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Aberrant Sialylation in Cancer: Therapeutic Opportunities. Cancers (Basel) 2022; 14:cancers14174248. [PMID: 36077781 PMCID: PMC9454432 DOI: 10.3390/cancers14174248] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 08/15/2022] [Accepted: 08/23/2022] [Indexed: 11/16/2022] Open
Abstract
The surface of every eukaryotic cell is coated in a thick layer of glycans that acts as a key interface with the extracellular environment. Cancer cells have a different ‘glycan coat’ to healthy cells and aberrant glycosylation is a universal feature of cancer cells linked to all of the cancer hallmarks. This means glycans hold huge potential for the development of new diagnostic and therapeutic strategies. One key change in tumour glycosylation is increased sialylation, both on N-glycans and O-glycans, which leads to a dense forest of sialylated structures covering the cell surface. This hypersialylation has far-reaching consequences for cancer cells, and sialylated glycans are fundamental in tumour growth, metastasis, immune evasion and drug resistance. The development of strategies to inhibit aberrant sialylation in cancer represents an important opportunity to develop new therapeutics. Here, I summarise recent advances to target aberrant sialylation in cancer, including the development of sialyltransferase inhibitors and strategies to inhibit Siglecs and Selectins, and discuss opportunities for the future.
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2
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Domingues LN, Bendele KG, Halos L, Moreno Y, Epe C, Figueiredo M, Liebstein M, Guerrero FD. Identification of anti-horn fly vaccine antigen candidates using a reverse vaccinology approach. Parasit Vectors 2021; 14:442. [PMID: 34479607 PMCID: PMC8414034 DOI: 10.1186/s13071-021-04938-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 08/09/2021] [Indexed: 01/01/2023] Open
Abstract
Background The horn fly, Haematobia irritans irritans, causes significant production losses to the cattle industry. Horn fly control relies on insecticides; however, alternative control methods such as vaccines are needed due to the fly's capacity to quickly develop resistance to insecticides, and the pressure for eco-friendly options. Methods We used a reverse vaccinology approach comprising three vaccine prediction and 11 annotation tools to evaluate and rank 79,542 translated open reading frames (ORFs) from the horn fly's transcriptome, and selected 10 transcript ORFs as vaccine candidates for expression in Pichia pastoris. The expression of the 10 selected transcripts and the proteins that they encoded were investigated in adult flies by reverse transcription polymerase chain reaction (RT-PCR) and mass spectrometry, respectively. Then, we evaluated the immunogenicity of a vaccine candidate in an immunization trial and the antigen’s effects on horn fly mortality and fecundity in an in vitro feeding assay. Results Six of the ten vaccine candidate antigens were successfully expressed in P. pastoris. RT-PCR confirmed the expression of all six ORFs in adult fly RNA. One of the vaccine candidate antigens, BI-HS009, was expressed in sufficient quantity for immunogenicity and efficacy trials. The IgG titers of animals vaccinated with BI-HS009 plus adjuvant were significantly higher than those of animals vaccinated with buffer plus adjuvant only from days 42 to 112, with a peak on day 56. Progeny of horn flies feeding upon blood from animals vaccinated with BI-HS009 plus adjuvant collected on day 56 had 63% lower pupariation rate and 57% lower adult emergence than the control group (ANOVA: F(1, 6) = 8.221, P = 0.028 and F(1, 6) = 8.299, P = 0.028, respectively). Conclusions The reverse vaccinology approach streamlined the discovery process by prioritizing possible vaccine antigen candidates. Through a thoughtful process of selection and in vivo and in vitro evaluations, we were able to identify a promising antigen for an anti-horn fly vaccine. Graphical abstract ![]()
Supplementary Information The online version contains supplementary material available at 10.1186/s13071-021-04938-5.
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Affiliation(s)
- Luísa N Domingues
- USDA-ARS Knipling-Bushland U. S. Livestock Insects Research Lab, 2700 Fredericksburg Road, Kerrville, TX, USA. .,Texas A&M University, Department of Entomology, 2475 TAMU, College Station, TX, USA.
| | - Kylie G Bendele
- USDA-ARS Knipling-Bushland U. S. Livestock Insects Research Lab, 2700 Fredericksburg Road, Kerrville, TX, USA.
| | - Lénaïg Halos
- Boehringer Ingelheim Animal Health, 29 Avenue Tony Garnier, 69007, Lyon, France.,Bill and Melinda Gates Foundation, Seattle, WA, USA
| | - Yovany Moreno
- Boehringer Ingelheim Animal Health, Pharmaceutical Discovery and Research, 3239 Satellite Blvd. Bldg. 600, Duluth, GA, USA
| | - Christian Epe
- Boehringer Ingelheim Animal Health, Pharmaceutical Discovery and Research, 3239 Satellite Blvd. Bldg. 600, Duluth, GA, USA
| | - Monica Figueiredo
- Boehringer Ingelheim Animal Health, Pharmaceutical Discovery and Research, 3239 Satellite Blvd. Bldg. 600, Duluth, GA, USA
| | - Martin Liebstein
- Boehringer Ingelheim Animal Health Missouri Research Center, 6498 Jade Rd, Fulton, MO, USA
| | - Felix D Guerrero
- USDA-ARS Knipling-Bushland U. S. Livestock Insects Research Lab, 2700 Fredericksburg Road, Kerrville, TX, USA
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3
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Structural characterization and antioxidant activity of a glycoprotein isolated from Camellia oleifera Abel seeds against D-galactose-induced oxidative stress in mice. J Funct Foods 2020. [DOI: 10.1016/j.jff.2019.103594] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
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4
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Manabe S, Yamaguchi Y, Matsumoto K, Fuchigami H, Kawase T, Hirose K, Mitani A, Sumiyoshi W, Kinoshita T, Abe J, Yasunaga M, Matsumura Y, Ito Y. Characterization of Antibody Products Obtained through Enzymatic and Nonenzymatic Glycosylation Reactions with a Glycan Oxazoline and Preparation of a Homogeneous Antibody-Drug Conjugate via Fc N-Glycan. Bioconjug Chem 2019; 30:1343-1355. [PMID: 30938513 DOI: 10.1021/acs.bioconjchem.9b00132] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Glycan engineering of antibodies has received considerable attention. Although various endo-β- N-acetylglucosaminidase mutants have been developed for glycan remodeling, a side reaction has been reported between glycan oxazoline and amino groups. In this study, we performed a detailed characterization for antibody products obtained through enzymatic and nonenzymatic reactions with the aim of maximizing the efficiency of the glycosylation reaction with fewer side products. The reactions were monitored by an ultraperformance liquid chromatography system using an amide-based wide-pore column. The products were characterized by liquid chromatography coupled with tandem mass spectrometry. The side reactions were suppressed by adding glycan oxazoline in a stepwise manner under slightly acidic conditions. Through a combination of an azide-carrying glycan transfer reaction under optimized conditions and a bio-orthogonal reaction, a potent cytotoxic agent monomethyl auristatin E was site-specifically conjugated at N-glycosylated Asn297 with a drug-to-antibody ratio of 4. The prepared antibody-drug conjugate exhibited cytotoxicity against HER2-expressing cells.
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Affiliation(s)
- Shino Manabe
- Synthetic Cellular Chemistry Laboratory , RIKEN , Hirosawa, Wako , Saitama , 351-0198 Japan
| | - Yoshiki Yamaguchi
- Synthetic Cellular Chemistry Laboratory , RIKEN , Hirosawa, Wako , Saitama , 351-0198 Japan.,Structural Glycobiology Team , RIKEN , Hirosawa, Wako , Saitama , 351-0198 Japan
| | - Kana Matsumoto
- Structural Glycobiology Team , RIKEN , Hirosawa, Wako , Saitama , 351-0198 Japan
| | - Hirobumi Fuchigami
- Exploratory Oncology Research & Clinical Trial Center , National Cancer Center , Kashiwanoha, Kashiwa , Chiba 277-8577 Japan
| | - Taiji Kawase
- Nihon Waters KK, Kitashinagawa, Shinagawa, Tokyo , 140-0001 Japan
| | - Kenji Hirose
- Nihon Waters KK, Kitashinagawa, Shinagawa, Tokyo , 140-0001 Japan
| | - Ai Mitani
- Fushimi Pharmaceutical Co. Ltd., Nakatsu, Marugame , Kagawa , 763-8605 Japan
| | - Wataru Sumiyoshi
- Fushimi Pharmaceutical Co. Ltd., Nakatsu, Marugame , Kagawa , 763-8605 Japan
| | - Takashi Kinoshita
- Fushimi Pharmaceutical Co. Ltd., Nakatsu, Marugame , Kagawa , 763-8605 Japan
| | - Junpei Abe
- Synthetic Cellular Chemistry Laboratory , RIKEN , Hirosawa, Wako , Saitama , 351-0198 Japan
| | - Masahiro Yasunaga
- Exploratory Oncology Research & Clinical Trial Center , National Cancer Center , Kashiwanoha, Kashiwa , Chiba 277-8577 Japan
| | - Yasuhiro Matsumura
- Exploratory Oncology Research & Clinical Trial Center , National Cancer Center , Kashiwanoha, Kashiwa , Chiba 277-8577 Japan
| | - Yukishige Ito
- Synthetic Cellular Chemistry Laboratory , RIKEN , Hirosawa, Wako , Saitama , 351-0198 Japan
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5
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Kolli V, Schumacher KN, Dodds ED. Ion mobility-resolved collision-induced dissociation and electron transfer dissociation of N-glycopeptides: gathering orthogonal connectivity information from a single mass-selected precursor ion population. Analyst 2018; 142:4691-4702. [PMID: 29119999 DOI: 10.1039/c7an01196b] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Glycopeptide-level mass spectrometry (MS) and tandem mass spectrometry (MS/MS) analyses are commonly performed to establish site-specific protein glycosylation profiles that are of central importance to gaining structure-function insights on glycoproteins. Confoundingly, the complete characterization of glycopeptide connectivity usually requires the acquisition of multiple MS/MS fragmentation spectra. Complementary ion fragmentation techniques such as collision-induced dissociation (CID) and electron transfer dissociation (ETD) are often applied in concert to address this need. While structurally informative, the requirement for acquisition of two MS/MS spectra per analyte places considerable limitations upon the breadth and depth of large-scale glycoproteomic inquiry. Here, a previously developed method of multiplexing CID and ETD is applied to the study of glycopeptides for the first time. Integration of the two dissociation methods was accomplished through addition of an ion mobility (IM) dimension that disperses the two stages of MS/MS in time. This allows the two MS/MS spectra to be acquired within a few milliseconds of one another, and to be deconvoluted in post-processing. Furthermore, the method allows both fragmentation readouts to be obtained from the same precursor ion packet, thus reducing the inefficiencies imposed by separate CID and ETD acquisitions and the relatively poor precursor ion to fragment ion conversion typical of ETD. N-Linked glycopeptide ions ranging in molecular weight from 1.8 to 6.5 kDa were generated from four model glycoproteins that collectively encompassed paucimannosidic, high mannose, and complex types of N-glycosylation. In each case, IM-resolved CID and ETD events provided complete coverage of the glycan topology and peptide sequence coverages ranging from 48.4% (over 32 amino acid residues) to 85.7% (over eight amino acid residues). The potential of this method for large-scale glycoproteomic analysis is discussed.
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Affiliation(s)
- Venkata Kolli
- Department of Chemistry, University of Nebraska - Lincoln, Lincoln, NE 68588-0304, USA.
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6
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Feng HT, Li P, Rui G, Stray J, Khan S, Chen SM, Li SFY. Multiplexing N-glycan analysis by DNA analyzer. Electrophoresis 2017; 38:1788-1799. [PMID: 28426178 DOI: 10.1002/elps.201600404] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Revised: 04/03/2017] [Accepted: 04/08/2017] [Indexed: 12/25/2022]
Abstract
Analysis of N-glycan structures has been gaining attentions over the years due to their critical importance to biopharma-based applications and growing roles in biological research. Glycan profiling is also critical to the development of biosimilar drugs. The detailed characterization of N-glycosylation is mandatory because it is a nontemplate driven process and that significantly influences critical properties such as bio-safety and bio-activity. The ability to comprehensively characterize highly complex mixtures of N-glycans has been analytically challenging and stimulating because of the difficulties in both the structure complexity and time-consuming sample pretreatment procedures. CE-LIF is one of the typical techniques for N-glycan analysis due to its high separation efficiency. In this paper, a 16-capillary DNA analyzer was coupled with a magnetic bead glycan purification method to accelerate the sample preparation procedure and therefore increase N-glycan assay throughput. Routinely, the labeling dye used for CE-LIF is 8-aminopyrene-1,3,6-trisulfonic acid, while the typical identification method involves matching migration times with database entries. Two new fluorescent dyes were used to either cross-validate and increase the glycan identification precision or simplify sample preparation steps. Exoglycosidase studies were carried out using neuramididase, galactosidase, and fucosidase to confirm the results of three dye cross-validation. The optimized method combines the parallel separation capacity of multiple-capillary separation with three labeling dyes, magnetic bead assisted preparation, and exoglycosidase treatment to allow rapid and accurate analysis of N-glycans. These new methods provided enough useful structural information to permit N-glycan structure elucidation with only one sample injection.
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Affiliation(s)
- Hua-Tao Feng
- Department of Chemistry, National University of Singapore, Singapore.,NUS Environmental Research Institute, National University of Singapore, Singapore
| | - Pingjing Li
- NUS Environmental Research Institute, National University of Singapore, Singapore
| | - Guo Rui
- NUS Environmental Research Institute, National University of Singapore, Singapore
| | - James Stray
- Thermo Fisher Scientific, South San Francisco, CA, USA
| | - Shaheer Khan
- Thermo Fisher Scientific, South San Francisco, CA, USA
| | | | - Sam F Y Li
- Department of Chemistry, National University of Singapore, Singapore.,NUS Environmental Research Institute, National University of Singapore, Singapore
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7
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: An update for 2011-2012. MASS SPECTROMETRY REVIEWS 2017; 36:255-422. [PMID: 26270629 DOI: 10.1002/mas.21471] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2014] [Accepted: 01/15/2015] [Indexed: 06/04/2023]
Abstract
This review is the seventh update of the original article published in 1999 on the application of MALDI mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2012. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, and fragmentation are covered in the first part of the review and applications to various structural types constitute the remainder. The main groups of compound are oligo- and poly-saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2015 Wiley Periodicals, Inc. Mass Spec Rev 36:255-422, 2017.
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Affiliation(s)
- David J Harvey
- Department of Biochemistry, Oxford Glycobiology Institute, University of Oxford, Oxford, OX1 3QU, UK
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8
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Lobo MDP, Moreno FBMB, Souza GHMF, Verde SMML, Moreira RDA, Monteiro-Moreira ACDO. Label-Free Proteome Analysis of Plasma from Patients with Breast Cancer: Stage-Specific Protein Expression. Front Oncol 2017; 7:14. [PMID: 28210565 PMCID: PMC5288737 DOI: 10.3389/fonc.2017.00014] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/18/2017] [Indexed: 11/13/2022] Open
Abstract
Breast cancer is one of the most commonly diagnosed types of cancer among women. Breast cancer mortality rates remain high probably because its diagnosis is hampered by inaccurate detection methods. Since changes in protein expression as well as modifications in protein glycosylation have been frequently reported in cancer development, the aim of this work was to study the differential expression as well as modifications of glycosylation of proteins from plasma of women with breast cancer at different stages of disease (n = 30) compared to healthy women (n = 10). A proteomics approach was used that depleted albumin and IgG from plasma followed by glycoprotein enrichment using immobilized Moraceae lectin (frutalin)-affinity chromatography and data-independent label-free mass spectrometric analysis. Data are available via ProteomeXchange with identifier PXD003106. As result, 57,016 peptides and 4,175 proteins among all samples were identified. From this, 40 proteins present in unbound (PI—proteins that did not interact with lectin) and bound (PII—proteins that interacted with lectin) fractions were differentially expressed. High levels of apolipoprotein A-II were detected here that were elevated significantly in the early and advanced stages of the disease. Apolipoprotein C-III was detected in both fractions, and its level was increased slightly in the PI fraction of patients with early-stage breast cancer and expressed at higher levels in the PII fraction of patients with early and intermediate stages. Clusterin was present at higher levels in both fractions of patients with early and intermediate stages of breast cancer. Our findings reveal a correlation between alterations in protein glycosylation, lipid metabolism, and the progression of breast cancer.
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Affiliation(s)
- Marina Duarte Pinto Lobo
- Department of Biochemistry and Molecular Biology, Federal University of Ceará (UFC), Fortaleza, Brazil; Center of Experimental Biology (Nubex), University of Fortaleza (UNIFOR), Fortaleza, Brazil
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9
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Feng HT, Su M, Rifai FN, Li P, Li SFY. Parallel analysis and orthogonal identification of N-glycans with different capillary electrophoresis mechanisms. Anal Chim Acta 2016; 953:79-86. [PMID: 28010746 DOI: 10.1016/j.aca.2016.11.043] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2016] [Revised: 11/16/2016] [Accepted: 11/19/2016] [Indexed: 10/20/2022]
Abstract
The deep involvement of glycans or carbohydrate moieties in biological processes makes glycan patterns an important direction for the clinical and medicine researches. A multiplexing CE mapping method for glycan analysis was developed in this study. By applying different CE separation mechanisms, the potential of combined parallel applications of capillary zone electrophoresis (CZE), micellar electrokinetic chromatography (MEKC) and capillary gel electrophoresis (CGE) for rapid and accurate identification of glycan was investigated. The combination of CZE and MEKC demonstrated enhancing chromatography separation capacity without the compromises of sample pre-treatment and glycan concentration. The separation mechanisms for multiplexing platform were selected based on the orthogonalities of the separation of glycan standards. MEKC method exhibited promising ability for the analysis of small GU value glycans and thus complementing the unavailability of CZE. The method established required only small amount of samples, simple instrument and single fluorescent labelling for sensitive detection. This integrated method can be used to search important glycan patterns appearing in biopharmaceutical products and other glycoproteins with clinical importance.
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Affiliation(s)
- Hua-Tao Feng
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore; NUS Environmental Research Institute, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore
| | - Min Su
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Farida Nur Rifai
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore
| | - Pingjing Li
- NUS Environmental Research Institute, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore
| | - Sam F Y Li
- Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543, Singapore; NUS Environmental Research Institute, 5A Engineering Drive 1, T-Lab Building, Singapore 117411, Singapore.
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10
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Ferreira JA, Peixoto A, Neves M, Gaiteiro C, Reis CA, Assaraf YG, Santos LL. Mechanisms of cisplatin resistance and targeting of cancer stem cells: Adding glycosylation to the equation. Drug Resist Updat 2016; 24:34-54. [DOI: 10.1016/j.drup.2015.11.003] [Citation(s) in RCA: 113] [Impact Index Per Article: 14.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2015] [Revised: 11/09/2015] [Accepted: 11/18/2015] [Indexed: 02/06/2023]
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11
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Zhao Y, Law HC, Zhang Z, Lam HC, Quan Q, Li G, Chu IK. Online coupling of hydrophilic interaction/strong cation exchange/reversed-phase liquid chromatography with porous graphitic carbon liquid chromatography for simultaneous proteomics and N-glycomics analysis. J Chromatogr A 2015; 1415:57-66. [DOI: 10.1016/j.chroma.2015.08.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 07/20/2015] [Accepted: 08/10/2015] [Indexed: 11/25/2022]
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12
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Shu L, Suter MJF, Räsänen K. Evolution of egg coats: linking molecular biology and ecology. Mol Ecol 2015; 24:4052-73. [DOI: 10.1111/mec.13283] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 06/12/2015] [Accepted: 06/17/2015] [Indexed: 12/18/2022]
Affiliation(s)
- Longfei Shu
- Department of Aquatic Ecology; Swiss Federal Institute of Aquatic Science and Technology; Eawag; 8600 Duebendorf Switzerland
- Institute of Integrative Biology; ETH Zurich; 8092 Zurich Switzerland
| | - Marc J.-F. Suter
- Department of Environmental Toxicology; Swiss Federal Institute of Aquatic Science and Technology; Eawag; 8600 Duebendorf Switzerland
- Department of Environmental Systems Science; Swiss Federal Institute of Technology; ETH Zurich; 8092 Zurich Switzerland
| | - Katja Räsänen
- Department of Aquatic Ecology; Swiss Federal Institute of Aquatic Science and Technology; Eawag; 8600 Duebendorf Switzerland
- Institute of Integrative Biology; ETH Zurich; 8092 Zurich Switzerland
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13
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Ali F, Cheong WJ. Open tubular capillary electrochromatography with an N
-phenylacrylamide-styrene copolymer-based stationary phase for the separation of anomers of glucose and structural isomers of maltotriose. J Sep Sci 2015; 38:1763-70. [DOI: 10.1002/jssc.201401356] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 02/23/2015] [Accepted: 02/24/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Faiz Ali
- Department of Chemistry; Inha University; Namku Incheon South Korea
| | - Won Jo Cheong
- Department of Chemistry; Inha University; Namku Incheon South Korea
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14
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Development of Monolithic Column Materials for the Separation and Analysis of Glycans. CHROMATOGRAPHY 2015. [DOI: 10.3390/chromatography2010020] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Lynn KS, Chen CC, Lih TM, Cheng CW, Su WC, Chang CH, Cheng CY, Hsu WL, Chen YJ, Sung TY. MAGIC: An Automated N-Linked Glycoprotein Identification Tool Using a Y1-Ion Pattern Matching Algorithm and in Silico MS2 Approach. Anal Chem 2015; 87:2466-73. [DOI: 10.1021/ac5044829] [Citation(s) in RCA: 58] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Ke-Shiuan Lynn
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Chen-Chun Chen
- Genomics
Research Center, Academia Sinica, Taipei 11529, Taiwan
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - T. Mamie Lih
- Bioinformatics
Program, Taiwan International Graduate Program, Institute of Information
Science, Academia Sinica, Taipei 11529, Taiwan
- Institute
of Biomedical Informatics, National Yang-Ming University, Taipei 11221, Taiwan
| | - Cheng-Wei Cheng
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Wan-Chih Su
- Institute
of Chemistry, Academia Sinica, Taipei 11529, Taiwan
| | - Chun-Hao Chang
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Chia-Ying Cheng
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Wen-Lian Hsu
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
| | - Yu-Ju Chen
- Institute
of Chemistry, Academia Sinica, Taipei 11529, Taiwan
- Department
of Chemistry, National Taiwan University, Taipei 10617, Taiwan
| | - Ting-Yi Sung
- Institute
of Information Science, Academia Sinica, Taipei 11529, Taiwan
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16
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Zhang YW, Zhao MZ, Liu JX, Zhou YL, Zhang XX. Double-layer poly(vinyl alcohol)-coated capillary for highly sensitive and stable capillary electrophoresis and capillary electrophoresis with mass spectrometry glycan analysis. J Sep Sci 2015; 38:475-82. [DOI: 10.1002/jssc.201401025] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2014] [Revised: 11/12/2014] [Accepted: 11/13/2014] [Indexed: 01/15/2023]
Affiliation(s)
- Yi-Wei Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS); MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering; College of Chemistry, Peking University; Beijing China
| | - Ming-Zhe Zhao
- Beijing National Laboratory for Molecular Sciences (BNLMS); MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering; College of Chemistry, Peking University; Beijing China
| | - Jing-Xin Liu
- Beijing National Laboratory for Molecular Sciences (BNLMS); MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering; College of Chemistry, Peking University; Beijing China
| | - Ying-Lin Zhou
- Beijing National Laboratory for Molecular Sciences (BNLMS); MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering; College of Chemistry, Peking University; Beijing China
| | - Xin-Xiang Zhang
- Beijing National Laboratory for Molecular Sciences (BNLMS); MOE Key Laboratory of Bioorganic Chemistry and Molecular Engineering; College of Chemistry, Peking University; Beijing China
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17
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Rajabi K. Mass spectrometric study of gas-phase ions of acid β-glucosidase (Cerezyme) and iminosugar pharmacological chaperones. JOURNAL OF MASS SPECTROMETRY : JMS 2014; 49:1002-1009. [PMID: 25303390 DOI: 10.1002/jms.3412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Revised: 06/13/2014] [Accepted: 06/14/2014] [Indexed: 06/04/2023]
Abstract
The effect on the conformations and stability of gas-phase ions of Cerezyme, a glycoprotein, when bound to three small-molecule chaperones has been studied using intact ESI MS, collision cross section and MS/MS measurements. To distinguish between the peaks from apo and small-molecule complex ions, Cerezyme is deglycosylated (dg-Cer). ESI MS of dg-Cer reveals that glycosylation accounts for 8.5% of the molecular weight. When excess chaperone, either covalent (2FGF) or noncovalent (A and B iminosugars), is added to solutions of dg-Cer, mass spectra show peaks from 1:1 chaperone-enzyme complexes as well as free enzyme. On average, ions of the apoenzyme have 1.6 times higher cross sections when activated in the source region of the mass spectrometer. For a given charge state, ions of complexes of 2FGF and B have about 30% and 8.4% lower cross sections, respectively, compared to the apoenzyme. Thus, binding the chaperones causes the gas-phase protein to adopt more compact conformations. The noncovalent complex ions dissociate by the loss of charged chaperones. In the gas phase, the relative stability of dg-Cer with B is higher than that with the A, whereas in solution A binds enzyme more strongly than B. Nevertheless, the disagreement is explained based on the greater number of contacts between the B and dg-Cer than the A and dg-Cer (13 vs. 8), indicating the importance of noncovalent interactions within the protein-chaperone complex in the absence of solvent. Findings in this work suggest a hypothesis towards predicting a consistent correlation between gas-phase properties to solution binding properties.
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Affiliation(s)
- Khadijeh Rajabi
- Department of Chemistry, University of British Columbia (UBC), 2036 Mail Mall, Vancouver, BC, V6T 1Z1, Canada; Astbury Centre for Structural Molecular Biology (ACSMB), University of Leeds, Leeds, West Yorkshire, LS2 9JT, UK
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18
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Huang BY, Yang CK, Liu CP, Liu CY. Stationary phases for the enrichment of glycoproteins and glycopeptides. Electrophoresis 2014; 35:2091-107. [PMID: 24729282 DOI: 10.1002/elps.201400034] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2013] [Revised: 03/25/2014] [Accepted: 04/04/2014] [Indexed: 12/20/2022]
Abstract
The analysis of protein glycosylation is important for biomedical and biopharmaceutical research. Recent advances in LC-MS analysis have enabled the identification of glycosylation sites, the characterisation of glycan structures and the identification and quantification of glycoproteins and glycopeptides. However, this type of analysis remains challenging due to the low abundance of glycopeptides in complex protein digests, the microheterogeneity at glycosylation sites, ion suppression effects and the competition for ionisation by co-eluting peptides. Specific sample preparation is necessary for comprehensive and site-specific glycosylation analyses using MS. Therefore, researchers continue to pursue new columns to broaden their applications. The current manuscript covers recent literature published from 2008 to 2013. The stationary phases containing various chemical bonding methods or ligands immobilisation strategies on solid supports that selectively enrich N-linked or sialylated N-glycopeptides are categorised with either physical or chemical modes of binding. These categories include lectin affinity, hydrophilic interactions, boronate affinity, titanium dioxide affinity, hydrazide chemistry and other separation techniques. This review should aid in better understanding the syntheses and physicochemical properties of each type of stationary phases for enriching glycoproteins and glycopeptides.
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Affiliation(s)
- Bao-Yu Huang
- Department of Chemistry, National Taiwan University, Taipei, Taiwan
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19
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One-pot synthesis of magnetic colloidal nanocrystal clusters coated with chitosan for selective enrichment of glycopeptides. Anal Chim Acta 2014; 841:99-105. [PMID: 25109867 DOI: 10.1016/j.aca.2014.05.037] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2014] [Revised: 05/09/2014] [Accepted: 05/25/2014] [Indexed: 12/19/2022]
Abstract
Selective enrichment of glycopeptides prior to the mass spectrometry (MS) analysis is essential due to ion suppression effect during ionization caused by the co-presence of non-glycosylated peptides. Among the enrichment approaches, hydrophilic interaction liquid chromatography (HILIC) based on magnetic separation has become a popular method in recent years. As the conventional synthesis procedures of these materials are tedious and time-consuming with at least four steps. Herein, magnetic colloidal nanocrystal clusters coated with chitosan (Fe3O4@CS MCNCs) have been successfully prepared by a simple one-pot method. The resulting Fe3O4@CS MCNCs demonstrated an excellent ability for glycopeptide enrichment with high selectivity, low detection limit and high binding capacity. Furthermore, in the analysis of real complicated biological sample, 283 unique N-glycosylation sites corresponding to 175 glycosylated proteins were identified in three replicate analyses of 45μg protein sample extracted from HeLa cells, indicating the great potential in detection and identification of low abundant glycopeptides in glycoproteome analysis.
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20
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Baycin Hizal D, Wolozny D, Colao J, Jacobson E, Tian Y, Krag SS, Betenbaugh MJ, Zhang H. Glycoproteomic and glycomic databases. Clin Proteomics 2014; 11:15. [PMID: 24725457 PMCID: PMC3996109 DOI: 10.1186/1559-0275-11-15] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2013] [Accepted: 02/20/2014] [Indexed: 11/17/2022] Open
Abstract
Protein glycosylation serves critical roles in the cellular and biological processes of many organisms. Aberrant glycosylation has been associated with many illnesses such as hereditary and chronic diseases like cancer, cardiovascular diseases, neurological disorders, and immunological disorders. Emerging mass spectrometry (MS) technologies that enable the high-throughput identification of glycoproteins and glycans have accelerated the analysis and made possible the creation of dynamic and expanding databases. Although glycosylation-related databases have been established by many laboratories and institutions, they are not yet widely known in the community. Our study reviews 15 different publicly available databases and identifies their key elements so that users can identify the most applicable platform for their analytical needs. These databases include biological information on the experimentally identified glycans and glycopeptides from various cells and organisms such as human, rat, mouse, fly and zebrafish. The features of these databases - 7 for glycoproteomic data, 6 for glycomic data, and 2 for glycan binding proteins are summarized including the enrichment techniques that are used for glycoproteome and glycan identification. Furthermore databases such as Unipep, GlycoFly, GlycoFish recently established by our group are introduced. The unique features of each database, such as the analytical methods used and bioinformatical tools available are summarized. This information will be a valuable resource for the glycobiology community as it presents the analytical methods and glycosylation related databases together in one compendium. It will also represent a step towards the desired long term goal of integrating the different databases of glycosylation in order to characterize and categorize glycoproteins and glycans better for biomedical research.
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Affiliation(s)
- Deniz Baycin Hizal
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Daniel Wolozny
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Joseph Colao
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Elena Jacobson
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Yuan Tian
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
| | - Sharon S Krag
- Department of Biochemistry and Molecular Biology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Michael J Betenbaugh
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD, USA
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21
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Cao L, Yu L, Guo Z, Shen A, Guo Y, Liang X. N-Glycosylation Site Analysis of Proteins from Saccharomyces cerevisiae by Using Hydrophilic Interaction Liquid Chromatography-Based Enrichment, Parallel Deglycosylation, and Mass Spectrometry. J Proteome Res 2014; 13:1485-93. [DOI: 10.1021/pr401049e] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Liwei Cao
- Key Laboratory of Separation
Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Long Yu
- Key Laboratory of Separation
Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhimou Guo
- Key Laboratory of Separation
Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Aijin Shen
- Key Laboratory of Separation
Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Yunü Guo
- Key Laboratory of Separation
Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Xinmiao Liang
- Key Laboratory of Separation
Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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22
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Ali F, Kim YS, Cheong WJ. Immobilization of Styrene-acrylamide Co-polymer on Either Silica Particles or Inner Surface of Silica Capillary for the Separation of D-Glucose Anomers. B KOREAN CHEM SOC 2014. [DOI: 10.5012/bkcs.2014.35.2.539] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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23
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Wang J, Zhou C, Zhang W, Yao J, Lu H, Dong Q, Zhou H, Qin L. An integrative strategy for quantitative analysis of the N-glycoproteome in complex biological samples. Proteome Sci 2014; 12:4. [PMID: 24428921 PMCID: PMC3923275 DOI: 10.1186/1477-5956-12-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2013] [Accepted: 12/27/2013] [Indexed: 12/23/2022] Open
Abstract
Background The complexity of protein glycosylation makes it difficult to characterize glycosylation patterns on a proteomic scale. In this study, we developed an integrated strategy for comparatively analyzing N-glycosylation/glycoproteins quantitatively from complex biological samples in a high-throughput manner. This strategy entailed separating and enriching glycopeptides/glycoproteins using lectin affinity chromatography, and then tandem labeling them with 18O/16O to generate a mass shift of 6 Da between the paired glycopeptides, and finally analyzing them with liquid chromatography-mass spectrometry (LC-MS) and the automatic quantitative method we developed based on Mascot Distiller. Results The accuracy and repeatability of this strategy were first verified using standard glycoproteins; linearity was maintained within a range of 1:10–10:1. The peptide concentration ratios obtained by the self-build quantitative method were similar to both the manually calculated and theoretical values, with a standard deviation (SD) of 0.023–0.186 for glycopeptides. The feasibility of the strategy was further confirmed with serum from hepatocellular carcinoma (HCC) patients and healthy individuals; the expression of 44 glycopeptides and 30 glycoproteins were significantly different between HCC patient and control serum. Conclusions This strategy is accurate, repeatable, and efficient, and may be a useful tool for identification of disease-related N-glycosylation/glycoprotein changes.
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Affiliation(s)
| | | | | | | | | | | | - Haijun Zhou
- Department of Surgery, Huashan Hospital, Fudan University, Shanghai 200040, China.
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24
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Chen CC, Su WC, Huang BY, Chen YJ, Tai HC, Obena RP. Interaction modes and approaches to glycopeptide and glycoprotein enrichment. Analyst 2014; 139:688-704. [DOI: 10.1039/c3an01813j] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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25
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Lei C, Qian K, Noonan O, Nouwens A, Yu C. Applications of nanomaterials in mass spectrometry analysis. NANOSCALE 2013; 5:12033-12042. [PMID: 24162102 DOI: 10.1039/c3nr04194h] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
Mass spectrometry (MS) based analyses have received intense research interest in a series of rapidly developing disciplines. Although current MS techniques have enjoyed great successes, several key challenges still remain in practical applications, especially for the detection of biomolecules in biological systems. The use of nanomaterials in MS based analysis provides a promising approach due to their unique physical and chemical properties. In this review, nanomaterials with different compositions and nanostructures employed in MS applications are summarised and classified by their functions. Such an integrated and wide reaching review will provide a comprehensive handbook to researchers with various backgrounds working in this exciting interdisciplinary area.
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Affiliation(s)
- Chang Lei
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD 4072, Australia.
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26
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Sanda M, Pompach P, Benicky J, Goldman R. LC-MS3 quantification of O-glycopeptides in human serum. Electrophoresis 2013; 34:2342-9. [PMID: 23765987 PMCID: PMC3808000 DOI: 10.1002/elps.201200658] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2012] [Revised: 05/03/2013] [Accepted: 05/04/2013] [Indexed: 12/30/2022]
Abstract
Quantitative analysis of site-specific glycosylation of proteins is a challenging part of glycoproteomic research. Multiple enrichment steps are typically required in the analytical workflows to achieve adequate characterization of the site-specific glycoforms. In spite of recent advances, quantitative workflows need further development. Here, we report a selective and sensitive MS2 followed by further fragmentation in the linear IT-MS analyzer (MS3) multiple reaction monitoring workflow mass spectrometric method for direct analysis of O-glycopeptides in difficult matrix such as serum. Method optimization was performed using two serum glycoproteins, hemopexin (HPX) and sex hormone binding globulin. With the optimized MS3 workflow, we were able to analyze major glycoforms of HPX directly in human serum. Quantification of the minor glycoforms of HPX and glycoforms of sex hormone binding globulin required enrichment of the protein because these analytes were below the sensitivity of the 4000 quadrupole ion trap hybrid mass spectrometer in the complex serum background. In conclusion, we present a quantitative method for site-specific analysis of O-glycosylation with general applicability to mucin-type glycoproteins. Our results document reliable application of the optimized MS3 multiple reaction monitoring workflow to the relative quantification of O-glycosylation microheterogeneity of HPX in human serum. Introduction of isotopically labeled standards would be desirable to achieve absolute quantification of the analytes. The possibility to analyze serum samples directly represents a significant improvement of the quantitative glycopeptide workflows with the potential for use in clinical applications.
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Affiliation(s)
- Miloslav Sanda
- Department of Oncology, Georgetown University, Washington, DC 20057, USA
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27
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Reuel NF, Mu B, Zhang J, Hinckley A, Strano MS. Nanoengineered glycan sensors enabling native glycoprofiling for medicinal applications: towards profiling glycoproteins without labeling or liberation steps. Chem Soc Rev 2013; 41:5744-79. [PMID: 22868627 DOI: 10.1039/c2cs35142k] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Nanoengineered glycan sensors may help realize the long-held goal of accurate and rapid glycoprotein profiling without labeling or glycan liberation steps. Current methods of profiling oligosaccharides displayed on protein surfaces, such as liquid chromatography, mass spectrometry, capillary electrophoresis, and microarray methods, are limited by sample pretreatment and quantitative accuracy. Microarrayed platforms can be improved with methods that better estimate kinetic parameters rather than simply reporting relative binding information. These quantitative glycan sensors are enabled by an emerging class of nanoengineered materials that differ in their mode of signal transduction from traditional methods. Platforms that respond to mass changes include a quartz crystal microbalance and cantilever sensors. Electronic response can be detected from electrochemical, field effect transistor, and pore impedance sensors. Optical methods include fluorescent frontal affinity chromatography, surface plasmon resonance methods, and fluorescent carbon nanotubes. After a very brief primer on glycobiology and its connection to medicine, these emerging systems are critically reviewed for their potential use as core sensors in future glycoprofiling tools.
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Affiliation(s)
- Nigel F Reuel
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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28
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Liu J, Wang F, Lin H, Zhu J, Bian Y, Cheng K, Zou H. Monolithic Capillary Column Based Glycoproteomic Reactor for High-Sensitive Analysis of N-Glycoproteome. Anal Chem 2013; 85:2847-52. [DOI: 10.1021/ac400315n] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Jing Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Fangjun Wang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Hui Lin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jun Zhu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yangyang Bian
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Kai Cheng
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanfa Zou
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
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29
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Switzar L, Giera M, Niessen WMA. Protein Digestion: An Overview of the Available Techniques and Recent Developments. J Proteome Res 2013; 12:1067-77. [DOI: 10.1021/pr301201x] [Citation(s) in RCA: 164] [Impact Index Per Article: 14.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Linda Switzar
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Martin Giera
- Division of Molecular Cell Physiology,
Faculty of Earth and Life Sciences, VU University Amsterdam, De Boelelaan 1085, 1081 HV, Amsterdam, The Netherlands
- Biomolecular Mass Spectrometry
Unit, Department of Parasitology, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Wilfried M. A. Niessen
- AIMMS Division of BioMolecular
Analysis, Faculty of Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
- hyphen MassSpec, de Wetstraat 8, 2332 XT Leiden, The Netherlands
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30
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Sun B, Ma L, Yan X, Lee D, Alexander V, Hohmann LJ, Lorang C, Chandrasena L, Tian Q, Hood L. N-glycoproteome of E14.Tg2a mouse embryonic stem cells. PLoS One 2013; 8:e55722. [PMID: 23405203 PMCID: PMC3565968 DOI: 10.1371/journal.pone.0055722] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2012] [Accepted: 12/29/2012] [Indexed: 11/19/2022] Open
Abstract
E14.Tg2a mouse embryonic stem (mES) cells are a widely used host in gene trap and gene targeting techniques. Molecular characterization of host cells will provide background information for a better understanding of functions of the knockout genes. Using a highly selective glycopeptide-capture approach but ordinary liquid chromatography coupled mass spectrometry (LC-MS), we characterized the N-glycoproteins of E14.Tg2a cells and analyzed the close relationship between the obtained N-glycoproteome and cell-surface proteomes. Our results provide a global view of cell surface protein molecular properties, in which receptors seem to be much more diverse but lower in abundance than transporters on average. In addition, our results provide a systematic view of the E14.Tg2a N-glycosylation, from which we discovered some striking patterns, including an evolutionarily preserved and maybe functionally selected complementarity between N-glycosylation and the transmembrane structure in protein sequences. We also observed an environmentally influenced N-glycosylation pattern among glycoenzymes and extracellular matrix proteins. We hope that the acquired information enhances our molecular understanding of mES E14.Tg2a as well as the biological roles played by N-glycosylation in cell biology in general.
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Affiliation(s)
- Bingyun Sun
- Institute for Systems Biology, Seattle, Washington, United States of America
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail: (LH); (BS)
| | - Li Ma
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Xiaowei Yan
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Denis Lee
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Vinita Alexander
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Laura J. Hohmann
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Cynthia Lorang
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Lalangi Chandrasena
- Department of Chemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Qiang Tian
- Institute for Systems Biology, Seattle, Washington, United States of America
| | - Leroy Hood
- Institute for Systems Biology, Seattle, Washington, United States of America
- * E-mail: (LH); (BS)
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31
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Ye H, Boyne MT, Buhse LF, Hill J. Direct Approach for Qualitative and Quantitative Characterization of Glycoproteins Using Tandem Mass Tags and an LTQ Orbitrap XL Electron Transfer Dissociation Hybrid Mass Spectrometer. Anal Chem 2013; 85:1531-9. [DOI: 10.1021/ac3026465] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Hongping Ye
- U.S. Food and Drug Administration, CDER, DPA, St. Louis, Missouri 63101,
United States
| | - Michael T. Boyne
- U.S. Food and Drug Administration, CDER, DPA, St. Louis, Missouri 63101,
United States
| | - Lucinda F. Buhse
- U.S. Food and Drug Administration, CDER, DPA, St. Louis, Missouri 63101,
United States
| | - John Hill
- U.S. Food and Drug Administration, CDER, ONDQA/DPAII, Silver Spring, Maryland
20993, United States
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32
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Zamfir AD, Flangea C, Serb A, Zagrean AM, Rizzi AM, Sisu E. Separation and identification of glycoforms by capillary electrophoresis with electrospray ionization mass spectrometric detection. Methods Mol Biol 2013; 951:145-169. [PMID: 23296530 DOI: 10.1007/978-1-62703-146-2_11] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Capillary electrophoresis (CE) is a resourceful and versatile separation method for the analysis of complex carbohydrate mixtures. In combination with electrospray ionization (ESI) mass spectrometry (MS), CE enables fast, sensitive, and efficient separations for the accurate identification of a large variety of glycoform mixture types. In this chapter several reliable off- and on-line CE-based methods for the analysis of glycoforms with ESI MS/MS are presented. The first part of this chapter is dedicated to the application of off-line CE/ESI MS to complex mixtures of O-glycopeptides and mixtures of proteoglycan-derived O-glycans, i.e., glycosaminoglycans such as depolymerized hybrid chains of chondroitin sulfate (CS) and dermatan sulfate (DS). Procedures for off-line fractionation of these heterogeneous mixtures followed by ESI MS screening and sequencing of single glycoforms by collision-induced dissociation (CID) at low energies are also described. Ample sections are further devoted to on-line CE/ESI MS technique and its application to separation and identification of O-glycopeptides and CS/DS oligosaccharides. The concept and construction principles of two different sheathless CE/ESI MS interfaces together with the protocols to be applied for successful on-line analysis of O-glycopeptides and CS/DS oligosaccharides are presented in details in the last part of the chapter.
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Affiliation(s)
- Alina D Zamfir
- Department of Chemical and Biological Sciences, "Aurel Vlaicu" University of Arad, Timisoara, Romania.
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33
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Li F, Glinskii OV, Glinsky VV. Glycobioinformatics: Current strategies and tools for data mining in MS-based glycoproteomics. Proteomics 2012; 13:341-54. [DOI: 10.1002/pmic.201200149] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2012] [Revised: 10/06/2012] [Accepted: 11/06/2012] [Indexed: 12/18/2022]
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34
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Malerod H, Graham RLJ, Sweredoski MJ, Hess S. Comprehensive Profiling of N-Linked Glycosylation Sites in HeLa Cells Using Hydrazide Enrichment. J Proteome Res 2012. [DOI: 10.1021/pr300859k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Helle Malerod
- Department
of Chemistry, University of Oslo, P.O.
Box 1033 Blindern, 0315 Oslo,
Norway
| | - Robert L. J. Graham
- Proteome Exploration
Laboratory,
Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Michael J. Sweredoski
- Proteome Exploration
Laboratory,
Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
| | - Sonja Hess
- Proteome Exploration
Laboratory,
Beckman Institute, California Institute of Technology, Pasadena, California 91125, United States
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35
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Lazar IM, Lee W, Lazar AC. Glycoproteomics on the rise: established methods, advanced techniques, sophisticated biological applications. Electrophoresis 2012; 34:113-25. [PMID: 23161435 DOI: 10.1002/elps.201200445] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2012] [Revised: 10/07/2012] [Accepted: 10/07/2012] [Indexed: 02/05/2023]
Abstract
Glycosylation is the most complex form of protein PTMs. Affected proteins may carry dozens of glycosylation sites with tens to hundreds of glycan residues attached to every site. Glycosylated proteins have many important functions in biology, from cellular to organismal levels, being involved in cell-cell signaling, cell adhesion, immune response, host-pathogen interactions, and development and growth. Glycosylation, however, expands the biological functional diversity of proteins at the expense of a tremendous increase in structural heterogeneity. Aberrant glycosylation of cell surface proteins, as well as their detectable fingerprint in plasma samples, has been associated with cancer, inflammatory and degenerative diseases, and congenital disorders of glycosylation. Therefore, there are on-going efforts directed toward developing new technologies and approaches for glycan sequencing and high-throughput analysis of glycosylated proteins in complex samples with simultaneous characterization of both the protein and glycan moieties. This work is aimed primarily at pinpointing the challenges associated with the large-scale analysis of glycoproteins and the latest developments in glycoproteomic research, with focus on recent advancements (2011-2012) in microcolumn separations and MS detection.
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Affiliation(s)
- Iulia M Lazar
- Department of Biological Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061, USA.
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36
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Partyka J, Foret F. Cationic labeling of oligosaccharides for electrophoretic preconcentration and separation with contactless conductivity detection. J Chromatogr A 2012; 1267:116-20. [DOI: 10.1016/j.chroma.2012.06.044] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2012] [Revised: 06/13/2012] [Accepted: 06/14/2012] [Indexed: 01/12/2023]
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37
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Kim JY, Kim SK, Kang D, Moon MH. Dual lectin-based size sorting strategy to enrich targeted N-glycopeptides by asymmetrical flow field-flow fractionation: profiling lung cancer biomarkers. Anal Chem 2012; 84:5343-50. [PMID: 22616828 DOI: 10.1021/ac300772w] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A dual lectin-based size sorting and simultaneous enrichment strategy for selectively isolating N-linked glycopeptides was developed using asymmetrical flow field-flow fractionation (AF4). AF4 is an elution-based method for separating biological macromolecules that has been utilized for the separation of lectin-glycopeptide complexes formed by mixing serum peptides with lectin cocktails according to the difference in diffusion coefficients. It has also been used for simultaneous depletion of nonglycosylated peptides. The dual lectin-based enrichment method was applied to proteolytic peptides from lung cancer serum samples with two lectins (WGA, GlcNAc-specific, and SNA, Sia-specific), and the whole mixture was separated by AF4. The lectin-glycopeptide complex fractions collected during AF4 separation were endoglycosidically digested with PNGase F. The resulting deamidated glycopeptides were analyzed by nanoflow liquid chromatography-electrospray ionization-tandem mass spectrometry (nLC-ESI-MS-MS) to semiquantitatively profile the N-linked glycopeptides from the sera of lung cancer patients and healthy controls. The AF4 enrichment strategy coupled with nLC-ESI-MS-MS identified 16/24 (up/down-regulated by at least 10-fold compared to normal sera) N-linked glycopeptides from a WGA complex fraction of lung cancer sera and 18/3 from a SNA fraction.
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Affiliation(s)
- Jin Yong Kim
- Department of Chemistry, Yonsei University, Seoul, 120-749, Korea
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38
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The major autolysin Acm2 from Lactobacillus plantarum undergoes cytoplasmic O-glycosylation. J Bacteriol 2011; 194:325-33. [PMID: 22081384 DOI: 10.1128/jb.06314-11] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The major autolysin Acm2 from the probiotic strain Lactobacillus plantarum WCFS1 contains high proportions of alanine, serine, and threonine in its N-terminal so-called AST domain. It has been suggested that this extracellular protein might be glycosylated, but this has not been experimentally verified. We used high-resolution liquid chromatography-tandem mass spectrometry (LC-MS/MS) to study the possible occurrence of glycans on peptides generated from lactobacillary surface proteins by protease treatment. This approach yielded five glycopeptides in various glycoforms, all derived from the AST domain of Acm2. All five glycopeptides contained the hydroxy-amino acids serine and threonine, suggesting that Acm2 is O-glycosylated. By using lectin blotting with succinylated wheat germ agglutinin, and by comparing the wild-type strain with an Acm2-negative derivative (NZ3557), we found that the attached N-acetylhexosamines are most likely N-acetylglucosamines (GlcNAc). NZ3557 was further used as a genetic background to express an Acm2 variant lacking its secretion signal, resulting in intracellular expression of Acm2. We show that this intracellular version of Acm2 is also glycosylated, indicating that the GlcNAc modification is an intracellular process.
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39
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Darville LN, Merchant ME, Murray KK. A mass spectrometry approach for the study of deglycosylated proteins. Microchem J 2011. [DOI: 10.1016/j.microc.2011.05.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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40
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Reuel NF, Ahn JH, Kim JH, Zhang J, Boghossian AA, Mahal LK, Strano MS. Transduction of Glycan–Lectin Binding Using Near-Infrared Fluorescent Single-Walled Carbon Nanotubes for Glycan Profiling. J Am Chem Soc 2011; 133:17923-33. [DOI: 10.1021/ja2074938] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Nigel F. Reuel
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jin-Ho Ahn
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Jong-Ho Kim
- Department of Chemical Engineering, Hanyang University, Ansan 426-791, Republic of Korea
| | - Jingqing Zhang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Ardemis A. Boghossian
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Lara K. Mahal
- Department of Chemistry, New York University, New York, New York 10003, United States
| | - Michael S. Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Ferreira JA, Daniel-da-Silva AL, Alves RMP, Duarte D, Vieira I, Santos LL, Vitorino R, Amado F. Synthesis and Optimization of Lectin Functionalized Nanoprobes for the Selective Recovery of Glycoproteins from Human Body Fluids. Anal Chem 2011; 83:7035-43. [DOI: 10.1021/ac200916j] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- José A. Ferreira
- Experimental Pathology and Therapeutics Group, Research Centre, Portuguese Oncology Institute, 4200-072 Porto, Portugal
| | | | | | | | | | - Lúcio Lara Santos
- Experimental Pathology and Therapeutics Group, Research Centre, Portuguese Oncology Institute, 4200-072 Porto, Portugal
- University of Fernando Pessoa, Porto, Portugal
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42
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Sisu E, Flangea C, Serb A, Rizzi A, Zamfir AD. High-performance separation techniques hyphenated to mass spectrometry for ganglioside analysis. Electrophoresis 2011; 32:1591-609. [DOI: 10.1002/elps.201100067] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2011] [Revised: 03/09/2011] [Accepted: 03/09/2011] [Indexed: 11/06/2022]
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43
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Cortes DF, Kabulski JL, Lazar AC, Lazar IM. Recent advances in the MS analysis of glycoproteins: Capillary and microfluidic workflows. Electrophoresis 2011; 32:14-29. [PMID: 21171110 PMCID: PMC3717299 DOI: 10.1002/elps.201000394] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2010] [Revised: 09/21/2010] [Accepted: 09/21/2010] [Indexed: 12/26/2022]
Abstract
Recent developments in bioanalytical instrumentation, MS detection, and computational data analysis approaches have provided researchers with capabilities for interrogating the complex cellular glycoproteome, to help gain a better insight into the cellular and physiological processes that are associated with a disease and to facilitate the efforts centered on identifying disease-specific biomarkers. This review describes the progress achieved in the characterization of protein glycosylation by using advanced capillary and microfluidic MS technologies. The major steps involved in large-scale glycoproteomic analysis approaches are discussed, with special emphasis given to workflows that have evolved around complex MS detection functions. In addition, quantitative analysis strategies are assessed, and the bioinformatics aspects of glycoproteomic data processing are summarized. The developments in commercial and custom fabricated microfluidic front-end platforms to ESI- and MALDI-MS instrumentation, for addressing major challenges in carbohydrate analysis such as sensitivity, throughput, and ability to perform structural characterization, are further evaluated and illustrated with relevant examples.
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Affiliation(s)
- Diego F. Cortes
- Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University Washington St. Bio II/283, Blacksburg, VA 24061
| | - Jarod L. Kabulski
- Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University Washington St. Bio II/283, Blacksburg, VA 24061
| | | | - Iulia M. Lazar
- Virginia Bioinformatics Institute Virginia Polytechnic Institute and State University Washington St. Bio II/283, Blacksburg, VA 24061
- Department of Biological Sciences, Virginia Polytechnic Institute and State University Washington St. Bio II/283, Blacksburg, VA 24061
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