confidently identified the 1,4-α-glucosidase as the major "active" starch hydrolysis enzyme (R = 0.96) and the endoglucanase as the major "active" cellulose hydrolysis enzyme (R = 0.97). The results demonstrated that the ACPP facilitated the discovery of bioactive enzymes from complex protein samples in a high-throughput, multiplexing, and untargeted fashion. Graphical Abstract ᅟ.
- Published
- 2017
16. Peroxymonosulfate Oxidizes Amino Acids in Water without Activation
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Daniel G. Delafield, Lingjun Li, Yi Yang, Joseph J. Pignatello, Christian A. Lochbaum, Joel A. Pedersen, and Mercedes Ruiz
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chemistry.chemical_classification ,Methionine ,Singlet oxygen ,Tryptophan ,Water ,General Chemistry ,010501 environmental sciences ,01 natural sciences ,Amino acid ,Peroxides ,chemistry.chemical_compound ,chemistry ,Oxidizing agent ,Environmental Chemistry ,Organic chemistry ,Tyrosine ,Amino Acids ,Oxidation-Reduction ,Histidine ,0105 earth and related environmental sciences ,Cysteine - Abstract
A variety of peptidic and proteinaceous contaminants (e.g., proteins, toxins, pathogens) present in the environment may pose risk to human health and wildlife. Peroxymonosulfate is a strong oxidant (EH0 = 1.82 V for HSO5-, the predominant species at environmental pH values) that may hold promise for the deactivation of proteinaceous contaminants. Relatively little quantitative information exists on the rates of peroxymonosulfate reactions with free amino acids. Here, we studied the oxidation of 19 of the 20 standard proteinogenic amino acids (all except cysteine) by peroxymonosulfate without explicit activation. Reaction half-lives at pH 7 ranged from milliseconds to hours. Amino acids possessing sulfur-containing, heteroaromatic, or substituted aromatic side chains were the most susceptible to oxidation by peroxymonosulfate, with rates of transformation decreasing in the order methionine > tryptophan > tyrosine > histidine. The rate of tryptophan oxidation did not decrease in the presence of an aquatic natural organic matter. Singlet oxygen resulting from peroxymonosulfate self-decomposition, while detected by electron paramagnetic resonance spectroscopy, was unlikely to be the principal reactive species. Our results demonstrate that peroxymonosulfate is capable of oxidizing 19 amino acids without explicit activation and that solvent-exposed methionine and tryptophan residues are likely initial targets of oxidation in peptides and proteins.
- Published
- 2019
17. Improved structural elucidation of peptide isomers and their receptors using advanced ion mobility-mass spectrometry
- Author
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Gongyu Li, Lingjun Li, and Daniel G. Delafield
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chemistry.chemical_classification ,Ion-mobility spectrometry ,Biomolecule ,010401 analytical chemistry ,Analytical technique ,Nanotechnology ,Peptide ,Mass spectrometry ,01 natural sciences ,0104 chemical sciences ,Analytical Chemistry ,Characterization (materials science) ,chemistry ,Receptor ,Spectroscopy - Abstract
Ion mobility-mass spectrometry (IM-MS) has emerged as a highly important analytical technique for the structural elucidation of a wide range of biomolecules, including neuropeptides, proteins and protein complexes. However, though the inherent value presented by powerful ion mobility techniques has garnered significant interest and spurred on the development of novel and increasingly powerful IM-MS regimes, modern commercial implementations continually fall short in the effort to fully resolve subtle structural variations of biologically-relevant analytes, including peptide stereoisomers. Presented here is a review of emerging instrumentation, computational strategies, and methods of data analysis vital to the integration and development of IM-MS workflows for structural characterization. Furthermore, we explore the usefulness of ion mobility techniques in probing structurally-critical biomolecules, examining the ability of current methods to elucidate neuropeptide stereoisomers and receptors.
- Published
- 2020
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