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Trevisan França de Lima L, Crawford DH, Broszczak DA, Zhang X, Bridle R. K, Punyadeera C. A salivary biomarker panel to detect liver cirrhosis. iScience 2023; 26:107015. [PMID: 37360686 PMCID: PMC10285560 DOI: 10.1016/j.isci.2023.107015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 04/14/2023] [Accepted: 05/29/2023] [Indexed: 06/28/2023] Open
Abstract
Limited access to diagnostic tests for liver fibrosis remains one of the main reasons for late diagnosis, especially in rural and remote communities. Saliva diagnostics is accessible with excellent patient compliance. The aim of this study was to develop a saliva-based diagnostic tool for liver fibrosis/cirrhosis. Salivary concentrations of hyaluronic acid (HA), tissue inhibitor of metalloproteinase-1 (TIMP-1), and α-2-macroglobulin (A2MG) were significantly increased (p < 0.05) in patients with liver fibrosis/cirrhosis. By combining these biomarkers, we developed the Saliva Liver Fibrosis (SALF) score, which identified patients with liver cirrhosis with an area under the receiver operating characteristic curve (AUROC) of 0.970 and 0.920 in a discovery and validation cohorts, respectively. The SALF score had a performance that was similar to that of the current Fibrosis-4 (AUROC:0.740) and Hepascore (AUROC:0.979). We demonstrated the clinical utility of saliva to diagnose liver fibrosis/cirrhosis with a potential to improve the screening for cirrhosis in asymptomatic populations.
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Affiliation(s)
- Lucas Trevisan França de Lima
- The School of Environment and Science, Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, QLD, Australia
- Gallipoli Medical Research Foundation, Greenslopes Private Hospital, Greenslopes, QLD, Australia
| | - Darrell H.G. Crawford
- Gallipoli Medical Research Foundation, Greenslopes Private Hospital, Greenslopes, QLD, Australia
- The University of Queensland, Faculty of Medicine, Herston, QLD, Australia
| | - Daniel A. Broszczak
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Kelvin Grove Campus, Brisbane, QLD, Australia
| | - Xi Zhang
- The School of Environment and Science, Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, QLD, Australia
| | - Kim Bridle R.
- Gallipoli Medical Research Foundation, Greenslopes Private Hospital, Greenslopes, QLD, Australia
- The University of Queensland, Faculty of Medicine, Herston, QLD, Australia
| | - Chamindie Punyadeera
- The School of Environment and Science, Griffith Institute for Drug Discovery (GRIDD), Griffith University, Brisbane, QLD, Australia
- Menzies Health Institute Queensland (MIHQ), Griffith University, Gold Coast, QLD, Australia
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2
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Wang X, Yue L, Zhang F, Tang Z, Chen Z, Li Z. A novel strategy for quantification of α2,3- and α2,6-linked sialic acids in sialylated glycoproteins. Carbohydr Res 2023; 531:108892. [PMID: 37429229 DOI: 10.1016/j.carres.2023.108892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 06/24/2023] [Accepted: 06/28/2023] [Indexed: 07/12/2023]
Abstract
Sialic acid, a monosaccharide containing nine carbon atoms, is widely distributed in eukaryotic cells. The bound sialic acids are mainly present at the glycan ends of glycoconjugates via α2-3 or α2-6 glycosidic bonds, and alterations in their expression levels and linkage types are associated with the progress of many diseases and tumors. The present study provides a new strategy for quantification of α2,3- and α2,6-linked sialic acids in sialylated glycoproteins. In fact, quantification of α2,3-linked sialic acids were based on the difference of the bound sialic acids in the sample before and after treatment with α2-3 neuraminidase, whereas the α2,6-linked sialic acids were equal to the bound sialic acids in the α2-3 neuraminidase-treated sample. Subsequently, α2,3/6-linked sialic acids in salivary glycoproteins from healthy volunteers and diabetic patients were quantified in accordance with this method. This work provides an accurate method for the quantification of α2,3- and α2,6-linked sialic acids in the sialoglycoproteins, which is more instructive for understanding the biological roles of α2,3/6-linked sialic acid in sialoglycoproteins.
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Affiliation(s)
- Xilong Wang
- College of Life Sciences and Technology, Longdong University, Qingyang, Gansu, China; Gansu Key Laboratory of Protection and Utilization for Biological Resources and Ecological Restoration, Qingyang, Gansu, China.
| | - Lixin Yue
- Department of Dermatology, Xijing Hospital, Fourth Military Medical University, Xi'an, Shaanxi, China
| | - Fan Zhang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Zhen Tang
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Zhuo Chen
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
| | - Zheng Li
- Laboratory for Functional Glycomics, College of Life Sciences, Northwest University, Xi'an, Shaanxi, China
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3
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Shu J, Xiong W, Zhang R, Ma S, Zhou K, Wang X, Yan F, Huang D, Li J, Wu Y, He J. Glycan-selective in-situ growth of thermoresponsive polymers for thermoprecipitation and enrichment of N-glycoprotein/glycopeptides. Talanta 2023; 253:123956. [PMID: 36167012 DOI: 10.1016/j.talanta.2022.123956] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 09/13/2022] [Accepted: 09/19/2022] [Indexed: 12/13/2022]
Abstract
In view of the biological significance and micro-heterogeneity of protein glycosylation for human health, specific enrichment of N-glycosylated proteins/peptides from complex biological samples is a prerequisite for the discovery of disease biomarkers and clinical diagnosis. In this work, we propose a "grafting-from" N-glycoprotein enriching method based on the in-situ growth of thermoresponsive polymer brushes from the N-glycosylated site of proteins. The initiator was first attached to the pre-oxidized glycan moieties by hydrazide chemistry, from which the thermoresponsive polymers can be grown to form giant protein-polymer conjugates (PPC). The thermosensitive PPC can be precipitated and separated by raising the temperature to above its lower critical solubility temperature (LCST). Mass spectrometry verified 210 N-glycopeptides corresponding to 136 N-glycoproteins in the rabbit serum. These results demonstrate the capability of the tandem thermoprecipitation strategy to enrich and separate N-glycoprotein/glycopeptide. Due to its simplicity and efficiency specifically, this method holds the potential for identifying biomarkers from biological samples in N-glycoproteome analysis.
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Affiliation(s)
- Jingjing Shu
- Research Institute of Photocatalysis, College of Biological Science and Engineering, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350108, China
| | - Wenli Xiong
- Research Institute of Photocatalysis, College of Biological Science and Engineering, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350108, China
| | - Ran Zhang
- Central Laboratory of Health Quarantine, International Travel Health Care Center, Shenzhen Customs District. 1011 Fuqiang Road, Shenzhen, 518045, China
| | - Shanyun Ma
- Research Institute of Photocatalysis, College of Biological Science and Engineering, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350108, China
| | - Kaiqiang Zhou
- Research Institute of Photocatalysis, College of Biological Science and Engineering, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350108, China
| | - Xuwei Wang
- Research Institute of Photocatalysis, College of Biological Science and Engineering, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350108, China
| | - Fen Yan
- Research Institute of Photocatalysis, College of Biological Science and Engineering, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350108, China
| | - Da Huang
- Research Institute of Photocatalysis, College of Biological Science and Engineering, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350108, China
| | - Jianhua Li
- Research Institute of Photocatalysis, College of Biological Science and Engineering, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350108, China
| | - Yuanzi Wu
- Research Institute of Photocatalysis, College of Biological Science and Engineering, Fuzhou University, 2 Xueyuan Road, Fuzhou, 350108, China.
| | - Jian'an He
- Central Laboratory of Health Quarantine, International Travel Health Care Center, Shenzhen Customs District. 1011 Fuqiang Road, Shenzhen, 518045, China.
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4
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Overexpression of miRNA-9 enhances galectin-3 levels in oral cavity cancers. Mol Biol Rep 2021; 48:3979-3989. [PMID: 34021445 DOI: 10.1007/s11033-021-06398-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/03/2021] [Indexed: 12/13/2022]
Abstract
Oral cavity cancer (OCC) is the predominant subtype of head and neck cancer (HNC) and has up to 50% mortality. Genome-wide microRNA (miR) sequencing data indicates overexpression of miR-9-5p in HNC tumours, however, the biological role of miR-9-5p in OCC is complex; it can either act as a tumour suppressor or an oncomir, regulating many target genes at the post-transcriptional level. We have investigated the overexpression of miR-9-5p in three OCC cell lines. We have evaluated its expression levels and Galectin-3 as potential biomarkers in saliva samples collected from controls and OCC patients. We found that over expression of miR-9-5p in OCC cell lines resulted in a significant reduction in cell proliferation and migration, and an increase in apoptosis, which was paralleled by an increase in Galectin-3 secretion and export of Galectin-3 protein. Our data are consistent with miR-9-5p being a modulator of Galectin-3 via the AKT/γ-catenin pathway. In addition, the positive correlation between the levels of miR-9-5p expression and secreted Galectin-3 in saliva reflects a similar relationship in vivo, and supports the utility of their integrative evaluation in OCC. Our findings indicate that both miR-9-5p and Galectin-3 are critical biomolecules in the progression of OCC.
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5
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Pegg CL, Phung TK, Caboche CH, Niamsuphap S, Bern M, Howell K, Schulz BL. Quantitative Data-Independent Acquisition Glycoproteomics of Sparkling Wine. Mol Cell Proteomics 2020; 20:100020. [PMID: 32938748 PMCID: PMC8724608 DOI: 10.1074/mcp.ra120.002181] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/26/2020] [Accepted: 09/16/2020] [Indexed: 11/16/2022] Open
Abstract
Sparkling wine is an alcoholic beverage enjoyed around the world. The sensory properties of sparkling wine depend on a complex interplay between the chemical and biochemical components in the final product. Glycoproteins have been linked to positive and negative qualities in sparkling wine, but the glycosylation profiles of sparkling wine have not been previously investigated in detail. We analyzed the glycoproteome of sparkling wines using protein- and glycopeptide-centric approaches. We developed an automated workflow that created ion libraries to analyze sequential window acquisition of all theoretical mass spectra data-independent acquisition mass spectrometry data based on glycopeptides identified by Byonic (Protein Metrics; version 2.13.17). We applied our workflow to three pairs of experimental sparkling wines to assess the effects of aging on lees and of different yeast strains used in the liqueur de tirage for secondary fermentation. We found that aging a cuvée on lees for 24 months compared with 8 months led to a dramatic decrease in overall protein abundance and an enrichment in large glycans at specific sites in some proteins. Secondary fermentation of a Riesling wine with Saccharomyces cerevisiae yeast strain Siha4 produced more yeast proteins and glycoproteins than with S. cerevisiae yeast strain DV10. The abundance and glycosylation profiles of grape glycoproteins were also different between grape varieties. To our knowledge, this work represents the first in-depth study into protein- and peptide-specific glycosylation in sparkling wines and describes a quantitative glycoproteomic sequential window acquisition of all theoretical mass spectra/data-independent acquisition workflow that is broadly applicable to other sample types. Development of an automated glycoproteomic sequential window acquisition of all theoretical mass spectra workflow. Application to three pairs of commercial-scale experimental sparkling wines. Decreased protein abundance in cuvée during the aging process. Different yeast strains produce varying levels of yeast proteins.
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Affiliation(s)
- Cassandra L Pegg
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Toan K Phung
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Christopher H Caboche
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Suchada Niamsuphap
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia; Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | | | - Kate Howell
- Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, VIC, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia; Centre for Biopharmaceutical Innovation, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia.
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6
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Rasheduzzaman M, Kulasinghe A, Dolcetti R, Kenny L, Johnson NW, Kolarich D, Punyadeera C. Protein glycosylation in head and neck cancers: From diagnosis to treatment. Biochim Biophys Acta Rev Cancer 2020; 1874:188422. [PMID: 32853734 DOI: 10.1016/j.bbcan.2020.188422] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2020] [Revised: 08/20/2020] [Accepted: 08/21/2020] [Indexed: 12/24/2022]
Abstract
Glycosylation is the most common post-translational modification (PTM) of proteins. Malignant tumour cells frequently undergo an alteration in surface protein glycosylation. This phenomenon is also common in cancers of the head and neck, most of which are squamous cell carcinomas (HNSCC). It affects cell functions, including proliferation, motility and invasiveness, thus increasing the propensity to metastasise. HNSCC represents the sixth most frequent malignancy worldwide. These neoplasms, which arise from the mucous membranes of the various anatomical subsites of the upper aero-digestive tract, are heterogeneous in terms of aetiology and clinico-pathologic features. With current treatments, only about 50% of HNSCC patients survive beyond 5-years. Therefore, there is the pressing need to dissect NHSCC heterogeneity to inform treatment choices. In particular, reliable biomarkers of predictive and prognostic value are eagerly needed. This review describes the current state of the art and bio-pathological meaning of glycosylation signatures associated with HNSCC and explores the possible role of tumour specific glycoproteins as potential biomarkers and attractive therapeutic targets. We have also compiled data relating to altered glycosylation and the nature of glycoproteins as tools for the identification of circulating tumour cells (CTCs) in the new era of liquid biopsy.
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Affiliation(s)
- Mohammad Rasheduzzaman
- Saliva and Liquid Biopsy Translational Laboratory, The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia; Translational Research Institute, Woolloongabba, QLD, Australia
| | - Arutha Kulasinghe
- Saliva and Liquid Biopsy Translational Laboratory, The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia; Translational Research Institute, Woolloongabba, QLD, Australia
| | - Riccardo Dolcetti
- Translational Research Institute, Woolloongabba, QLD, Australia.; The University of Queensland Diamantina Institute, 37 Kent Street Woolloongabba, QLD 4102, Australia
| | - Liz Kenny
- Department of Radiation Oncology, Cancer Care Services, Royal Brisbane and Women's Hospital, Joyce Tweddell Building, Herston, QLD, 4029, Australia
| | - Newell W Johnson
- Menzies Health Institute Queensland, Griffith University, Southport, Queensland, Australia; Faculty of Dentistry, Oral and Craniofacial Sciences, King's College, London, United Kingdom
| | - Daniel Kolarich
- Institute for Glycomics, Griffith University, Gold Coast, QLD, Australia; ARC Centre of Excellence for Nanoscale BioPhotonics, Griffith University, QLD, Australia.
| | - Chamindie Punyadeera
- Saliva and Liquid Biopsy Translational Laboratory, The School of Biomedical Sciences, Institute of Health and Biomedical Innovation, Queensland University of Technology, Kelvin Grove, QLD, Australia; Translational Research Institute, Woolloongabba, QLD, Australia..
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7
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Santorelli L, Capitoli G, Chinello C, Piga I, Clerici F, Denti V, Smith A, Grasso A, Raimondo F, Grasso M, Magni F. In-Depth Mapping of the Urinary N-Glycoproteome: Distinct Signatures of ccRCC-related Progression. Cancers (Basel) 2020; 12:E239. [PMID: 31963743 PMCID: PMC7016614 DOI: 10.3390/cancers12010239] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 01/12/2020] [Accepted: 01/14/2020] [Indexed: 12/15/2022] Open
Abstract
Protein N-glycosylation is one of the most important post-translational modifications and is involved in many biological processes, with aberrant changes in protein N-glycosylation patterns being closely associated with several diseases, including the progression and spreading of tumours. In light of this, identifying these aberrant protein glycoforms in tumours could be useful for understanding the molecular mechanism of this multifactorial disease, developing specific biomarkers and finding novel therapeutic targets. We investigated the urinary N-glycoproteome of clear cell renal cell carcinoma (ccRCC) patients at different stages (n = 15 at pT1 and n = 15 at pT3), and of non-ccRCC subjects (n = 15), using an N-glyco-FASP-based method. Using label-free nLC-ESI MS/MS, we identified and quantified several N-glycoproteins with altered expression and abnormal changes affecting the occupancy of the glycosylation site in the urine of RCC patients compared to control. In particular, nine of them had a specific trend that was directly related to the stage progression: CD97, COCH and P3IP1 were up-expressed whilst APOB, FINC, CERU, CFAH, HPT and PLTP were down-expressed in ccRCC patients. Overall, these results expand our knowledge related to the role of this post-translational modification in ccRCC and translation of this information into pre-clinical studies could have a significant impact on the discovery of novel biomarkers and therapeutic target in kidney cancer.
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Affiliation(s)
- Lucia Santorelli
- Clinical Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy; (C.C.); (I.P.); (F.C.); (V.D.); (A.S.); (F.R.); (F.M.)
| | - Giulia Capitoli
- Centre of Biostatistics for Clinical Epidemiology, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy;
| | - Clizia Chinello
- Clinical Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy; (C.C.); (I.P.); (F.C.); (V.D.); (A.S.); (F.R.); (F.M.)
| | - Isabella Piga
- Clinical Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy; (C.C.); (I.P.); (F.C.); (V.D.); (A.S.); (F.R.); (F.M.)
| | - Francesca Clerici
- Clinical Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy; (C.C.); (I.P.); (F.C.); (V.D.); (A.S.); (F.R.); (F.M.)
| | - Vanna Denti
- Clinical Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy; (C.C.); (I.P.); (F.C.); (V.D.); (A.S.); (F.R.); (F.M.)
| | - Andrew Smith
- Clinical Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy; (C.C.); (I.P.); (F.C.); (V.D.); (A.S.); (F.R.); (F.M.)
| | - Angelica Grasso
- Urology Service, Department of Surgery, EOC Beata Vergine Regional Hospital, 23, 6850 Mendrisio, Switzerland;
| | - Francesca Raimondo
- Clinical Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy; (C.C.); (I.P.); (F.C.); (V.D.); (A.S.); (F.R.); (F.M.)
| | - Marco Grasso
- Urology Unit, S. Gerardo Hospital, 20900 Monza, Italy;
| | - Fulvio Magni
- Clinical Proteomics and Metabolomics Unit, School of Medicine and Surgery, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy; (C.C.); (I.P.); (F.C.); (V.D.); (A.S.); (F.R.); (F.M.)
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8
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Evaluation of sample preparation methods for label-free quantitative profiling of salivary proteome. J Proteomics 2020; 210:103532. [DOI: 10.1016/j.jprot.2019.103532] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2019] [Revised: 09/07/2019] [Accepted: 09/19/2019] [Indexed: 01/17/2023]
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9
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Li L, Ren M, Xu Y, Jin C, Zhang W, Dong X. Enhanced glycosylation of an S-layer protein enables a psychrophilic methanogenic archaeon to adapt to elevated temperatures in abundant substrates. FEBS Lett 2019; 594:665-677. [PMID: 31665542 DOI: 10.1002/1873-3468.13650] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/09/2019] [Accepted: 10/10/2019] [Indexed: 12/15/2022]
Abstract
Adaptation to higher temperatures would increase the environmental competitiveness of psychrophiles, organisms that thrive in low-temperature environments. Methanolobus psychrophilus, a cold wetland methanogen, 'evolved' as a mesophile, growing optimally at 30 °C after subculturings, and cells grown with ample substrates exhibited higher integrity. Here, we investigated N-glycosylation of S-layer proteins, the major archaeal envelope component, with respect to mesophilic adaptation. Lectin affinity enriched a glycoprotein in cells grown at 30 °C under ample substrate availability, which was identified as the S-layer protein Mpsy_1486. Four N-glycosylation sites were identified on Mpsy_1486, which exhibited different glycosylation profiles, with N94 only found in cells cultured at 30 °C. An N-linked glycosylation inhibitor, tunicamycin, reduced glycosylation levels of Mpsy_1486 and growth at 30 °C, thus establishing a link between S-layer protein glycosylation and higher temperature adaptation of the psychrophilic archaeon M. psychrophilus.
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Affiliation(s)
- Lingyan Li
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Mifang Ren
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Yueqiang Xu
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Cheng Jin
- University of Chinese Academy of Sciences, Beijing, China.,State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,Guangxi Academy of Sciences, Nanning, China
| | - Wenhao Zhang
- MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University, Beijing, China
| | - Xiuzhu Dong
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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10
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Sun S, Hu Y, Ao M, Shah P, Chen J, Yang W, Jia X, Tian Y, Thomas S, Zhang H. N-GlycositeAtlas: a database resource for mass spectrometry-based human N-linked glycoprotein and glycosylation site mapping. Clin Proteomics 2019; 16:35. [PMID: 31516400 PMCID: PMC6731604 DOI: 10.1186/s12014-019-9254-0] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 08/14/2019] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND N-linked glycoprotein is a highly interesting class of proteins for clinical and biological research. The large-scale characterization of N-linked glycoproteins accomplished by mass spectrometry-based glycoproteomics has provided valuable insights into the interdependence of glycoprotein structure and protein function. However, these studies focused mainly on the analysis of specific sample type, and lack the integration of glycoproteomic data from different tissues, body fluids or cell types. METHODS In this study, we collected the human glycosite-containing peptides identified through their de-glycosylated forms by mass spectrometry from over 100 publications and unpublished datasets generated from our laboratory. A database resource termed N-GlycositeAtlas was created and further used for the distribution analyses of glycoproteins among different human cells, tissues and body fluids. Finally, a web interface of N-GlycositeAtlas was created to maximize the utility and value of the database. RESULTS The N-GlycositeAtlas database contains more than 30,000 glycosite-containing peptides (representing > 14,000 N-glycosylation sites) from more than 7200 N-glycoproteins from different biological sources including human-derived tissues, body fluids and cell lines from over 100 studies. CONCLUSIONS The entire human N-glycoproteome database as well as 22 sub-databases associated with individual tissues or body fluids can be downloaded from the N-GlycositeAtlas website at http://nglycositeatlas.biomarkercenter.org.
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Affiliation(s)
- Shisheng Sun
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
- College of Life Science, Northwest University, Xi’an, 710069 Shaanxi China
| | - Yingwei Hu
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Minghui Ao
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Punit Shah
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Jing Chen
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Weiming Yang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Xingwang Jia
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Yuan Tian
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Stefani Thomas
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21287 USA
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11
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Berg P, McConnell EW, Hicks LM, Popescu SC, Popescu GV. Evaluation of linear models and missing value imputation for the analysis of peptide-centric proteomics. BMC Bioinformatics 2019; 20:102. [PMID: 30871482 PMCID: PMC6419331 DOI: 10.1186/s12859-019-2619-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Several methods to handle data generated from bottom-up proteomics via liquid chromatography-mass spectrometry, particularly for peptide-centric quantification dealing with post-translational modification (PTM) analysis like reversible cysteine oxidation are evaluated. The paper proposes a pipeline based on the R programming language to analyze PTMs from peptide-centric label-free quantitative proteomics data. RESULTS Our methodology includes variance stabilization, normalization, and missing data imputation to account for the large dynamic range of PTM measurements. It also corrects biases from an enrichment protocol and reduces the random and systematic errors associated with label-free quantification. The performance of the methodology is tested by performing proteome-wide differential PTM quantitation using linear models analysis (limma). We objectively compare two imputation methods along with significance testing when using multiple-imputation for missing data. CONCLUSION Identifying PTMs in large-scale datasets is a problem with distinct characteristics that require new methods for handling missing data imputation and differential proteome analysis. Linear models in combination with multiple-imputation could significantly outperform a t-test-based decision method.
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Affiliation(s)
- Philip Berg
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA.,Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, USA
| | - Evan W McConnell
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Leslie M Hicks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Sorina C Popescu
- Department of Biochemistry, Molecular Biology, Entomology, and Plant Pathology, Mississippi State University, Mississippi State, MS, USA
| | - George V Popescu
- Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS, USA. .,The National Institute for Laser, Plasma & Radiation Physics, Bucharest, Romania.
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12
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Magnetite nanoparticles coated with mercaptosuccinic acid-modified mesoporous titania as a hydrophilic sorbent for glycopeptides and phosphopeptides prior to their quantitation by LC-MS/MS. Mikrochim Acta 2019; 186:159. [DOI: 10.1007/s00604-019-3274-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Accepted: 01/20/2019] [Indexed: 11/26/2022]
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13
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Gutiérrez A, Cerón JJ, Razzazi-Fazeli E, Schlosser S, Tecles F. Influence of different sample preparation strategies on the proteomic identification of stress biomarkers in porcine saliva. BMC Vet Res 2017; 13:375. [PMID: 29202764 PMCID: PMC5716369 DOI: 10.1186/s12917-017-1296-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Accepted: 11/22/2017] [Indexed: 02/06/2023] Open
Abstract
Background The influence of two different sample treatments comprising the enrichment of glycoproteins by boronic acid and dynamic range compression by hexapeptide libraries, on the detection of stress markers in saliva of pigs was evaluated in this study. For this purpose, saliva samples collected before and after the application of an acute stress model consisting of nasal restraining in pigs were processed without any treatment and with the two different treatments mentioned above. Protein separation by two-dimensional gel electrophoresis (2-DE) followed by identification of proteins using MALDI-TOF/TOF mass spectrometry (MS) was used as proteomic technique. Results The application of each of the two different sample treatment protocols allowed the identification of unique proteins that could be potential salivary acute stress markers in pigs: lipocalin 1, protein S100-A8 and immunoglobulin M by enrichment of glycoproteins; protein S100-A9, double headed protease inhibitor submandibular gland, and haemoglobin by dynamic range compression; and protein S100-A12 by both protocols. Salivary lipocalin, prolactin inducible protein, light chain of immunoglobulins, adenosine deaminase and carbonic anhydrase VI were identified as potential markers in untreated saliva as well as one of the other treatments. Conclusion The use of different procedures allowed the detection of different potential stress markers. Although from a practical point of view, the use of saliva without further treatment as well as the enrichment of glycoproteins are less expensive and easy to do procedures.
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Affiliation(s)
- Ana Gutiérrez
- Department of Animal Medicine and Surgery, Regional Campus of International Excellence "Campus Mare Nostrum", Hospital Veterinario 4 planta, University of Murcia, 30100, Espinardo, Murcia, Spain
| | - José Joaquín Cerón
- Department of Animal Medicine and Surgery, Regional Campus of International Excellence "Campus Mare Nostrum", Hospital Veterinario 4 planta, University of Murcia, 30100, Espinardo, Murcia, Spain
| | - Ebrahim Razzazi-Fazeli
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Veterinaerplatz 1, A-1210, Vienna, Austria
| | - Sarah Schlosser
- VetCore Facility for Research, University of Veterinary Medicine Vienna, Veterinaerplatz 1, A-1210, Vienna, Austria
| | - Fernando Tecles
- Department of Animal Medicine and Surgery, Regional Campus of International Excellence "Campus Mare Nostrum", Hospital Veterinario 4 planta, University of Murcia, 30100, Espinardo, Murcia, Spain.
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14
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Du X, He Q, Zhang L, Liu C, Zhu J, Kuang B, Zeng S, Chen B, Yin D, Zeng Y. Selective and Cleavable Extraction of Sialo-glycoproteins by Disulfide-Linked Amino-oxy-Functionalized Fe 3O 4 Magnetic Nanoparticles. Bioconjug Chem 2017; 28:2514-2517. [PMID: 28876900 DOI: 10.1021/acs.bioconjchem.7b00339] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The low abundance of sialo-glycoprotein hampered the separation, enrichment, and analysis of sialo-glycoproteins, which are critical for studying their functions. Here, we designed cleavable amino-oxy functionalized magnetic materials and employed to fast and selective isolate sialo-glycoproteins. This includes the ligation of disulfide-linked amino-oxy-functionalized magnetic nanoparticles with periodate-treated glycoproteins or cells, followed by magnetic separation. A reductive reagent could release the sialo-glycoproteins with small molecular fragments on the terminal of glycan chains, and the sialo-glycoproteins were analyzed by sodium dodecyl sulfate polyacrylamide gel electrophoresis. On-bead digestion of the peptides were analyzed by tandem mass spectrometry. The results indicated that this method could selectively separate the majority of cell-surface sialo-glycoproteins.
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Affiliation(s)
- Xiufang Du
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education of China, College of Chemistry and Chemical Engineering, Hunan Normal University , No. 36, Lushan Road, Changsha, China 410081
| | - Qingke He
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education of China, College of Chemistry and Chemical Engineering, Hunan Normal University , No. 36, Lushan Road, Changsha, China 410081
| | - Lixia Zhang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education of China, College of Chemistry and Chemical Engineering, Hunan Normal University , No. 36, Lushan Road, Changsha, China 410081
| | - Changgeng Liu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education of China, College of Chemistry and Chemical Engineering, Hunan Normal University , No. 36, Lushan Road, Changsha, China 410081
| | - Junling Zhu
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education of China, College of Chemistry and Chemical Engineering, Hunan Normal University , No. 36, Lushan Road, Changsha, China 410081
| | - Bin Kuang
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education of China, College of Chemistry and Chemical Engineering, Hunan Normal University , No. 36, Lushan Road, Changsha, China 410081
| | - Sheng Zeng
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education of China, College of Chemistry and Chemical Engineering, Hunan Normal University , No. 36, Lushan Road, Changsha, China 410081
| | - Bo Chen
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education of China, College of Chemistry and Chemical Engineering, Hunan Normal University , No. 36, Lushan Road, Changsha, China 410081
| | - Dulin Yin
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education of China, College of Chemistry and Chemical Engineering, Hunan Normal University , No. 36, Lushan Road, Changsha, China 410081
| | - Ying Zeng
- Key Laboratory of Chemical Biology and Traditional Chinese Medicine Research, Ministry of Education of China, College of Chemistry and Chemical Engineering, Hunan Normal University , No. 36, Lushan Road, Changsha, China 410081
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15
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Poljak K, Selevsek N, Ngwa E, Grossmann J, Losfeld ME, Aebi M. Quantitative Profiling of N-linked Glycosylation Machinery in Yeast Saccharomyces cerevisiae. Mol Cell Proteomics 2017; 17:18-30. [PMID: 28993419 DOI: 10.1074/mcp.ra117.000096] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2017] [Indexed: 11/06/2022] Open
Abstract
Asparagine-linked glycosylation is a common posttranslational protein modification regulating the structure, stability and function of many proteins. The N-linked glycosylation machinery involves enzymes responsible for the assembly of the lipid-linked oligosaccharide (LLO), which is then transferred to the asparagine residues on the polypeptides by the enzyme oligosaccharyltransferase (OST). A major goal in the study of protein glycosylation is to establish quantitative methods for the analysis of site-specific extent of glycosylation. We developed a sensitive approach to examine glycosylation site occupancy in Saccharomyces cerevisiae by coupling stable isotope labeling (SILAC) approach to parallel reaction monitoring (PRM) mass spectrometry (MS). We combined the method with genetic tools and validated the approach with the identification of novel glycosylation sites dependent on the Ost3p and Ost6p regulatory subunits of OST. Based on the observations that alternations in LLO substrate structure and OST subunits activity differentially alter the systemic output of OST, we conclude that sequon recognition is a direct property of the catalytic subunit Stt3p, auxiliary subunits such as Ost3p and Ost6p extend the OST substrate range by modulating interfering pathways such as protein folding. In addition, our proteomics approach revealed a novel regulatory network that connects isoprenoid lipid biosynthesis and LLO substrate assembly.
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Affiliation(s)
- Kristina Poljak
- From the ‡Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Nathalie Selevsek
- §Functional Genomics Center Zurich, UZH/ETH Zurich, CH-8057 Zurich, Switzerland
| | - Elsy Ngwa
- From the ‡Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Jonas Grossmann
- §Functional Genomics Center Zurich, UZH/ETH Zurich, CH-8057 Zurich, Switzerland
| | - Marie Estelle Losfeld
- From the ‡Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland
| | - Markus Aebi
- From the ‡Institute of Microbiology, ETH Zurich, Vladimir-Prelog-Weg 4, CH-8093 Zurich, Switzerland;
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Zhang X, Walsh T, Atherton JJ, Kostner K, Schulz B, Punyadeera C. Identification and Validation of a Salivary Protein Panel to Detect Heart Failure Early. Am J Cancer Res 2017; 7:4350-4358. [PMID: 29158831 PMCID: PMC5695135 DOI: 10.7150/thno.21727] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 08/24/2017] [Indexed: 01/10/2023] Open
Abstract
BACKGROUND Over 26 million people suffer from heart failure (HF) globally. Current diagnosis of HF relies on clinical evaluation, blood assays and imaging techniques. Our aim is to develop a diagnostic assay to detect HF in at risk individuals within the community using human saliva as a medium, potentially leading to a simple, safe early warning system. METHODS Saliva samples were collected from healthy controls (n=36) and HF patients (n=75). Salivary proteome profiles were analysed by Sequential Window Acquisition of All Theoretical fragment ion spectra - Mass Spectrometry (SWATH-MS). A total of 738 proteins were quantified and 177 proteins demonstrated significant differences between HF patients and healthy controls. Candidate biomarkers were chosen based on their abundance and difference between the two cohorts. A multi-protein panel was developed using logistic regression analysis. The diagnostic performance of the multi-protein panel was assessed using receiver operative characteristic curves. The candidate proteins were further confirmed, using western blot analysis, and validated technically, using an independent biological cohort. RESULTS A group of six proteins were chosen in the discovery phase as potential candidates based on their differences in the abundance between the two cohorts. During the validation phase, two of the proteins were not detected with western blotting and as such were removed. The final panel consists of four proteins with sensitivity of 83.3%, specificity of 62.5% with an area under ROC curve of 0.78 in discriminating healthy controls from NYHA class I/II HF patients, and was validated in a second independent cohort study. CONCLUSION Analysis of salivary proteome using SWATH-MS revealed novel HF-specific protein candidates yielding high diagnostic performance. A multi-centre longitudinal clinical trial will be the next step before clinical implementation of this panel.
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17
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A New Clade of Insect-Specific Flaviviruses from Australian Anopheles Mosquitoes Displays Species-Specific Host Restriction. mSphere 2017; 2:mSphere00262-17. [PMID: 28713857 PMCID: PMC5506557 DOI: 10.1128/msphere.00262-17] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Accepted: 06/13/2017] [Indexed: 12/03/2022] Open
Abstract
Flaviviruses like dengue, Zika, or West Nile virus infect millions of people each year and are transmitted to humans via infected-mosquito bites. A subset of flaviviruses can only replicate in the mosquito host, and recent studies have shown that some can interfere with pathogenic flaviviruses in mosquitoes and limit the replication and transmission of the latter. The insect-specific flaviviruses (ISFs) reported here form a new Anopheles mosquito-associated clade separate from the Aedes- and Culex-associated ISF clades. The identification of distinct clades for each mosquito genus provides new insights into the evolution and ecology of flaviviruses. One of these viruses was shown to replicate in the midgut of the mosquito host and exhibit the most specialized host restriction reported to date for ISFs. Understanding this unprecedented host restriction in ISFs could help identify the mechanisms involved in the evolution of flaviviruses and their emergence as mosquito-borne pathogens. Flaviviruses are arthropod-borne viruses found worldwide and are responsible for significant human and veterinary diseases, including dengue, Zika, and West Nile fever. Some flaviviruses are insect specific and replicate only in mosquitoes. We report a genetically divergent group of insect-specific flaviviruses from Anopheles mosquitoes that do not replicate in arthropod cell lines or heterologous Anopheles species, exhibiting unprecedented specialization for their host species. Determination of the complete sequences of the RNA genomes of three of these viruses, Karumba virus (KRBV), Haslams Creek virus, and Mac Peak virus (McPV), that are found in high prevalence in some Anopheles mosquito populations and detection of virus-specific proteins, replicative double-stranded RNA, and small interfering RNA responses in the host mosquito species provided strong evidence of a functional replicating virus in the mosquito midgut. Analysis of nucleotide composition in the KRBV and McPV sequences also revealed a pattern consistent with the virus evolving to replicate only in insects. These findings represent a significant advance in our knowledge of mosquito-borne flavivirus ecology, host restriction, and evolution. IMPORTANCE Flaviviruses like dengue, Zika, or West Nile virus infect millions of people each year and are transmitted to humans via infected-mosquito bites. A subset of flaviviruses can only replicate in the mosquito host, and recent studies have shown that some can interfere with pathogenic flaviviruses in mosquitoes and limit the replication and transmission of the latter. The insect-specific flaviviruses (ISFs) reported here form a new Anopheles mosquito-associated clade separate from the Aedes- and Culex-associated ISF clades. The identification of distinct clades for each mosquito genus provides new insights into the evolution and ecology of flaviviruses. One of these viruses was shown to replicate in the midgut of the mosquito host and exhibit the most specialized host restriction reported to date for ISFs. Understanding this unprecedented host restriction in ISFs could help identify the mechanisms involved in the evolution of flaviviruses and their emergence as mosquito-borne pathogens.
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18
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Quantification of N-glycosylation site occupancy status based on labeling/label-free strategies with LC-MS/MS. Talanta 2017; 170:509-513. [PMID: 28501204 DOI: 10.1016/j.talanta.2017.04.053] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2017] [Revised: 04/18/2017] [Accepted: 04/21/2017] [Indexed: 12/30/2022]
Abstract
Protein N-glycosylation plays important roles in physiological and pathological processes. Characterizing the site-specific N-glycosylation including N-glycan macroheterogeneity (glycosylation site occupancy) and microheterogeneity (site-specific glycan structure) is important for understanding of glycoprotein biosynthesis and function. N-Glycan macroheterogeneity is a physiological property of glycoprotein and the technical obstacles have restricted research into the regulation and functions of this heterogeneity. Quantification of N-glycosylation site occupancy would uncover the critical role of macroheterogeneity in a variety of biological properties. Liquid chromatography (LC)- mass spectrometry (MS)-based quantification is emerging as a powerful tool for glycosylation characterization. This review summarizes the labeling and label-free quantitative MS approaches for quantifying N-glycosylation site occupancy, including its quantification for target glycoproteins in recent years.
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19
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Detection and first characterization of an uncommon haptoglobin in porcine saliva of pigs with rectal prolapse by using boronic acid sample enrichment. Animal 2017; 11:845-853. [DOI: 10.1017/s1751731116002159] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
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20
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Abstract
Chemical tools have accelerated progress in glycoscience, reducing experimental barriers to studying protein glycosylation, the most widespread and complex form of posttranslational modification. For example, chemical glycoproteomics technologies have enabled the identification of specific glycosylation sites and glycan structures that modulate protein function in a number of biological processes. This field is now entering a stage of logarithmic growth, during which chemical innovations combined with mass spectrometry advances could make it possible to fully characterize the human glycoproteome. In this review, we describe the important role that chemical glycoproteomics methods are playing in such efforts. We summarize developments in four key areas: enrichment of glycoproteins and glycopeptides from complex mixtures, emphasizing methods that exploit unique chemical properties of glycans or introduce unnatural functional groups through metabolic labeling and chemoenzymatic tagging; identification of sites of protein glycosylation; targeted glycoproteomics; and functional glycoproteomics, with a focus on probing interactions between glycoproteins and glycan-binding proteins. Our goal with this survey is to provide a foundation on which continued technological advancements can be made to promote further explorations of protein glycosylation.
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Affiliation(s)
- Krishnan K. Palaniappan
- Verily Life Sciences, 269 East Grand Ave., South San Francisco, California 94080, United States
| | - Carolyn R. Bertozzi
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
- Howard Hughes Medical Institute, Stanford University, Stanford, California 94305, United States
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21
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Yeo KB, Chrysanthopoulos PK, Nouwens AS, Marcellin E, Schulz BL. High-performance targeted mass spectrometry with precision data-independent acquisition reveals site-specific glycosylation macroheterogeneity. Anal Biochem 2016; 510:106-113. [DOI: 10.1016/j.ab.2016.06.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 06/06/2016] [Accepted: 06/07/2016] [Indexed: 12/13/2022]
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22
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Kerr ED, Schulz BL. Vegemite Beer: yeast extract spreads as nutrient supplements to promote fermentation. PeerJ 2016; 4:e2271. [PMID: 27602264 PMCID: PMC4991886 DOI: 10.7717/peerj.2271] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 06/29/2016] [Indexed: 01/01/2023] Open
Abstract
Vegemite is an iconic Australian food spread made from spent brewers' yeast extract, which has been reported to be used as an ingredient in illegal home brewing. In this study, we tested the utility of Vegemite and the similar spread Marmite in promoting fermentation. We could not culture microorganisms from either Vegemite or Marmite, consistent with these food-grade spreads being essentially sterile. To test if the addition of Vegemite or Marmite could assist in fermentation when additional viable yeast was also present, solutions containing glucose and a range of concentrations of either Vegemite or Marmite were inoculated with brewers' yeast. No fermentation occurred in any condition without addition of extra brewer's yeast. Fermentation did not occur when yeast was inoculated into solutions containing only glucose, but progressed efficiently with when Vegemite or Marmite was also added. Gas Chromatography confirmed that ethanol was present at ∼3% v/v post-fermentation in all samples which contained glucose, Vegemite or Marmite, and brewers' yeast. Trace amounts of methanol were also detected. Mass spectrometry proteomics identified abundant intracellular yeast proteins and barley proteins in Vegemite and Marmite, and abundant secreted yeast proteins from actively growing yeast in those samples to which extra brewers' yeast had been added. We estimate that the real-world cost of home brewed "Vegemite Beer" would be very low. Our results show that Vegemite or other yeast extract spreads could provide cheap and readily available sources of nutrient supplementation to increase the efficiency of fermentation in home brewing or other settings.
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Affiliation(s)
- Edward D Kerr
- School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane , Queensland , Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland , Brisbane , Queensland , Australia
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Thaysen-Andersen M, Packer NH, Schulz BL. Maturing Glycoproteomics Technologies Provide Unique Structural Insights into the N-glycoproteome and Its Regulation in Health and Disease. Mol Cell Proteomics 2016; 15:1773-90. [PMID: 26929216 PMCID: PMC5083109 DOI: 10.1074/mcp.o115.057638] [Citation(s) in RCA: 137] [Impact Index Per Article: 17.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/09/2016] [Indexed: 12/21/2022] Open
Abstract
The glycoproteome remains severely understudied because of significant analytical challenges associated with glycoproteomics, the system-wide analysis of intact glycopeptides. This review introduces important structural aspects of protein N-glycosylation and summarizes the latest technological developments and applications in LC-MS/MS-based qualitative and quantitative N-glycoproteomics. These maturing technologies provide unique structural insights into the N-glycoproteome and its synthesis and regulation by complementing existing methods in glycoscience. Modern glycoproteomics is now sufficiently mature to initiate efforts to capture the molecular complexity displayed by the N-glycoproteome, opening exciting opportunities to increase our understanding of the functional roles of protein N-glycosylation in human health and disease.
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Affiliation(s)
- Morten Thaysen-Andersen
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia;
| | - Nicolle H Packer
- From the ‡Department of Chemistry and Biomolecular Sciences, Macquarie University, Sydney, NSW, Australia
| | - Benjamin L Schulz
- §School of Chemistry & Molecular Biosciences, St Lucia, The University of Queensland, Brisbane, QLD, Australia
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Caragata M, Shah AK, Schulz BL, Hill MM, Punyadeera C. Enrichment and identification of glycoproteins in human saliva using lectin magnetic bead arrays. Anal Biochem 2015; 497:76-82. [PMID: 26743719 DOI: 10.1016/j.ab.2015.11.024] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/23/2015] [Accepted: 11/24/2015] [Indexed: 01/21/2023]
Abstract
Aberrant glycosylation of proteins is a hallmark of tumorigenesis and could provide diagnostic value in cancer detection. Human saliva is an ideal source of glycoproteins due to the relatively high proportion of glycosylated proteins in the salivary proteome. Moreover, saliva collection is noninvasive and technically straightforward, and the sample collection and storage is relatively easy. Although differential glycosylation of proteins can be indicative of disease states, identification of differential glycosylation from clinical samples is not trivial. To facilitate salivary glycoprotein biomarker discovery, we optimized a method for differential glycoprotein enrichment from human saliva based on lectin magnetic bead arrays (saLeMBA). Selected lectins from distinct reactivity groups were used in the saLeMBA platform to enrich salivary glycoproteins from healthy volunteer saliva. The technical reproducibility of saLeMBA was analyzed with liquid chromatography-tandem mass spectrometry (LC-MS/MS) to identify the glycosylated proteins enriched by each lectin. Our saLeMBA platform enabled robust glycoprotein enrichment in a glycoprotein- and lectin-specific manner consistent with known protein-specific glycan profiles. We demonstrated that saLeMBA is a reliable method to enrich and detect glycoproteins present in human saliva.
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Affiliation(s)
- Michael Caragata
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, 4102, Australia
| | - Alok K Shah
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, 4102, Australia
| | - Benjamin L Schulz
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Queensland, 4072, Australia
| | - Michelle M Hill
- The University of Queensland Diamantina Institute, The University of Queensland, Translational Research Institute, Woolloongabba, Queensland, 4102, Australia.
| | - Chamindie Punyadeera
- School of Biomedical Sciences, Institute of Biomedical Innovations, Queensland University of Technology, Kelvin Grove, and Translational Research Institute, Woolloongabba, Queensland, 4102, Australia.
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25
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Albertolle ME, Hassis ME, Ng CJ, Cuison S, Williams K, Prakobphol A, Dykstra AB, Hall SC, Niles RK, Ewa Witkowska H, Fisher SJ. Mass spectrometry-based analyses showing the effects of secretor and blood group status on salivary N-glycosylation. Clin Proteomics 2015; 12:29. [PMID: 26719750 PMCID: PMC4696288 DOI: 10.1186/s12014-015-9100-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 11/25/2015] [Indexed: 12/15/2022] Open
Abstract
Background The carbohydrate portions of salivary glycoproteins play important roles, including mediating bacterial and leukocyte adhesion. Salivary glycosylation is complex. Many of its glycoproteins present ABO and Lewis blood group determinants. An individual’s genetic complement and secretor status govern the expression of blood group antigens. We queried the extent to which salivary glycosylation varies
according to blood group and secretor status. First, we screened submandibular/sublingual and parotid salivas collected as ductal secretions for reactivity with a panel of 16 lectins. We selected three lectins that reacted with the largest number of glycoproteins and one that recognized uncommon lactosamine-containing structures. Ductal salivas representing a secretor with complex blood group expression and a nonsecretor with a simple pattern were separated by SDS-PAGE. Gel slices were trypsin digested and the glycopeptides were individually separated on each of the four lectins. The bound fractions were de-N-glycosylated. LC–MS/MS identified the original glycosylation sites, the peptide sequences, and the parent proteins. Results The results revealed novel salivary N-glycosites and glycoproteins not previously reported. As compared to the secretor, nonsecretor saliva had higher levels of N-glycosylation albeit with simpler structures. Conclusions Together, the results suggested a molecular basis for inter-individual variations in salivary protein glycosylation with functional implications for oral health. Electronic supplementary material The online version of this article (doi:10.1186/s12014-015-9100-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew E Albertolle
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143 USA.,Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143 USA
| | - Maria E Hassis
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143 USA.,Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143 USA
| | - Connie Jen Ng
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143 USA.,Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143 USA
| | - Severino Cuison
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143 USA.,Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143 USA
| | - Katherine Williams
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143 USA.,Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143 USA
| | - Akraporn Prakobphol
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143 USA.,Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143 USA
| | - Andrew B Dykstra
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143 USA.,Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143 USA
| | - Steven C Hall
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143 USA.,Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143 USA
| | - Richard K Niles
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143 USA.,Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143 USA
| | - H Ewa Witkowska
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143 USA.,Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143 USA
| | - Susan J Fisher
- Department of Obstetrics, Gynecology, and Reproductive Sciences, University of California San Francisco, San Francisco, CA 94143 USA.,Sandler-Moore Mass Spectrometry Core Facility, University of California San Francisco, San Francisco, CA 94143 USA
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Zacchi LF, Schulz BL. N-glycoprotein macroheterogeneity: biological implications and proteomic characterization. Glycoconj J 2015; 33:359-76. [DOI: 10.1007/s10719-015-9641-3] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2015] [Revised: 11/04/2015] [Accepted: 11/20/2015] [Indexed: 10/22/2022]
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Li D, Chen Y, Liu Z. Boronate affinity materials for separation and molecular recognition: structure, properties and applications. Chem Soc Rev 2015; 44:8097-123. [PMID: 26377373 DOI: 10.1039/c5cs00013k] [Citation(s) in RCA: 373] [Impact Index Per Article: 41.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Boronate affinity materials, as unique sorbents, have emerged as important media for the selective separation and molecular recognition of cis-diol-containing compounds. With the introduction of boronic acid functionality, boronate affinity materials exhibit several significant advantages, including broad-spectrum selectivity, reversible covalent binding, pH-controlled capture/release, fast association/desorption kinetics, and good compatibility with mass spectrometry. Because cis-diol-containing biomolecules, including nucleosides, saccharides, glycans, glycoproteins and so on, are the important targets in current research frontiers such as metabolomics, glycomics and proteomics, boronate affinity materials have gained rapid development and found increasing applications in the last decade. In this review, we critically survey recent advances in boronate affinity materials. We focus on fundamental considerations as well as important progress and new boronate affinity materials reported in the last decade. We particularly discuss on the effects of the structure of boronate ligands and supporting materials on the properties of boronate affinity materials, such as binding pH, affinity, selectivity, binding capacity, tolerance for interference and so on. A variety of promising applications, including affinity separation, proteomics, metabolomics, disease diagnostics and aptamer selection, are introduced with main emphasis on how boronate affinity materials can solve the issues in the applications and what merits boronate affinity materials can provide.
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Affiliation(s)
- Daojin Li
- State Key Laboratory of Analytical Chemistry for Life Science and Collaborative Innovation Center of Chemistry for Life Sciences, School of Chemistry and Chemical Engineering, Nanjing University, 22 Hankou Road, Nanjing 210093, China.
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Abstract
Protein glycosylation is one of the most important protein modifications. Glycosylation site occupancy alteration has been implicated in human diseases and cancers. However, current glycoproteomic methods focus on the identification and quantification of glycosylated peptides and glycosylation sites but not glycosylation occupancy or glycoform stoichiometry. Here we describe a method for large-scale determination of the absolute glycosylation stoichiometry using three independent relative ratios. Using this method, we determined 117 absolute N-glycosylation occupancies in OVCAR-3 cells. Finally, we investigated the possible functions and the determinants for partial glycosylation.
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Affiliation(s)
- Shisheng Sun
- Department of Pathology, Johns Hopkins University, 400 North Broadway, Smith Building, Room 4011, Baltimore, Maryland 21287, United States
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, 400 North Broadway, Smith Building, Room 4011, Baltimore, Maryland 21287, United States
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Xu Y, Bailey UM, Schulz BL. Automated measurement of site-specific N
-glycosylation occupancy with SWATH-MS. Proteomics 2015; 15:2177-86. [DOI: 10.1002/pmic.201400465] [Citation(s) in RCA: 73] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 01/08/2015] [Accepted: 02/27/2015] [Indexed: 12/21/2022]
Affiliation(s)
- Ying Xu
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
| | - Ulla-Maja Bailey
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
| | - Benjamin L. Schulz
- School of Chemistry and Molecular Biosciences; The University of Queensland; Brisbane Queensland Australia
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Goyallon A, Cholet S, Chapelle M, Junot C, Fenaille F. Evaluation of a combined glycomics and glycoproteomics approach for studying the major glycoproteins present in biofluids: Application to cerebrospinal fluid. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:461-473. [PMID: 26160412 DOI: 10.1002/rcm.7125] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 12/08/2014] [Accepted: 12/14/2014] [Indexed: 06/04/2023]
Abstract
RATIONALE Glycosylation is one of the most complex types of post-translational modifications of proteins. The alteration of glycans bound to proteins from cerebrospinal fluid (CSF) in relation to disorders of the central nervous system is a highly relevant subject, but only few studies have focused on the glycosylation of CSF proteins. METHODS Reproducible profiles of CSF N-glycans were first obtained by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry after permethylation. Tryptic glycopeptides from CSF proteins were also enriched by hydrophilic interaction, and the resulting extracts divided into two equal aliquots. A first aliquot was enzymatically deglycosylated and analyzed by nano-liquid chromatography/tandem mass spectrometry while the second one, containing intact enriched glycopeptides, was directly analyzed. Site-specific data were obtained by combining the data from these three experiments. RESULTS We describe the development of a versatile approach for obtaining site-specific information on the N-glycosylation of CSF glycoproteins. Under these conditions, 124 N-glycopeptides representing 55 N-glycosites from 36 glycoproteins were tentatively identified. Special emphasis was placed on the analysis of glycoproteins/glycopeptides bearing 'brain-type' N-glycans, representing potential biologically relevant structures in the field of neurodegenerative disorders. Using our workflow, only a few proteins were shown to carry such particular glycan motifs. CONCLUSIONS We developed an approach combining N-glycomics and N-glycoproteomics and underline its usefulness to study the site-specific glycosylation of major human CSF proteins. The final rather long-term objective is to combine these data with those from other omics approaches to delve deeper into the understanding of particular neurological disorders.
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Affiliation(s)
- Arnaud Goyallon
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
| | - Sophie Cholet
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
| | | | - Christophe Junot
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
| | - François Fenaille
- CEA, iBiTec-S, Service de Pharmacologie et d'Immunoanalyse, 91191, Gif-sur-Yvette, France
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Kumar A, Baycin-Hizal D, Shiloach J, Bowen MA, Betenbaugh MJ. Coupling enrichment methods with proteomics for understanding and treating disease. Proteomics Clin Appl 2015; 9:33-47. [PMID: 25523641 DOI: 10.1002/prca.201400097] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2014] [Revised: 11/12/2014] [Accepted: 12/15/2014] [Indexed: 12/17/2022]
Abstract
Owing to recent advances in proteomics analytical methods and bioinformatics capabilities there is a growing trend toward using these capabilities for the development of drugs to treat human disease, including target and drug evaluation, understanding mechanisms of drug action, and biomarker discovery. Currently, the genetic sequences of many major organisms are available, which have helped greatly in characterizing proteomes in model animal systems and humans. Through proteomics, global profiles of different disease states can be characterized (e.g. changes in types and relative levels as well as changes in PTMs such as glycosylation or phosphorylation). Although intracellular proteomics can provide a broad overview of physiology of cells and tissues, it has been difficult to quantify the low abundance proteins which can be important for understanding the diseased states and treatment progression. For this reason, there is increasing interest in coupling comparative proteomics methods with subcellular fractionation and enrichment techniques for membranes, nucleus, phosphoproteome, glycoproteome as well as low abundance serum proteins. In this review, we will provide examples of where the utilization of different proteomics-coupled enrichment techniques has aided target and biomarker discovery, understanding the drug targeting mechanism, and mAb discovery. Taken together, these improvements will help to provide a better understanding of the pathophysiology of various diseases including cancer, autoimmunity, inflammation, cardiovascular disease, and neurological conditions, and in the design and development of better medicines for treating these afflictions.
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Affiliation(s)
- Amit Kumar
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA; Antibody Discovery and Protein Engineering, MedImmune LLC, One MedImmune Way, Gaithersburg, MD, USA; Biotechnology Core Laboratory, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD, USA
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Randall SM, Koryakina I, Williams GJ, Muddiman DC. Evaluating nonpolar surface area and liquid chromatography/mass spectrometry response: an application for site occupancy measurements for enzyme intermediates in polyketide biosynthesis. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2014; 28:2511-2522. [PMID: 25366398 PMCID: PMC4230892 DOI: 10.1002/rcm.7051] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/07/2014] [Revised: 08/22/2014] [Accepted: 09/09/2014] [Indexed: 05/31/2023]
Abstract
RATIONALE Site occupancy measurements using liquid chromatography/mass spectrometry (LC/MS) are reported throughout the literature. However, site occupancy quantification suffers from ionization bias between modified and unmodified peptides containing the active site. In this study, we explore the MS signal as a function of nonpolar surface area (NPSA) in order to better understand this bias in electrospray response. The correlation between hydrophobicity and LC/MS response was evaluated and applied to study enzyme intermediates in polyketide synthases. METHODS Site occupancy methods were developed to study acyltransferase activity. To further evaluate these methods, several standard peptides containing one cysteine residue were modified with alkylation reagents of increasing hydrophobicity to study the MS signal as a function of NPSA. RESULTS A consistent trend in MS response was observed which is dependent on the NPSA of the analyte. An optimal NPSA zone was observed for the peptides studied. CONCLUSIONS Nonpolar surface area can be used as metric to determine relative LC/MS response for peptides and evaluate site occupancy measurements.
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Affiliation(s)
- Shan M. Randall
- W.M. Keck Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Irina Koryakina
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - Gavin J. Williams
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
| | - David C. Muddiman
- W.M. Keck Fourier Transform Mass Spectrometry Laboratory, Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
- Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, USA
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