151
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Zacharias LG, Hartmann AK, Song E, Zhao J, Zhu R, Mirzaei P, Mechref Y. HILIC and ERLIC Enrichment of Glycopeptides Derived from Breast and Brain Cancer Cells. J Proteome Res 2016; 15:3624-3634. [PMID: 27533485 DOI: 10.1021/acs.jproteome.6b00429] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Aberrant glycosylation has been linked to many different cancer types. The blood-brain barrier (BBB) is a region of the brain that regulates the entrance of ions, diseases, toxins, and so on. However, in breast cancer metastasis, the BBB fails to prevent the crossing of the cancer cells into the brain. Here we present a study of identifying and quantifying the glycosylation of six breast and brain cancer cell lines using hydrophilic interaction liquid chromatography (HILIC) and electrostatic repulsion liquid chromatography (ERLIC) enrichments and LC-MS/MS analysis. Qualitative and quantitative analyses of N-linked glycosylation were performed by both enrichment techniques for individual and complementary comparison. Potential cancer glycopeptide biomarkers were identified and confirmed by chemometric and statistical evaluations. A total of 497 glycopeptides were characterized, of which 401 were common glycopeptides (80.6% overlap) identified from both enrichment techniques. HILIC enrichment yielded 320 statistically significant glycopeptides in 231BR relative to the other cell lines out of 494 unique glycopeptides, and sequential HILIC-ERLIC enrichment yielded 214 statistically significant glycopeptides in 231BR compared with the other cell lines out of 404 unique glycopeptides. The results provide the first comprehensive glycopeptide listing for these six cell lines.
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Affiliation(s)
- Lauren G Zacharias
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States
| | - Alyssa K Hartmann
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States
| | - Ehwang Song
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States
| | - Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States
| | - Rui Zhu
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States
| | - Parvin Mirzaei
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University , Lubbock, Texas 79409, United States
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152
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Gudelj I, Baciarello M, Ugrina I, De Gregori M, Napolioni V, Ingelmo PM, Bugada D, De Gregori S, Đerek L, Pučić-Baković M, Novokmet M, Gornik O, Saccani Jotti G, Meschi T, Lauc G, Allegri M. Changes in total plasma and serum N-glycome composition and patient-controlled analgesia after major abdominal surgery. Sci Rep 2016; 6:31234. [PMID: 27501865 PMCID: PMC4977520 DOI: 10.1038/srep31234] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 07/15/2016] [Indexed: 12/21/2022] Open
Abstract
Systemic inflammation participates to the complex healing process occurring after major surgery, thus directly affecting the surgical outcome and patient recovery. Total plasma N-glycome might be an indicator of inflammation after major surgery, as well as an anti-inflammatory therapy response marker, since protein glycosylation plays an essential role in the inflammatory cascade. Therefore, we assessed the effects of surgery on the total plasma N-glycome and the association with self-administration of postoperative morphine in two cohorts of patients that underwent major abdominal surgery. We found that plasma N-glycome undergoes significant changes one day after surgery and intensifies one day later, thus indicating a systemic physiological response. In particular, we observed the increase of bisialylated biantennary glycan, A2G2S[3,6]2, 12 hours after surgery, which progressively increased until 48 postoperative hours. Most changes occurred 24 hours after surgery with the decrease of most core-fucosylated biantennary structures, as well as the increase in sialylated tetraantennary and FA3G3S[3,3,3]3 structures. Moreover, we observed a progressive increase of sialylated triantennary and tetraantennary structures two days after surgery, with a concomitant decrease of the structures containing bisecting N-acetylglucosamine along with bi- and trisialylated triantennary glycans. We did not find any statistically significant association between morphine consumption and plasma N-glycome.
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Affiliation(s)
- Ivan Gudelj
- Genos Glycoscience Research Laboratory, Zagreb, Croatia
| | - Marco Baciarello
- Department of Anesthesia, ICU and Pain Therapy, University Hospital of Parma, Parma, Italy.,SIMPAR Group (Study in Multidisciplinary Pain Research), Parma, Italy.,Department of Surgical Sciences, University of Parma, Parma, Italy
| | - Ivo Ugrina
- Genos Glycoscience Research Laboratory, Zagreb, Croatia.,University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Manuela De Gregori
- SIMPAR Group (Study in Multidisciplinary Pain Research), Parma, Italy.,Pain Therapy Service, Fondazione IRCCS Policlinico S. Matteo, Pavia, Italy.,YAP (Young Against Pain) group, Parma, Italy
| | - Valerio Napolioni
- SIMPAR Group (Study in Multidisciplinary Pain Research), Parma, Italy.,Department of Neurology and Neurological Sciences, Stanford University School of Medicine, Palo Alto, CA, USA
| | - Pablo M Ingelmo
- SIMPAR Group (Study in Multidisciplinary Pain Research), Parma, Italy.,Department of Anesthesia, Montreal Children's Hospital, Canada
| | - Dario Bugada
- Department of Anesthesia, ICU and Pain Therapy, University Hospital of Parma, Parma, Italy.,SIMPAR Group (Study in Multidisciplinary Pain Research), Parma, Italy.,Department of Surgical Sciences, University of Parma, Parma, Italy
| | - Simona De Gregori
- Clinical and Experimental Pharmacokinetics Unit, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Lovorka Đerek
- Department of Medical Biochemistry and Laboratory Medicine, Clinical Hospital Merkur, Zagreb, Croatia
| | | | | | - Olga Gornik
- University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Gloria Saccani Jotti
- Department of Biomedical, Biotechnological and Translational Science (S.Bi.Bi.T.), University of Parma, Parma, Italy
| | - Tiziana Meschi
- Department of Clinical and Experimental Medicine, University of Parma, Italy
| | - Gordan Lauc
- Genos Glycoscience Research Laboratory, Zagreb, Croatia.,University of Zagreb Faculty of Pharmacy and Biochemistry, Zagreb, Croatia
| | - Massimo Allegri
- Department of Anesthesia, ICU and Pain Therapy, University Hospital of Parma, Parma, Italy.,SIMPAR Group (Study in Multidisciplinary Pain Research), Parma, Italy.,Department of Surgical Sciences, University of Parma, Parma, Italy
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153
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Wang J, Wang Y, Gao M, Zhang X, Yang P. Versatile metal–organic framework-functionalized magnetic graphene nanoporous composites: As deft matrix for high-effective extraction and purification of the N-linked glycans. Anal Chim Acta 2016; 932:41-8. [DOI: 10.1016/j.aca.2016.05.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/16/2016] [Accepted: 05/17/2016] [Indexed: 01/07/2023]
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154
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Nasir W, Toledo AG, Noborn F, Nilsson J, Wang M, Bandeira N, Larson G. SweetNET: A Bioinformatics Workflow for Glycopeptide MS/MS Spectral Analysis. J Proteome Res 2016; 15:2826-40. [PMID: 27399812 DOI: 10.1021/acs.jproteome.6b00417] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Glycoproteomics has rapidly become an independent analytical platform bridging the fields of glycomics and proteomics to address site-specific protein glycosylation and its impact in biology. Current glycopeptide characterization relies on time-consuming manual interpretations and demands high levels of personal expertise. Efficient data interpretation constitutes one of the major challenges to be overcome before true high-throughput glycopeptide analysis can be achieved. The development of new glyco-related bioinformatics tools is thus of crucial importance to fulfill this goal. Here we present SweetNET: a data-oriented bioinformatics workflow for efficient analysis of hundreds of thousands of glycopeptide MS/MS-spectra. We have analyzed MS data sets from two separate glycopeptide enrichment protocols targeting sialylated glycopeptides and chondroitin sulfate linkage region glycopeptides, respectively. Molecular networking was performed to organize the glycopeptide MS/MS data based on spectral similarities. The combination of spectral clustering, oxonium ion intensity profiles, and precursor ion m/z shift distributions provided typical signatures for the initial assignment of different N-, O- and CS-glycopeptide classes and their respective glycoforms. These signatures were further used to guide database searches leading to the identification and validation of a large number of glycopeptide variants including novel deoxyhexose (fucose) modifications in the linkage region of chondroitin sulfate proteoglycans.
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Affiliation(s)
- Waqas Nasir
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
| | - Alejandro Gomez Toledo
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
| | - Fredrik Noborn
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
| | - Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
| | - Mingxun Wang
- Department of Computer Science and Engineering, Center for Computational Mass Spectrometry, CSE, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
| | - Nuno Bandeira
- Department of Computer Science and Engineering, Center for Computational Mass Spectrometry, CSE, and Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California, San Diego , La Jolla, California 92093, United States
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, Sahlgrenska Academy at the University of Gothenburg , SE 413 45 Gothenburg, Sweden
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155
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Yamamoto S, Kinoshita M, Suzuki S. Current landscape of protein glycosylation analysis and recent progress toward a novel paradigm of glycoscience research. J Pharm Biomed Anal 2016; 130:273-300. [PMID: 27461579 DOI: 10.1016/j.jpba.2016.07.015] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2016] [Revised: 07/09/2016] [Accepted: 07/09/2016] [Indexed: 12/25/2022]
Abstract
This review covers the basics and some applications of methodologies for the analysis of glycoprotein glycans. Analytical techniques used for glycoprotein glycans, including liquid chromatography (LC), capillary electrophoresis (CE), mass spectrometry (MS), and high-throughput analytical methods based on microfluidics, were described to supply the essentials about biopharmaceutical and biomarker glycoproteins. We will also describe the MS analysis of glycoproteins and glycopeptides as well as the chemical and enzymatic releasing methods of glycans from glycoproteins and the chemical reactions used for the derivatization of glycans. We hope the techniques have accommodated most of the requests from glycoproteomics researchers.
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Affiliation(s)
- Sachio Yamamoto
- Faculty of Pharmaceutical Sciences, Kinki University, 3-4-1, Kowakae, Higashi-osaka, Osaka, 577-8502, Japan.
| | - Mitsuhiro Kinoshita
- Faculty of Pharmaceutical Sciences, Kinki University, 3-4-1, Kowakae, Higashi-osaka, Osaka, 577-8502, Japan
| | - Shigeo Suzuki
- Faculty of Pharmaceutical Sciences, Kinki University, 3-4-1, Kowakae, Higashi-osaka, Osaka, 577-8502, Japan
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156
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Zhao M, Deng C. Fluorous modified magnetic mesoporous silica composites-incorporated fluorous solid-phase extraction for the specific enrichment of N-linked glycans with simultaneous exclusion of proteins. Talanta 2016; 159:111-116. [PMID: 27474286 DOI: 10.1016/j.talanta.2016.06.017] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/01/2016] [Accepted: 06/05/2016] [Indexed: 12/31/2022]
Abstract
Taking advantage of fluorine-fluorine interactions, fluorous solid-phase extraction (FSPE) is emerging as a novel approach in proteomics research. Notably, silica gel bound with perfluoroalkyl groups was applied to the FSPE of N-linked glycans. Based on previous studies, mesoporous silica coated magnetic nanoparticles bound with perfluoroalkyl groups were synthesized for the specific enrichment of N-linked glycans in this study. The magnetic nanoparticles-incorporated FSPE strategy successfully identified 22 N-linked glycans from the OVA digest with a concentration of 0.5μg/μL, and achieved a detection limit of 5ng/μL (with 16 N-linked glycans identified). It also showed good day-to-day reproducibility. Its selectivity towards BSA protein is 1:200 (molar ratio), showing excellent size-exclusion effect. In addition, the present method proved to be effective for the analysis of the human serum digest, opening up new prospect for the identification of glycans and proteins with other post-translational modifications in biological environment.
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Affiliation(s)
- Man Zhao
- Department of Chemistry and Institutes of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200433, China
| | - Chunhui Deng
- Department of Chemistry and Institutes of Biomedical Sciences, Collaborative Innovation Center of Genetics and Development, Fudan University, Shanghai 200433, China.
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157
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Zhao J, Song E, Zhu R, Mechref Y. Parallel data acquisition of in-source fragmented glycopeptides to sequence the glycosylation sites of proteins. Electrophoresis 2016; 37:1420-30. [PMID: 26957414 DOI: 10.1002/elps.201500562] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2015] [Revised: 02/28/2016] [Accepted: 02/28/2016] [Indexed: 11/11/2022]
Abstract
Glycosylation plays important roles in maintaining protein stability and controlling biological processes. In recent years, the correlation between aberrant glycoproteins and many diseases has been reported. Hence, qualitative and quantitative analyses of glycoproteins are necessary to understand physiological processes. LC-MS/MS analysis of glycopeptides is faced with the low glycopeptide signal intensities and low peptide sequence identification. In our study, in-source fragmentation (ISF) was used in conjunction with LC-MS/MS to facilitate the parallel acquisition of peptide backbone sequence and glycan composition information. In ISF method, the identification of glycosylation sites depended on the detection of Y1 ion (ion of peptide backbone with an N-acetylglucosamine attached). To attain dominant Y1 ions, a range of source fragmentation voltages was studied using fetuin. A 45 V ISF voltage was found to be the most efficient voltage for the analysis of glycoproteins. ISF was employed to study the glycosylation sites of three model glycoproteins, including fetuin, α1-acid glycoprotein and porcine thyroglobulin. The approach was then used to analyze blood serum samples. Y1 ions of glycopeptides in tryptic digests of samples were detected. Y1 ions of glycopeptides with different sialic acid groups are observed at different retention times, representing the various numbers of sialic acid moieties associated with the same peptide backbone sequence. With ISF facilitating the peptide backbone sequencing of glycopeptides, identified peptide sequence coverage was increased. For example, identified fetuin sequence percentage was improved from 39 to 80% in MASCOT database searching compared to conventional CID method. The formation of Y1 ions and oxonium ions in ISF facilitates glycopeptide sequencing and glycan composition identification.
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Affiliation(s)
- Jingfu Zhao
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Ehwang Song
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Rui Zhu
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
| | - Yehia Mechref
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, TX, USA
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158
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Woo CM, Bertozzi CR. Isotope Targeted Glycoproteomics (IsoTaG) to Characterize Intact, Metabolically Labeled Glycopeptides from Complex Proteomes. ACTA ACUST UNITED AC 2016; 8:59-82. [PMID: 26995354 DOI: 10.1002/9780470559277.ch150185] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Protein glycosylation plays many critical roles in biological function and creates the most diversity of all post-translational modifications (PTMs). Glycan structural diversity is directly correlated with difficulty in characterizing the intact glycoproteome by mass spectrometry (MS). In this protocol, we describe a novel mass-independent chemical glycoproteomics platform for characterizing intact, metabolically labeled glycopeptides from complex proteomes, termed Isotope Targeted Glycoproteomics (IsoTaG). To use IsoTaG, cell culture samples are metabolically labeled with an azido- or alkynyl-sugar. Metabolically labeled glycoproteins are then tagged using Click chemistry and enriched with an isotopic recoding biotin probe. Intact glycopeptides are recovered by cleavage of the probe, analyzed with directed MS, and assigned by targeted mass-independent data analysis. The outlined procedure is well defined in cell culture and has been executed with over 15 cell lines.
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Affiliation(s)
- Christina M Woo
- Department of Chemistry, Stanford University, Stanford, California
| | - Carolyn R Bertozzi
- Department of Chemistry, Stanford University, Stanford, California.,Department of Chemical and Systems Biology, Stanford University, Stanford, California.,Howard Hughes Medical Institute, Stanford, California
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159
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Hecht ES, McCord JP, Muddiman DC. A Quantitative Glycomics and Proteomics Combined Purification Strategy. J Vis Exp 2016. [PMID: 27023253 PMCID: PMC4828233 DOI: 10.3791/53735] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
There is a growing desire in the biological and clinical sciences to integrate and correlate multiple classes of biomolecules to unravel biology, define pathways, improve treatment, understand disease, and aid biomarker discovery. N-linked glycosylation is one of the most important and robust post-translational modifications on proteins and regulates critical cell functions such as signaling, adhesion, and enzymatic function. Analytical techniques to purify and analyze N-glycans have remained relatively static over the last decade. While accurate and effective, they commonly require significant expertise and resources. Though some high-throughput purification schemes have been developed, they have yet to find widespread adoption and often rely on the enrichment of glycopeptides. One promising method, developed by Thomas-Oates et al., filter aided N-glycan separation (FANGS), was qualitatively demonstrated on tissues. Herein, we adapted FANGS to plasma and coupled it to the individuality normalization when labeling with glycan hydrazide tags strategy in order to achieve accurate relative quantification by liquid chromatography mass spectrometry and enhanced electrospray ionization. Furthermore, we designed new functionality to the protocol by achieving tandem, shotgun proteomics and glycosylation site analysis on hen plasma. We showed that N-glycans purified on filter and derivatized by hydrophobic hydrazide tags were comparable in terms of abundance and class to those by solid phase extraction (SPE); the latter is considered a gold standard in the field. Importantly, the variability in the two protocols was not statistically different. Proteomic data that was collected in-line with glycomic data had the same depth compared to a standard trypsin digest. Peptide deamidation is minimized in the protocol, limiting non-specific deamidation detected at glycosylation motifs. This allowed for direct glycosylation site analysis, though the protocol can accommodate (18)O site labeling as well. Overall, we demonstrated a new in-line high-throughput, unbiased, filter based protocol for quantitative glycomics and proteomics analysis.
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Affiliation(s)
| | - James P McCord
- Department of Chemistry, North Carolina State University
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160
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Hinneburg H, Stavenhagen K, Schweiger-Hufnagel U, Pengelley S, Jabs W, Seeberger PH, Silva DV, Wuhrer M, Kolarich D. The Art of Destruction: Optimizing Collision Energies in Quadrupole-Time of Flight (Q-TOF) Instruments for Glycopeptide-Based Glycoproteomics. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:507-19. [PMID: 26729457 PMCID: PMC4756043 DOI: 10.1007/s13361-015-1308-6] [Citation(s) in RCA: 102] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 11/06/2015] [Accepted: 11/09/2015] [Indexed: 05/12/2023]
Abstract
In-depth site-specific investigations of protein glycosylation are the basis for understanding the biological function of glycoproteins. Mass spectrometry-based N- and O-glycopeptide analyses enable determination of the glycosylation site, site occupancy, as well as glycan varieties present on a particular site. However, the depth of information is highly dependent on the applied analytical tools, including glycopeptide fragmentation regimes and automated data analysis. Here, we used a small set of synthetic disialylated, biantennary N-glycopeptides to systematically tune Q-TOF instrument parameters towards optimal energy stepping collision induced dissociation (CID) of glycopeptides. A linear dependency of m/z-ratio and optimal fragmentation energy was found, showing that with increasing m/z-ratio, more energy is required for glycopeptide fragmentation. Based on these optimized fragmentation parameters, a method combining lower- and higher-energy CID was developed, allowing the online acquisition of glycan and peptide-specific fragments within a single tandem MS experiment. We validated this method analyzing a set of human immunoglobulins (IgA1+2, sIgA, IgG1+2, IgE, IgD, IgM) as well as bovine fetuin. These optimized fragmentation parameters also enabled software-assisted glycopeptide assignment of both N- and O-glycopeptides including information about the most abundant glycan compositions, peptide sequence and putative structures. Twenty-six out of 30 N-glycopeptides and four out of five O-glycopeptides carrying >110 different glycoforms could be identified by this optimized LC-ESI tandem MS method with minimal user input. The Q-TOF based glycopeptide analysis platform presented here opens the way to a range of different applications in glycoproteomics research as well as biopharmaceutical development and quality control.
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Affiliation(s)
- Hannes Hinneburg
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Kathrin Stavenhagen
- Division of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam, The Netherlands
| | | | | | | | - Peter H Seeberger
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
- Institute of Chemistry and Biochemistry, Freie Universität Berlin, Arnimallee 22, 14195, Berlin, Germany
| | - Daniel Varón Silva
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany
| | - Manfred Wuhrer
- Division of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam, The Netherlands
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Daniel Kolarich
- Department of Biomolecular Systems, Max Planck Institute of Colloids and Interfaces, 14424, Potsdam, Germany.
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161
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Lee CS, Taib NAM, Ashrafzadeh A, Fadzli F, Harun F, Rahmat K, Hoong SM, Abdul-Rahman PS, Hashim OH. Unmasking Heavily O-Glycosylated Serum Proteins Using Perchloric Acid: Identification of Serum Proteoglycan 4 and Protease C1 Inhibitor as Molecular Indicators for Screening of Breast Cancer. PLoS One 2016; 11:e0149551. [PMID: 26890881 PMCID: PMC4758733 DOI: 10.1371/journal.pone.0149551] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 02/02/2016] [Indexed: 12/29/2022] Open
Abstract
Heavily glycosylated mucin glycopeptides such as CA 27.29 and CA 15-3 are currently being used as biomarkers for detection and monitoring of breast cancer. However, they are not well detected at the early stages of the cancer. In the present study, perchloric acid (PCA) was used to enhance detection of mucin-type O-glycosylated proteins in the serum in an attempt to identify new biomarkers for early stage breast cancer. Sensitivity and specificity of an earlier developed sandwich enzyme-linked lectin assay were significantly improved with the use of serum PCA isolates. When a pilot case-control study was performed using the serum PCA isolates of normal participants (n = 105) and patients with stage 0 (n = 31) and stage I (n = 48) breast cancer, higher levels of total O-glycosylated proteins in sera of both groups of early stage breast cancer patients compared to the normal control women were demonstrated. Further analysis by gel-based proteomics detected significant inverse altered abundance of proteoglycan 4 and plasma protease C1 inhibitor in both the early stages of breast cancer patients compared to the controls. Our data suggests that the ratio of serum proteoglycan 4 to protease C1 inhibitor may be used for screening of early breast cancer although this requires further validation in clinically representative populations.
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Affiliation(s)
- Cheng-Siang Lee
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Nur Aishah Mohd Taib
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Ali Ashrafzadeh
- Medical Biotechnology Laboratory, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Farhana Fadzli
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Faizah Harun
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Kartini Rahmat
- Department of Biomedical Imaging, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - See Mee Hoong
- Department of Surgery, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Puteri Shafinaz Abdul-Rahman
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- University of Malaya Centre for Proteomics Research, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
| | - Onn Haji Hashim
- Department of Molecular Medicine, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- University of Malaya Centre for Proteomics Research, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia
- * E-mail:
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162
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Nguyen A, Hulleman JD. Evidence of Alternative Cystatin C Signal Sequence Cleavage Which Is Influenced by the A25T Polymorphism. PLoS One 2016; 11:e0147684. [PMID: 26845025 PMCID: PMC4741414 DOI: 10.1371/journal.pone.0147684] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Accepted: 01/07/2016] [Indexed: 11/19/2022] Open
Abstract
Cystatin C (Cys C) is a small, potent, cysteine protease inhibitor. An Ala25Thr (A25T) polymorphism in Cys C has been associated with both macular degeneration and late-onset Alzheimer's disease. Previously, studies have suggested that this polymorphism may compromise the secretion of Cys C. Interestingly, we found that untagged A25T, A25T tagged C-terminally with FLAG, or A25T FLAG followed by green fluorescent protein (GFP), were all secreted as efficiently from immortalized human cells as their wild-type (WT) counterparts (e.g., 112%, 100%, and 88% of WT levels from HEK-293T cells, respectively). Supporting these observations, WT and A25T Cys C variants also showed similar intracellular steady state levels. Furthermore, A25T Cys C did not activate the unfolded protein response and followed the same canonical endoplasmic reticulum (ER)-Golgi trafficking pathway as WT Cys C. WT Cys C has been shown to undergo signal sequence cleavage between residues Gly26 and Ser27. While the A25T polymorphism did not affect Cys C secretion, we hypothesized that it may alter where the Cys C signal sequence is preferentially cleaved. Under normal conditions, WT and A25T Cys C have the same signal sequence cleavage site after Gly26 (referred to as 'site 2' cleavage). However, in particular circumstances when the residues around site 2 are modified (such as by the presence of an N-terminal FLAG tag immediately after Gly26, or by a Gly26Lys (G26K) mutation), A25T has a significantly higher likelihood than WT Cys C of alternative signal sequence cleavage after Ala20 ('site 1') or even earlier in the Cys C sequence. Overall, our results indicate that the A25T polymorphism does not cause a significant reduction in Cys C secretion, but instead predisposes the protein to be cleaved at an alternative signal sequence cleavage site if site 2 is hindered. Additional N-terminal amino acids resulting from alternative signal sequence cleavage may, in turn, affect the protease inhibition function of Cys C.
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Affiliation(s)
- Annie Nguyen
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
| | - John D. Hulleman
- Department of Ophthalmology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
- Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, United States of America
- * E-mail:
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163
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Chakrabarti A, Halder S, Karmakar S. Erythrocyte and platelet proteomics in hematological disorders. Proteomics Clin Appl 2016; 10:403-14. [PMID: 26611378 DOI: 10.1002/prca.201500080] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 10/26/2015] [Accepted: 11/19/2015] [Indexed: 12/20/2022]
Abstract
Erythrocytes undergo ineffective erythropoesis, hemolysis, and premature eryptosis in sickle cell disease and thalassemia. Abnormal hemoglobin variants associated with hemoglobinopathy lead to vesiculation, membrane instability, and loss of membrane asymmetry with exposal of phosphatidylserine. This potentiates thrombin generation resulting in activation of the coagulation cascade responsible for subclinical phenotypes. Platelet activation also results in the release of microparticles, which express and transfer functional receptors from platelet membrane, playing key roles in vascular reactivity and activation of intracellular signaling pathways. Over the last decade, proteomics had proven to be an important field of research in studies of blood and blood diseases. Blood cells and its fluidic components have been proven to be easy systems for studying differential expressions of proteins in hematological diseases encompassing hemoglobinopathies, different types of anemias, myeloproliferative disorders, and coagulopathies. Proteomic studies of erythrocytes and platelets reported from several groups have highlighted various factors that intersect the signaling networks in these anucleate systems. In this review, we have elaborated on the current scenario of anucleate blood cell proteomes in normal and diseased individuals and the cross-talk between the two major constituent cell types of circulating blood.
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Affiliation(s)
- Abhijit Chakrabarti
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Suchismita Halder
- Crystallography and Molecular Biology Division, Saha Institute of Nuclear Physics, Kolkata, India
| | - Shilpita Karmakar
- Biophysics and Structural Genomics Division, Saha institute of Nuclear Physics, Kolkata, India
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164
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Liquid chromatography-tandem mass spectrometry-based fragmentation analysis of glycopeptides. Glycoconj J 2016; 33:261-72. [PMID: 26780731 DOI: 10.1007/s10719-016-9649-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 12/23/2015] [Accepted: 01/04/2016] [Indexed: 02/08/2023]
Abstract
The use of liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS(n)) for the glycoproteomic characterization of glycopeptides is a growing field of research. The N- and O-glycosylated peptides (N- and O-glycopeptides) analyzed typically originate from protease-digested glycoproteins where many of them are expected to be biomedically important. Examples of LC-MS(2) and MS(3) fragmentation strategies used to pursue glycan structure, peptide identity and attachment-site identification analyses of glycopeptides are described in this review. MS(2) spectra, using the CID and HCD fragmentation techniques of a complex biantennary N-glycopeptide and a core 1 O-glycopeptide, representing two examples of commonly studied glycopeptide types, are presented. A few practical tips for accomplishing glycopeptide analysis using reversed-phase LC-MS(n) shotgun proteomics settings, together with references to the latest glycoproteomic studies, are presented.
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165
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Darula Z, Sarnyai F, Medzihradszky KF. O-glycosylation sites identified from mucin core-1 type glycopeptides from human serum. Glycoconj J 2016; 33:435-45. [PMID: 26729242 DOI: 10.1007/s10719-015-9630-6] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 10/09/2015] [Accepted: 10/14/2015] [Indexed: 10/22/2022]
Abstract
In this work O-linked glycopeptides bearing mucin core-1 type structures were enriched from human serum. Since about 70 % of the O-glycans in human serum bind to the plant lectin Jacalin, we tested a previously successful protocol that combined Jacalin affinity enrichment on the protein- and peptide-level with ERLIC chromatography as a further enrichment step in between, to eliminate the high background of unmodified peptides. In parallel, we developed a simpler and significantly faster new workflow that used two lectins sequentially: wheat germ agglutinin and then Jacalin. The first lectin provides general glycopeptide enrichment, while the second specifically enriches O-linked glycopeptides with Galβ1-3GalNAcα structures. Mass spectrometric analysis of enriched samples showed that the new sample preparation method is more selective and sensitive than the former. Altogether, 52 unique glycosylation sites in 20 proteins were identified in this study.
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Affiliation(s)
- Zsuzsanna Darula
- Laboratory of Proteomics Research, Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biochemistry, Szeged, Hungary.
| | - Farkas Sarnyai
- Laboratory of Proteomics Research, Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biochemistry, Szeged, Hungary
| | - Katalin F Medzihradszky
- Laboratory of Proteomics Research, Biological Research Centre of the Hungarian Academy of Sciences, Institute of Biochemistry, Szeged, Hungary.,Department of Pharmaceutical Chemistry, University of California San Francisco, San Francisco, USA
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166
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Clark DJ, Mei Y, Sun S, Zhang H, Yang AJ, Mao L. Glycoproteomic Approach Identifies KRAS as a Positive Regulator of CREG1 in Non-small Cell Lung Cancer Cells. Am J Cancer Res 2016; 6:65-77. [PMID: 26722374 PMCID: PMC4679355 DOI: 10.7150/thno.12350] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2015] [Accepted: 09/09/2015] [Indexed: 01/05/2023] Open
Abstract
Protein glycosylation plays a fundamental role in a multitude of biological processes, and the associated aberrant expression of glycoproteins in cancer has made them attractive biomarkers and therapeutic targets. In this study, we examined differentially expressed glycoproteins in cell lines derived from three different states of lung tumorigenesis: an immortalized bronchial epithelial cell (HBE) line, a non-small cell lung cancer (NSCLC) cell line harboring a Kirsten rat sarcoma viral oncogene homolog (KRAS) activation mutation and a NSCLC cell line harboring an epidermal growth factor receptor (EGFR) activation deletion. Using a Triple SILAC proteomic quantification strategy paired with hydrazide chemistry N-linked glycopeptide enrichment, we quantified 118 glycopeptides in the three cell lines derived from 82 glycoproteins. Proteomic profiling revealed 27 glycopeptides overexpressed in both NSCLC cell lines, 6 glycopeptides overexpressed only in the EGFR mutant cells and 19 glycopeptides overexpressed only in the KRAS mutant cells. Further investigation of a panel of NSCLC cell lines found that Cellular repressor of E1A-stimulated genes (CREG1) overexpression was closely correlated with KRAS mutation status in NSCLC cells and could be down-regulated by inhibition of KRAS expression. Our results indicate that CREG1 is a down-stream effector of KRAS in a sub-type of NSCLC cells and a novel candidate biomarker or therapeutic target for KRAS mutant NSCLC.
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167
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Wang J, Wang Y, Gao M, Zhang X, Yang P. Facile synthesis of hydrophilic polyamidoxime polymers as a novel solid-phase extraction matrix for sequential characterization of glyco- and phosphoproteomes. Anal Chim Acta 2015; 907:69-76. [PMID: 26803004 DOI: 10.1016/j.aca.2015.12.015] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Revised: 11/02/2015] [Accepted: 12/01/2015] [Indexed: 11/15/2022]
Abstract
Selective enrichment of glycopeptides or phosphopeptides with great biological significance is essential for high-throughput mass spectrometry analysis. However, most previously reported methods only focused on enriching either glycopeptides or phosphopeptides rather than enriching them both. In this work, for the first time, a facile route was developed for the synthesis of polyamidoxime polymers with intrinsic hydrophilic skeletons and attractive long chain structure. The polyamidoxime materials (co-PAN) were synthesized from polyacrylonitrile (PAN) precursor and were successfully used for selective enrichment of glycopeptides. After that, co-PAN as a matrix functionalized with titanium ions (co-PAN@Ti(4+)) could efficiently enrich phosphopeptides. The performances of the polymers for sequential selective and effective enrichment of glycopeptides and phosphopeptides were evaluated with standard peptide mixtures and human serum. Moreover, the efficiency of enrichment of the material was still retained after being used repeatedly. These results demonstrated that the polymers showed great potential in the practical application of proteomics.
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Affiliation(s)
- Jiaxi Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Yanan Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Mingxia Gao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China.
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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168
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Yu J, Schorlemer M, Gomez Toledo A, Pett C, Sihlbom C, Larson G, Westerlind U, Nilsson J. Distinctive MS/MS Fragmentation Pathways of Glycopeptide-Generated Oxonium Ions Provide Evidence of the Glycan Structure. Chemistry 2015; 22:1114-24. [DOI: 10.1002/chem.201503659] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Indexed: 01/14/2023]
Affiliation(s)
- Jin Yu
- Gesellschaft zur Förderung der Analytischen Wissenschaften e.V. ISAS-Leibniz Institute for Analytical Sciences; 44227 Dortmund Germany
| | - Manuel Schorlemer
- Gesellschaft zur Förderung der Analytischen Wissenschaften e.V. ISAS-Leibniz Institute for Analytical Sciences; 44227 Dortmund Germany
| | - Alejandro Gomez Toledo
- Department of Clinical Chemistry and Transfusion Medicine; Institute of Biomedicine; University of Gothenburg; 40530 Gothenburg Sweden
| | - Christian Pett
- Gesellschaft zur Förderung der Analytischen Wissenschaften e.V. ISAS-Leibniz Institute for Analytical Sciences; 44227 Dortmund Germany
| | - Carina Sihlbom
- Proteomics Core Facility; University of Gothenburg; 40530 Gothenburg Sweden
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine; Institute of Biomedicine; University of Gothenburg; 40530 Gothenburg Sweden
| | - Ulrika Westerlind
- Gesellschaft zur Förderung der Analytischen Wissenschaften e.V. ISAS-Leibniz Institute for Analytical Sciences; 44227 Dortmund Germany
| | - Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine; Institute of Biomedicine; University of Gothenburg; 40530 Gothenburg Sweden
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169
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Hoffmann M, Marx K, Reichl U, Wuhrer M, Rapp E. Site-specific O-Glycosylation Analysis of Human Blood Plasma Proteins. Mol Cell Proteomics 2015; 15:624-41. [PMID: 26598643 PMCID: PMC4739677 DOI: 10.1074/mcp.m115.053546] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Indexed: 12/04/2022] Open
Abstract
Site-specific glycosylation analysis is key to investigate structure-function relationships of glycoproteins, e.g. in the context of antigenicity and disease progression. The analysis, though, is quite challenging and time consuming, in particular for O-glycosylated proteins. In consequence, despite their clinical and biopharmaceutical importance, many human blood plasma glycoproteins have not been characterized comprehensively with respect to their O-glycosylation. Here, we report on the site-specific O-glycosylation analysis of human blood plasma glycoproteins. To this end pooled human blood plasma of healthy donors was proteolytically digested using a broad-specific enzyme (Proteinase K), followed by a precipitation step, as well as a glycopeptide enrichment and fractionation step via hydrophilic interaction liquid chromatography, the latter being optimized for intact O-glycopeptides carrying short mucin-type core-1 and -2 O-glycans, which represent the vast majority of O-glycans on human blood plasma proteins. Enriched O-glycopeptide fractions were subjected to mass spectrometric analysis using reversed-phase liquid chromatography coupled online to an ion trap mass spectrometer operated in positive-ion mode. Peptide identity and glycan composition were derived from low-energy collision-induced dissociation fragment spectra acquired in multistage mode. To pinpoint the O-glycosylation sites glycopeptides were fragmented using electron transfer dissociation. Spectra were annotated by database searches as well as manually. Overall, 31 O-glycosylation sites and regions belonging to 22 proteins were identified, the majority being acute-phase proteins. Strikingly, also 11 novel O-glycosylation sites and regions were identified. In total 23 O-glycosylation sites could be pinpointed. Interestingly, the use of Proteinase K proved to be particularly beneficial in this context. The identified O-glycan compositions most probably correspond to mono- and disialylated core-1 mucin-type O-glycans (T-antigen). The developed workflow allows the identification and characterization of the major population of the human blood plasma O-glycoproteome and our results provide new insights, which can help to unravel structure-function relationships. The data were deposited to ProteomeXchange PXD003270.
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Affiliation(s)
- Marcus Hoffmann
- From the ‡Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, 39106 Magdeburg, Germany
| | | | - Udo Reichl
- From the ‡Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, 39106 Magdeburg, Germany; ¶Otto von Guericke University Magdeburg, Chair of Bioprocess Engineering, 39106 Magdeburg, Germany
| | - Manfred Wuhrer
- ‖Center for Proteomics and Metabolomics, Department of Rheumatology, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
| | - Erdmann Rapp
- From the ‡Max Planck Institute for Dynamics of Complex Technical Systems, Bioprocess Engineering, 39106 Magdeburg, Germany; **glyXera GmbH, Leipziger Strasse 44 (Zenit), 39120 Magdeburg, Germany
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170
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Sun S, Shah P, Eshghi ST, Yang W, Trikannad N, Yang S, Chen L, Aiyetan P, Höti N, Zhang Z, Chan DW, Zhang H. Comprehensive analysis of protein glycosylation by solid-phase extraction of N-linked glycans and glycosite-containing peptides. Nat Biotechnol 2015; 34:84-8. [PMID: 26571101 DOI: 10.1038/nbt.3403] [Citation(s) in RCA: 172] [Impact Index Per Article: 19.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 10/13/2015] [Indexed: 01/22/2023]
Abstract
Comprehensive characterization of protein glycosylation is critical for understanding the structure and function of glycoproteins. However, due to the complexity and heterogeneity of glycoprotein conformations, current glycoprotein analyses focus mainly on either the de-glycosylated glycosylation site (glycosite)-containing peptides or the released glycans. Here, we describe a chemoenzymatic method called solid phase extraction of N-linked glycans and glycosite-containing peptides (NGAG) for the comprehensive characterization of glycoproteins that is able to determine glycan heterogeneity for individual glycosites in addition to providing information about the total N-linked glycan, glycosite-containing peptide and glycoprotein content of complex samples. The NGAG method can also be applied to quantitatively detect glycoprotein alterations in total and site-specific glycan occupancies.
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Affiliation(s)
- Shisheng Sun
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Punit Shah
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Shadi Toghi Eshghi
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Weiming Yang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Namita Trikannad
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Shuang Yang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Lijun Chen
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Paul Aiyetan
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Naseruddin Höti
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Zhen Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
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171
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Zhang Y, Yu CY, Song E, Li SC, Mechref Y, Tang H, Liu X. Identification of Glycopeptides with Multiple Hydroxylysine O-Glycosylation Sites by Tandem Mass Spectrometry. J Proteome Res 2015; 14:5099-108. [DOI: 10.1021/acs.jproteome.5b00299] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yanlin Zhang
- Department
of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
- Department
of BioHealth Informatics, Indiana University−Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
| | - Chuan-Yih Yu
- School
of Informatics and Computing, Indiana University Bloomington, Bloomington, Indiana 47405, United States
| | - Ehwang Song
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Shuai Cheng Li
- Department
of Computer Science, City University of Hong Kong, Kowloon, Hong Kong
| | - Yehia Mechref
- Department
of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
| | - Haixu Tang
- School
of Informatics and Computing, Indiana University Bloomington, Bloomington, Indiana 47405, United States
| | - Xiaowen Liu
- Department
of BioHealth Informatics, Indiana University−Purdue University Indianapolis, Indianapolis, Indiana 46202, United States
- Center
for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, Indiana 46202, United States
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172
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Clerc F, Reiding KR, Jansen BC, Kammeijer GSM, Bondt A, Wuhrer M. Human plasma protein N-glycosylation. Glycoconj J 2015; 33:309-43. [PMID: 26555091 PMCID: PMC4891372 DOI: 10.1007/s10719-015-9626-2] [Citation(s) in RCA: 293] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 09/30/2015] [Accepted: 10/05/2015] [Indexed: 01/09/2023]
Abstract
Glycosylation is the most abundant and complex protein modification, and can have a profound structural and functional effect on the conjugate. The oligosaccharide fraction is recognized to be involved in multiple biological processes, and to affect proteins physical properties, and has consequentially been labeled a critical quality attribute of biopharmaceuticals. Additionally, due to recent advances in analytical methods and analysis software, glycosylation is targeted in the search for disease biomarkers for early diagnosis and patient stratification. Biofluids such as saliva, serum or plasma are of great use in this regard, as they are easily accessible and can provide relevant glycosylation information. Thus, as the assessment of protein glycosylation is becoming a major element in clinical and biopharmaceutical research, this review aims to convey the current state of knowledge on the N-glycosylation of the major plasma glycoproteins alpha-1-acid glycoprotein, alpha-1-antitrypsin, alpha-1B-glycoprotein, alpha-2-HS-glycoprotein, alpha-2-macroglobulin, antithrombin-III, apolipoprotein B-100, apolipoprotein D, apolipoprotein F, beta-2-glycoprotein 1, ceruloplasmin, fibrinogen, immunoglobulin (Ig) A, IgG, IgM, haptoglobin, hemopexin, histidine-rich glycoprotein, kininogen-1, serotransferrin, vitronectin, and zinc-alpha-2-glycoprotein. In addition, the less abundant immunoglobulins D and E are included because of their major relevance in immunology and biopharmaceutical research. Where available, the glycosylation is described in a site-specific manner. In the discussion, we put the glycosylation of individual proteins into perspective and speculate how the individual proteins may contribute to a total plasma N-glycosylation profile determined at the released glycan level.
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Affiliation(s)
- Florent Clerc
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Karli R Reiding
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Bas C Jansen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Guinevere S M Kammeijer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands
| | - Albert Bondt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands.,Department of Rheumatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC, Leiden, The Netherlands. .,Division of BioAnalytical Chemistry, VU University Amsterdam, Amsterdam, The Netherlands.
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173
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Yao Y, Huang J, Cheng K, Pan Y, Qin H, Ye M, Zou H. Specific Enrichment of Peptides with N-Terminal Serine/Threonine by a Solid-Phase Capture-Release Approach for Efficient Proteomics Analysis. Anal Chem 2015; 87:11353-60. [DOI: 10.1021/acs.analchem.5b02711] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yating Yao
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Junfeng Huang
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Kai Cheng
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yanbo Pan
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hongqiang Qin
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Mingliang Ye
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
| | - Hanfa Zou
- Key
Laboratory of Separation Science for Analytical Chemistry, Dalian
Institute of Chemical Physics, Chinese Academy of Sciences (CAS), Dalian, 116023, China
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174
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Narimatsu H. Development of M2BPGi: a novel fibrosis serum glyco-biomarker for chronic hepatitis/cirrhosis diagnostics. Expert Rev Proteomics 2015; 12:683-93. [PMID: 26394846 DOI: 10.1586/14789450.2015.1084874] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Many proteins in the living body are glycoproteins, which present glycans linked on their surface. Glycan structures reflect the degree of cell differentiation or canceration and are cell specific. These characteristics are advantageous in the development of various disease biomarkers. Glycoprotein-based biomarkers (glyco-biomarkers) are developed by utilizing the specific changes in the glycan structure on a glycoprotein secreted from the diseased cells of interest. Therefore, quantification of the altered glycan structures is the key to developing a new glyco-biomarker. Glycoscience is a relatively new area of molecular science, and recent advancement of glycotechnologies is remarkable. In the author's institute, new glycoscience technologies have been designed to be efficiently utilized for the development of new diagnostic agents. This paper introduces a strategy for glyco-biomarker development, which was successfully applied in the development of Wisteria floribunda agglutinin-positive Mac-2 binding protein M2BPGi, a liver fibrosis marker now commercially available for clinical use.
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Affiliation(s)
- Hisashi Narimatsu
- a Research Center for Medical Glycoscience (RCMG), National Institute of Advanced Industrial Science and Technology (AIST), Central 2, 1-1-1 Umezono, Tsukuba, Ibaraki, 305-8568, Japan
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175
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Sethi MK, Fanayan S. Using Single Lectins to Enrich Glycoproteins in Conditioned Media. ACTA ACUST UNITED AC 2015; 81:24.6.1-24.6.10. [DOI: 10.1002/0471140864.ps2406s81] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Manveen K. Sethi
- Department of Chemistry and Biomolecular Sciences, Macquarie University Sydney Australia
| | - Susan Fanayan
- Australian School of Advanced Medicine Macquarie University Sydney Australia
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176
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Wang J, Wang Y, Gao M, Zhang X, Yang P. Multilayer Hydrophilic Poly(phenol-formaldehyde resin)-Coated Magnetic Graphene for Boronic Acid Immobilization as a Novel Matrix for Glycoproteome Analysis. ACS APPLIED MATERIALS & INTERFACES 2015; 7:16011-7. [PMID: 26161682 DOI: 10.1021/acsami.5b04295] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Capturing glycopeptides selectively and efficiently from mixed biological samples has always been critical for comprehensive and in-depth glycoproteomics analysis, but the lack of materials with superior capture capacity and high specificity still makes it a challenge. In this work, we introduce a way first to synthesize a novel boronic-acid-functionalized magnetic graphene@phenolic-formaldehyde resin multilayer composites via a facile process. The as-prepared composites gathered excellent characters of large specific surface area and strong magnetic responsiveness of magnetic graphene, biocompatibility of resin, and enhanced affinity properties of boronic acid. Furthermore, the functional graphene composites were shown to have low detection limit (1 fmol) and good selectivity, even when the background nonglycopeptides has a concentration 100 fold higher. Additionally, enrichment efficiency of the composites was still retained after being used repeatedly (at least three times). Better yet, the practical applicability of this approach was evaluated by the enrichment of human serum with a low sample volume of 1 μL. All the results have illustrated that the magG@PF@APB has a great potential in glycoproteome analysis of complex biological samples.
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Affiliation(s)
- Jiaxi Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Yanan Wang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Mingxia Gao
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Xiangmin Zhang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai 200433, China
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177
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Analysis of differentially expressed novel post-translational modifications of plasma apolipoprotein E in Taiwanese females with breast cancer. J Proteomics 2015; 126:252-62. [PMID: 26079612 DOI: 10.1016/j.jprot.2015.05.038] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Revised: 05/07/2015] [Accepted: 05/24/2015] [Indexed: 12/22/2022]
Abstract
APOE ε2 or ε4 alleles being used as indicators of breast cancer risk are controversial in Taiwanese females. We provide a concept for relative comparisons of post-translational modifications (PTMs) of plasma apolipoprotein E (ApoE) between normal controls and breast cancer patients to investigate the association of ApoE with breast cancer risk. APOE polymorphisms (ApoE isoforms) were not assessed in this study. The relative modification ratio (%) of 15 targeted and 21 modified peptides were evaluated by 1D SDS-PAGE, in-gel digestion, and label-free nano-LC/MS to compare normal controls with breast cancer patients. Plasma levels of the ApoE protein did not significantly differ between normal controls and breast cancer patients. Eleven sites with novel PTMs were identified from 7 pairs of differentially expressed targeted and modified peptides according to the relative modification ratio including methylation at the E3 (↑1.45-fold), E7 (↑1.45-fold), E11 (↑1.19-fold), E77 (↑2.02-fold), E87 (↑2.02-fold), and Q98 (↑1.62-fold) residues; dimethylation at the Q187 (↑1.44-fold) residue; dihydroxylation at the R92 (↑1.25-fold), K95 (↑1.25-fold), and R103 (↑1.25-fold) residues; and glycosylation at the S129 (↑1.14-fold) residue. The clustered methylation and dihydroxylation of plasma ApoE proteins may play a role in breast cancer.
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178
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Kim EJ. The Utilities of Chemical Reactions and Molecular Tools for O-GlcNAc Proteomic Studies. Chembiochem 2015; 16:1397-409. [PMID: 26096757 DOI: 10.1002/cbic.201500183] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 11/05/2022]
Abstract
The post-translational modification of nuclear and cytoplasmic proteins with O-linked β-N-acetylglucosamine (O-GlcNAc) is involved in a wide variety of cellular processes and is associated with the pathological progression of chronic diseases. Considering its emerging biological significance, systematic identification, site mapping, and quantification of O-GlcNAc proteins are essential and have led to the development of several approaches for O-GlcNAc protein profiling. This minireview mainly focuses on the various useful chemical reactions and molecular tools with detailed reaction mechanisms widely adopted for O-GlcNAc protein/peptide enrichment and its quantification for comprehensive O-GlcNAc protein profiling.
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Affiliation(s)
- Eun Ju Kim
- Department of Science Education-Chemistry Major, Daegu University, Gyeongsan-si, GyeongBuk 712-714 (Republic of Korea). ,
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179
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Bai H, Fan C, Zhang W, Pan Y, Ma L, Ying W, Wang J, Deng Y, Qian X, Qin W. A pH-responsive soluble polymer-based homogeneous system for fast and highly efficient N-glycoprotein/glycopeptide enrichment and identification by mass spectrometry. Chem Sci 2015; 6:4234-4241. [PMID: 29218189 PMCID: PMC5707513 DOI: 10.1039/c5sc00396b] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2015] [Accepted: 04/21/2015] [Indexed: 12/24/2022] Open
Abstract
A homogeneous reaction system was developed for facile and highly efficient enrichment of biomolecules by exploiting the reversible self-assembly of a stimuli-responsive polymer.
Liquid phase homogeneous reactions using soluble polymer supports have found numerous applications in homogeneous catalysis and organic synthesis because of their advantages of no interface mass transfer limitation and a high conversion rate. However, their application in analytical separation is limited by the inefficient/inconvenient recovery of the target molecules from the extremely complex biological samples. Here, we report a stimuli-responsive polymer system for facile and efficient enrichment of trace amounts of biomolecules from complex biological samples. The soluble polymer supports provide a homogeneous reaction system with fast mass transfer and facilitate interactions between the supports and the target molecules. More importantly, the stimuli-responsive polymers exhibit reversible self-assembly and phase separation under pH variations, which leads to facial sample recovery with a high yield of the target biomolecules. The stimuli-responsive polymer is successfully applied to the enrichment of low abundant N-glycoproteins/glycopeptides, which play crucial roles in various key biological processes in mammals and are closely correlated with the occurrence, progression and metastasis of cancer. N-Glycoprotein is coupled to the stimuli-responsive polymer using the reported hydrazide chemistry with pre-oxidation of the oligosaccharide structure. Highly efficient enrichment of N-glycoproteins/N-glycopeptides with >95% conversion rate is achieved within 1 h, which is eight times faster than using solid/insoluble hydrazide enrichment materials. Mass spectrometry analysis achieves low femtomolar identification sensitivity and obtained 1317 N-glycopeptides corresponding to 458 N-glycoproteins in mouse brain, which is more than twice the amount obtained after enrichment using commercial solid/insoluble materials. These results demonstrate the capability of this “smart” polymer system to combine stimuli-responsive and target-enrichment moieties to achieve improved identification of key biological and disease related biomolecules.
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Affiliation(s)
- Haihong Bai
- National Center for Protein Sciences Beijing , State Key Laboratory of Proteomics , Beijing Proteome Research Center , Tianjin Baodi Hospital , Beijing Institute of Radiation Medicine , China . ; .,School of Life Science and Technology , Beijing Institute of Technology , Beijing , China
| | - Chao Fan
- National Center for Protein Sciences Beijing , State Key Laboratory of Proteomics , Beijing Proteome Research Center , Tianjin Baodi Hospital , Beijing Institute of Radiation Medicine , China . ;
| | - Wanjun Zhang
- National Center for Protein Sciences Beijing , State Key Laboratory of Proteomics , Beijing Proteome Research Center , Tianjin Baodi Hospital , Beijing Institute of Radiation Medicine , China . ;
| | - Yiting Pan
- National Center for Protein Sciences Beijing , State Key Laboratory of Proteomics , Beijing Proteome Research Center , Tianjin Baodi Hospital , Beijing Institute of Radiation Medicine , China . ; .,School of Life Science and Technology , Beijing Institute of Technology , Beijing , China
| | - Lin Ma
- Research Center for Analytical Sciences , College of Sciences , Northeastern University , Shenyang , China
| | - Wantao Ying
- National Center for Protein Sciences Beijing , State Key Laboratory of Proteomics , Beijing Proteome Research Center , Tianjin Baodi Hospital , Beijing Institute of Radiation Medicine , China . ;
| | - Jianhua Wang
- Research Center for Analytical Sciences , College of Sciences , Northeastern University , Shenyang , China
| | - Yulin Deng
- School of Life Science and Technology , Beijing Institute of Technology , Beijing , China
| | - Xiaohong Qian
- National Center for Protein Sciences Beijing , State Key Laboratory of Proteomics , Beijing Proteome Research Center , Tianjin Baodi Hospital , Beijing Institute of Radiation Medicine , China . ;
| | - Weijie Qin
- National Center for Protein Sciences Beijing , State Key Laboratory of Proteomics , Beijing Proteome Research Center , Tianjin Baodi Hospital , Beijing Institute of Radiation Medicine , China . ;
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180
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Huang J, Qin H, Sun Z, Huang G, Mao J, Cheng K, Zhang Z, Wan H, Yao Y, Dong J, Zhu J, Wang F, Ye M, Zou H. A peptide N-terminal protection strategy for comprehensive glycoproteome analysis using hydrazide chemistry based method. Sci Rep 2015; 5:10164. [PMID: 25959593 PMCID: PMC4426672 DOI: 10.1038/srep10164] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2014] [Accepted: 04/01/2015] [Indexed: 01/01/2023] Open
Abstract
Enrichment of glycopeptides by hydrazide chemistry (HC) is a popular method for glycoproteomics analysis. However, possible side reactions of peptide backbones during the glycan oxidation in this method have not been comprehensively studied. Here, we developed a proteomics approach to locate such side reactions and found several types of the side reactions that could seriously compromise the performance of glycoproteomics analysis. Particularly, the HC method failed to identify N-terminal Ser/Thr glycopeptides because the oxidation of vicinal amino alcohol on these peptides generates aldehyde groups and after they are covalently coupled to HC beads, these peptides cannot be released by PNGase F for identification. To overcome this drawback, we apply a peptide N-terminal protection strategy in which primary amine groups on peptides are chemically blocked via dimethyl labeling, thus the vicinal amino alcohols on peptide N-termini are eliminated. Our results showed that this strategy successfully prevented the oxidation of peptide N-termini and significantly improved the coverage of glycoproteome.
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Affiliation(s)
- Junfeng Huang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongqiang Qin
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
| | - Zhen Sun
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Guang Huang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jiawei Mao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, 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, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Zhang Zhang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hao Wan
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- Shanghai Key Laboratory of Functional Materials Chemistry, East China University of Science and Technology
| | - Yating Yao
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Jing Dong
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 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, China
- University of Chinese Academy of Sciences, Beijing, 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, China
| | - Mingliang Ye
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry, National Chromatographic R&A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 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, China
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181
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Harvey DJ. Analysis of carbohydrates and glycoconjugates by matrix-assisted laser desorption/ionization mass spectrometry: an update for 2009-2010. MASS SPECTROMETRY REVIEWS 2015; 34:268-422. [PMID: 24863367 PMCID: PMC7168572 DOI: 10.1002/mas.21411] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2013] [Revised: 07/16/2013] [Accepted: 07/16/2013] [Indexed: 05/07/2023]
Abstract
This review is the sixth 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 2010. General aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, arrays and fragmentation are covered in the first part of the review and applications to various structural typed constitutes the remainder. The main groups of compound that are discussed in this section are oligo and polysaccharides, glycoproteins, glycolipids, glycosides and biopharmaceuticals. Many of these applications are presented in tabular form. Also discussed are medical and industrial applications of the technique, studies of enzyme reactions and applications to chemical synthesis.
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Affiliation(s)
- David J. Harvey
- Department of BiochemistryOxford Glycobiology InstituteUniversity of OxfordOxfordOX1 3QUUK
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182
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Sun N, Zhang X, Deng C. Designed synthesis of MOF-derived magnetic nanoporous carbon materials for selective enrichment of glycans for glycomics analysis. NANOSCALE 2015; 7:6487-6491. [PMID: 25805188 DOI: 10.1039/c5nr00244c] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In this work, magnetic nanoporous carbon (NPC) materials were synthesized by choosing a MOF as a sacrificial template and a carbon precursor. The obtained Co-ZIF-67 materials showed strong magnetic response, high surface area, a uniform size of mesopores and high carbon content. The Co-ZIF-67 materials were successfully applied to glycomics analysis by enriching N-linked glycans in bio-samples with high selectivity and efficiency.
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Affiliation(s)
- Nianrong Sun
- Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433, China.
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183
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Woo CM, Iavarone AT, Spiciarich DR, Palaniappan KK, Bertozzi CR. Isotope-targeted glycoproteomics (IsoTaG): a mass-independent platform for intact N- and O-glycopeptide discovery and analysis. Nat Methods 2015; 12:561-7. [PMID: 25894945 DOI: 10.1038/nmeth.3366] [Citation(s) in RCA: 201] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 02/24/2015] [Indexed: 12/24/2022]
Abstract
Protein glycosylation is a heterogeneous post-translational modification (PTM) that plays an essential role in biological regulation. However, the diversity found in glycoproteins has undermined efforts to describe the intact glycoproteome via mass spectrometry (MS). We present IsoTaG, a mass-independent chemical glycoproteomics platform for characterization of intact, metabolically labeled glycopeptides at the whole-proteome scale. In IsoTaG, metabolic labeling of the glycoproteome is combined with (i) chemical enrichment and isotopic recoding of glycopeptides to select peptides for targeted glycoproteomics using directed MS and (ii) mass-independent assignment of intact glycopeptides. We structurally assigned 32 N-glycopeptides and over 500 intact and fully elaborated O-glycopeptides from 250 proteins across three human cancer cell lines and also discovered unexpected peptide sequence polymorphisms (pSPs). The IsoTaG platform is broadly applicable to the discovery of PTM sites that are amenable to chemical labeling, as well as previously unknown protein isoforms including pSPs.
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Affiliation(s)
- Christina M Woo
- Department of Chemistry, University of California, Berkeley, California, USA
| | - Anthony T Iavarone
- QB3/Chemistry Mass Spectrometry Facility, University of California, Berkeley, California, USA
| | - David R Spiciarich
- Department of Chemistry, University of California, Berkeley, California, USA
| | | | - Carolyn R Bertozzi
- 1] Department of Chemistry, University of California, Berkeley, California, USA. [2] Department of Molecular and Cell Biology, University of California, Berkeley, California, USA. [3] Howard Hughes Medical Institute, Berkeley, California, USA
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184
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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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185
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Ahn YH, Kim JY, Yoo JS. Quantitative mass spectrometric analysis of glycoproteins combined with enrichment methods. MASS SPECTROMETRY REVIEWS 2015; 34:148-65. [PMID: 24889823 PMCID: PMC4340049 DOI: 10.1002/mas.21428] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2013] [Accepted: 11/20/2013] [Indexed: 05/12/2023]
Abstract
Mass spectrometry (MS) has been a core technology for high sensitive and high-throughput analysis of the enriched glycoproteome in aspects of quantitative assays as well as qualitative profiling of glycoproteins. Because it has been widely recognized that aberrant glycosylation in a glycoprotein may involve in progression of a certain disease, the development of efficient analysis tool for the aberrant glycoproteins is very important for deep understanding about pathological function of the glycoprotein and new biomarker development. This review first describes the protein glycosylation-targeting enrichment technologies mainly employing solid-phase extraction methods such as hydrizide-capturing, lectin-specific capturing, and affinity separation techniques based on porous graphitized carbon, hydrophilic interaction chromatography, or immobilized boronic acid. Second, MS-based quantitative analysis strategies coupled with the protein glycosylation-targeting enrichment technologies, by using a label-free MS, stable isotope-labeling, or targeted multiple reaction monitoring (MRM) MS, are summarized with recent published studies.
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Affiliation(s)
- Yeong Hee Ahn
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
| | - Jin Young Kim
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
| | - Jong Shin Yoo
- Division of Mass Spectrometry, Korea Basic Science InstituteCheongwon-Gun, 363-883, Republic of Korea
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186
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Goldman R, Sanda M. Targeted methods for quantitative analysis of protein glycosylation. Proteomics Clin Appl 2015; 9:17-32. [PMID: 25522218 PMCID: PMC5780646 DOI: 10.1002/prca.201400152] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Revised: 11/15/2014] [Accepted: 12/11/2014] [Indexed: 12/17/2022]
Abstract
Quantification of proteins by LC-MS/MS-MRM has become a standard method with broad projected clinical applicability. MRM quantification of protein modifications is, however, far less utilized, especially in the case of glycoproteins. This review summarizes current methods for quantitative analysis of protein glycosylation with a focus on MRM methods. We describe advantages of this quantitative approach, analytical parameters that need to be optimized to achieve reliable measurements, and point out the limitations. Differences between major classes of N- and O-glycopeptides are described and class-specific glycopeptide assays are demonstrated.
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Affiliation(s)
- Radoslav Goldman
- Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, DC, USA
- Department of Biochemistry and Molecular and Cellular Biology, Georgetown University, Washington, DC, USA
| | - Miloslav Sanda
- Department of Oncology, Lombardi Comprehensive Cancer Center, Washington, DC, USA
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187
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Bai X, Li D, Zhu J, Guan Y, Zhang Q, Chi L. From individual proteins to proteomic samples: characterization of O-glycosylation sites in human chorionic gonadotropin and human-plasma proteins. Anal Bioanal Chem 2015; 407:1857-69. [DOI: 10.1007/s00216-014-8439-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2014] [Accepted: 12/19/2014] [Indexed: 12/27/2022]
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188
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Zhang Y, Zhang C, Jiang H, Yang P, Lu H. Fishing the PTM proteome with chemical approaches using functional solid phases. Chem Soc Rev 2015; 44:8260-87. [DOI: 10.1039/c4cs00529e] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Currently available chemical approaches for the enrichment and separation of a PTM proteome using functional solid phases were reviewed.
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Affiliation(s)
- Ying Zhang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
- Key Laboratory of Glycoconjugates Research Ministry of Public Health
| | - Cheng Zhang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
| | - Hucong Jiang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
| | - Pengyuan Yang
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
| | - Haojie Lu
- Department of Chemistry and Institutes of Biomedical Sciences
- Fudan University
- Shanghai 200032
- P. R. China
- Key Laboratory of Glycoconjugates Research Ministry of Public Health
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189
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Wan H, Huang J, Liu Z, Li J, Zhang W, Zou H. A dendrimer-assisted magnetic graphene–silica hydrophilic composite for efficient and selective enrichment of glycopeptides from the complex sample. Chem Commun (Camb) 2015; 51:9391-4. [DOI: 10.1039/c5cc01980j] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
A novel composite demonstrates the efficient hydrophilic enrichment of glycopeptides from the complex sample.
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Affiliation(s)
- Hao Wan
- Shanghai Key Laboratory of Functional Materials Chemistry
- East China University of Science and Technology
- Shanghai 200237
- China
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
| | - Junfeng Huang
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Zhongshan Liu
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Jinan Li
- CAS Key Laboratory of Separation Sciences for Analytical Chemistry
- National Chromatographic R&A Center
- Dalian Institute of Chemical Physics
- Chinese Academy of Sciences (CAS)
- Dalian 116023
| | - Weibing Zhang
- Shanghai Key Laboratory of Functional Materials Chemistry
- East China University of Science and Technology
- Shanghai 200237
- 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 (CAS)
- Dalian 116023
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190
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Wang P, Nilsson J, Brinkmalm G, Larson G, Huang X. Synthesis aided structural determination of amyloid-β(1-15) glycopeptides, new biomarkers for Alzheimer's disease. Chem Commun (Camb) 2014; 50:15067-70. [PMID: 25329175 PMCID: PMC4221429 DOI: 10.1039/c4cc05085a] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Unique tyrosine glycosylated amyloid-β(1-15) glycopeptides were synthesized with well-defined stereochemistry at the glycosidic linkages. Aided by these glycopeptides and tandem mass spectrometry analysis, the naturally existing amyloid-β glycopeptides, isolated from Alzheimer's disease patients, were determined to contain an α-linked N-acetyl galactosamine at the modified tyrosine 10 residue. Glycosylation can significantly impact the properties of amyloid-β as the glycopeptide has much lower affinity for Cu(+) ions.
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Affiliation(s)
- Peng Wang
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East
Lansing, Michigan 48824, USA
| | - Jonas Nilsson
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska
Academy at the University of Gothenburg Sweden
| | - Gunnar Brinkmalm
- Department of Psychiatry and Neurochemistry, Sahlgrenska Academy at the
University of Gothenburg Sweden
| | - Göran Larson
- Department of Clinical Chemistry and Transfusion Medicine, Sahlgrenska
Academy at the University of Gothenburg Sweden
| | - Xuefei Huang
- Department of Chemistry, Michigan State University, 578 S. Shaw Lane, East
Lansing, Michigan 48824, USA
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191
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Yang Z, Halim A, Narimatsu Y, Jitendra Joshi H, Steentoft C, Schjoldager KTBG, Alder Schulz M, Sealover NR, Kayser KJ, Paul Bennett E, Levery SB, Vakhrushev SY, Clausen H. The GalNAc-type O-Glycoproteome of CHO cells characterized by the SimpleCell strategy. Mol Cell Proteomics 2014; 13:3224-35. [PMID: 25092905 PMCID: PMC4256479 DOI: 10.1074/mcp.m114.041541] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2014] [Revised: 07/31/2014] [Indexed: 12/16/2022] Open
Abstract
The Chinese hamster ovary cell (CHO) is the major host cell factory for recombinant production of biological therapeutics primarily because of its "human-like" glycosylation features. CHO is used for production of several O-glycoprotein therapeutics including erythropoietin, coagulation factors, and chimeric receptor IgG1-Fc-fusion proteins, however, some O-glycoproteins are not produced efficiently in CHO. We have previously shown that the capacity for O-glycosylation of proteins can be one limiting parameter for production of active proteins in CHO. Although the capacity of CHO for biosynthesis of glycan structures (glycostructures) on glycoproteins are well established, our knowledge of the capacity of CHO cells for attaching GalNAc-type O-glycans to proteins (glycosites) is minimal. This type of O-glycosylation is one of the most abundant forms of glycosylation, and it is differentially regulated in cells by expression of a subset of homologous polypeptide GalNAc-transferases. Here, we have genetically engineered CHO cells to produce homogeneous truncated O-glycans, so-called SimpleCells, which enabled lectin enrichment of O-glycoproteins and characterization of the O-glycoproteome. We identified 738 O-glycoproteins (1548 O-glycosites) in cell lysates and secretomes providing the first comprehensive insight into the O-glycosylation capacity of CHO (http://glycomics.ku.dk/o-glycoproteome_db/).
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Affiliation(s)
- Zhang Yang
- From the ‡Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; §Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | - Adnan Halim
- From the ‡Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; §Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | - Yoshiki Narimatsu
- From the ‡Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; §Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | - Hiren Jitendra Joshi
- From the ‡Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; §Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | - Catharina Steentoft
- From the ‡Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Katrine Ter-Borch Gram Schjoldager
- From the ‡Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Morten Alder Schulz
- From the ‡Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Natalie R Sealover
- ¶Cell Sciences and Development, SAFC/Sigma-Aldrich, 2909 Laclede Avenue, St. Louis, Missouri 63103
| | - Kevin J Kayser
- ¶Cell Sciences and Development, SAFC/Sigma-Aldrich, 2909 Laclede Avenue, St. Louis, Missouri 63103
| | - Eric Paul Bennett
- From the ‡Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; §Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark
| | - Steven B Levery
- From the ‡Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- From the ‡Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark;
| | - Henrik Clausen
- From the ‡Center for Glycomics, Departments of Cellular and Molecular Medicine and School of Dentistry, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark; §Novo Nordisk Foundation Center for Biosustainability, Danish Technical University, Lyngby, Denmark;
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192
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Saraswat M, Joenväära S, Musante L, Peltoniemi H, Holthofer H, Renkonen R. N-linked (N-) glycoproteomics of urinary exosomes. [Corrected]. Mol Cell Proteomics 2014; 14:263-76. [PMID: 25452312 DOI: 10.1074/mcp.m114.040345] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Epithelial cells lining the urinary tract secrete urinary exosomes (40-100 nm) that can be targeted to specific cells modulating their functionality. One potential targeting mechanism is adhesion between vesicle surface glycoproteins and target cells. This makes the glycopeptide analysis of exosomes important. Exosomes reflect the physiological state of the parent cells; therefore, they are a good source of biomarkers for urological and other diseases. Moreover, the urine collection is easy and noninvasive and urinary exosomes give information about renal and systemic organ systems. Accordingly, multiple studies on proteomic characterization of urinary exosomes in health and disease have been published. However, no systematic analysis of their glycoproteomic profile has been carried out to date, whereas a conserved glycan signature has been found for exosomes from urine and other sources including T cell lines and human milk. Here, we have enriched and identified the N-glycopeptides from these vesicles. These enriched N-glycopeptides were solved for their peptide sequence, glycan composition, structure, and glycosylation site using collision-induced dissociation MS/MS (CID-tandem MS) data interpreted by a publicly available software GlycopeptideId. Released glycans from the same sample was also analyzed with MALDI-MS. We have identified the N-glycoproteome of urinary exosomes. In total 126 N-glycopeptides from 51 N-glycosylation sites belonging to 37 glycoproteins were found in our results. The peptide sequences of these N-glycopeptides were identified unambiguously and their glycan composition (for 125 N-glycopeptides) and structures (for 87 N-glycopeptides) were proposed. A corresponding glycomic analysis with released N-glycans was also performed. We identified 66 unique nonmodified N-glycan compositions and in addition 13 sulfated/phosphorylated glycans were also found. This is the first systematic analysis of N-glycoproteome of urinary exosomes.
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Affiliation(s)
- Mayank Saraswat
- From the ‡Transplantation Laboratory, Haartman Institute, PO Box 21, Haartmaninkatu 3, FI-00014 University of Helsinki, Finland
| | - Sakari Joenväära
- §HUSLAB, Helsinki University Central Hospital, Helsinki, Finland
| | - Luca Musante
- ¶Centre for Bioanalytical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Hannu Peltoniemi
- ‖Applied Numerics Ltd, Nuottapolku 10 A 8, 00330 Helsinki, Finland
| | - Harry Holthofer
- ¶Centre for Bioanalytical Sciences, Dublin City University, Glasnevin, Dublin 9, Ireland
| | - Risto Renkonen
- From the ‡Transplantation Laboratory, Haartman Institute, PO Box 21, Haartmaninkatu 3, FI-00014 University of Helsinki, Finland; §HUSLAB, Helsinki University Central Hospital, Helsinki, Finland;
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193
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van der Post S, Thomsson KA, Hansson GC. Multiple enzyme approach for the characterization of glycan modifications on the C-terminus of the intestinal MUC2mucin. J Proteome Res 2014; 13:6013-23. [PMID: 25406038 PMCID: PMC4261943 DOI: 10.1021/pr500874f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
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The
polymeric mucin MUC2 constitutes the main structural component
of the mucus that covers the colon epithelium. The protein’s
central mucin domain is highly O-glycosylated and binds water to provide
lubrication and prevent dehydration, binds bacteria, and separates
the bacteria from the epithelial cells. Glycosylation outside the
mucin domain is suggested to be important for proper protein folding
and protection against intestinal proteases. However, glycosylation
of these regions of the MUC2 has not been extensively studied. A purified
250 kDa recombinant protein containing the last 981 amino acids of
human MUC2 was produced in CHO-K1 cells. The protein was analyzed
before and after PNGase F treatment, followed by in-gel digestion
with trypsin, chymotrypsin, subtilisin, or Asp-N. Peptides were analyzed
by nLC/MS/MS using a combination of CID, ETD, and HCD fragmentation.
The multiple enzyme approach increased peptide coverage from 36% when
only using trypsin, to 86%. Seventeen of the 18 N-glycan consensus sites were identified as glycosylated. Fifty-six N-glycopeptides covering 10 N-glycan sites,
and 14 O-glycopeptides were sequenced and characterized.
The presented method of protein digestion can be used to gain better
insights into the density and complexity of glycosylation of complex
glycoproteins such as mucins.
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Affiliation(s)
- Sjoerd van der Post
- Department of Medical Biochemistry, University of Gothenburg , Box 440, 405 30 Gothenburg, Sweden
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194
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Halim A, Westerlind U, Pett C, Schorlemer M, Rüetschi U, Brinkmalm G, Sihlbom C, Lengqvist J, Larson G, Nilsson J. Assignment of saccharide identities through analysis of oxonium ion fragmentation profiles in LC-MS/MS of glycopeptides. J Proteome Res 2014; 13:6024-32. [PMID: 25358049 DOI: 10.1021/pr500898r] [Citation(s) in RCA: 105] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Protein glycosylation plays critical roles in the regulation of diverse biological processes, and determination of glycan structure-function relationships is important to better understand these events. However, characterization of glycan and glycopeptide structural isomers remains challenging and often relies on biosynthetic pathways being conserved. In glycoproteomic analysis with liquid chromatography-tandem mass spectrometry (LC-MS/MS) using collision-induced dissociation (CID), saccharide oxonium ions containing N-acetylhexosamine (HexNAc) residues are prominent. Through analysis of beam-type CID spectra and ion trap CID spectra of synthetic and natively derived N- and O-glycopeptides, we found that the fragmentation patterns of oxonium ions characteristically differ between glycopeptides terminally substituted with GalNAcα1-O-, GlcNAcβ1-O-, Galβ3GalNAcα1-O-, Galβ4GlcNAcβ-O-, and Galβ3GlcNAcβ-O- structures. The difference in the oxonium ion fragmentation profiles of such glycopeptides may thus be used to distinguish among these glycan structures and could be of importance in LC-MS/MS-based glycoproteomic studies.
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Affiliation(s)
- Adnan Halim
- Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, ‡Department of Neurochemistry, Institute of Neuroscience and Physiology, University of Gothenburg , SE-41345 Gothenburg, Sweden
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195
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Autelitano F, Loyaux D, Roudières S, Déon C, Guette F, Fabre P, Ping Q, Wang S, Auvergne R, Badarinarayana V, Smith M, Guillemot JC, Goldman SA, Natesan S, Ferrara P, August P. Identification of novel tumor-associated cell surface sialoglycoproteins in human glioblastoma tumors using quantitative proteomics. PLoS One 2014; 9:e110316. [PMID: 25360666 PMCID: PMC4216004 DOI: 10.1371/journal.pone.0110316] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2014] [Accepted: 09/11/2014] [Indexed: 11/21/2022] Open
Abstract
Glioblastoma multiform (GBM) remains clinical indication with significant “unmet medical need”. Innovative new therapy to eliminate residual tumor cells and prevent tumor recurrences is critically needed for this deadly disease. A major challenge of GBM research has been the identification of novel molecular therapeutic targets and accurate diagnostic/prognostic biomarkers. Many of the current clinical therapeutic targets of immunotoxins and ligand-directed toxins for high-grade glioma (HGG) cells are surface sialylated glycoproteins. Therefore, methods that systematically and quantitatively analyze cell surface sialoglycoproteins in human clinical tumor samples would be useful for the identification of potential diagnostic markers and therapeutic targets for malignant gliomas. In this study, we used the bioorthogonal chemical reporter strategy (BOCR) in combination with label-free quantitative mass spectrometry (LFQ-MS) to characterize and accurately quantify the individual cell surface sialoproteome in human GBM tissues, in fetal, adult human astrocytes, and in human neural progenitor cells (NPCs). We identified and quantified a total of 843 proteins, including 801 glycoproteins. Among the 843 proteins, 606 (72%) are known cell surface or secreted glycoproteins, including 156 CD-antigens, all major classes of cell surface receptor proteins, transporters, and adhesion proteins. Our findings identified several known as well as new cell surface antigens whose expression is predominantly restricted to human GBM tumors as confirmed by microarray transcription profiling, quantitative RT-PCR and immunohistochemical staining. This report presents the comprehensive identification of new biomarkers and therapeutic targets for the treatment of malignant gliomas using quantitative sialoglycoproteomics with clinically relevant, patient derived primary glioma cells.
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Affiliation(s)
- François Autelitano
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, Toulouse, France
- * E-mail:
| | - Denis Loyaux
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, Toulouse, France
| | - Sébastien Roudières
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, Toulouse, France
| | - Catherine Déon
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, Toulouse, France
| | - Frédérique Guette
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, Toulouse, France
| | - Philippe Fabre
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, Toulouse, France
| | - Qinggong Ping
- ALS Therapy Development Institute, Cambridge, Massachusetts, United States of America
| | - Su Wang
- Department of Neurology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, New York, United States of America
| | - Romane Auvergne
- Department of Neurology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, New York, United States of America
| | | | - Michael Smith
- Sanofi Tucson Research Center, Oro Valley, Arizona, United States of America
| | | | - Steven A. Goldman
- Department of Neurology, University of Rochester Medical Center, School of Medicine and Dentistry, Rochester, New York, United States of America
| | | | - Pascual Ferrara
- Sanofi-Aventis Recherche & Développement, Centre de Toulouse, Toulouse, France
| | - Paul August
- Sanofi Tucson Research Center, Oro Valley, Arizona, United States of America
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196
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Noborn F, Gomez Toledo A, Sihlbom C, Lengqvist J, Fries E, Kjellén L, Nilsson J, Larson G. Identification of chondroitin sulfate linkage region glycopeptides reveals prohormones as a novel class of proteoglycans. Mol Cell Proteomics 2014; 14:41-9. [PMID: 25326458 DOI: 10.1074/mcp.m114.043703] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Vertebrates produce various chondroitin sulfate proteoglycans (CSPGs) that are important structural components of cartilage and other connective tissues. CSPGs also contribute to the regulation of more specialized processes such as neurogenesis and angiogenesis. Although many aspects of CSPGs have been studied extensively, little is known of where the CS chains are attached on the core proteins and so far, only a limited number of CSPGs have been identified. Obtaining global information on glycan structures and attachment sites would contribute to our understanding of the complex proteoglycan structures and may also assist in assigning CSPG specific functions. In the present work, we have developed a glycoproteomics approach that characterizes CS linkage regions, attachment sites, and identities of core proteins. CSPGs were enriched from human urine and cerebrospinal fluid samples by strong-anion-exchange chromatography, digested with chondroitinase ABC, a specific CS-lyase used to reduce the CS chain lengths and subsequently analyzed by nLC-MS/MS with a novel glycopeptide search algorithm. The protocol enabled the identification of 13 novel CSPGs, in addition to 13 previously established CSPGs, demonstrating that this approach can be routinely used to characterize CSPGs in complex human samples. Surprisingly, five of the identified CSPGs are traditionally defined as prohormones (cholecystokinin, chromogranin A, neuropeptide W, secretogranin-1, and secretogranin-3), typically stored and secreted from granules of endocrine cells. We hypothesized that the CS side chain may influence the assembly and structural organization of secretory granules and applied surface plasmon resonance spectroscopy to show that CS actually promotes the assembly of chromogranin A core proteins in vitro. This activity required mild acidic pH and suggests that the CS-side chains may also influence the self-assembly of chromogranin A in vivo giving a possible explanation to previous observations that chromogranin A has an inherent property to assemble in the acidic milieu of secretory granules.
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Affiliation(s)
- Fredrik Noborn
- From the ‡Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, SE-413 45 Gothenburg, Sweden
| | - Alejandro Gomez Toledo
- From the ‡Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, SE-413 45 Gothenburg, Sweden
| | - Carina Sihlbom
- §Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Box 413, SE-405 30, Sweden
| | - Johan Lengqvist
- §Proteomics Core Facility, Sahlgrenska Academy, University of Gothenburg, Box 413, SE-405 30, Sweden
| | - Erik Fries
- ¶Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Lena Kjellén
- ¶Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23 Uppsala, Sweden
| | - Jonas Nilsson
- From the ‡Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, SE-413 45 Gothenburg, Sweden
| | - Göran Larson
- From the ‡Department of Clinical Chemistry and Transfusion Medicine, Institute of Biomedicine, University of Gothenburg, Sahlgrenska University Hospital, SE-413 45 Gothenburg, Sweden;
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197
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Levery SB, Steentoft C, Halim A, Narimatsu Y, Clausen H, Vakhrushev SY. Advances in mass spectrometry driven O-glycoproteomics. Biochim Biophys Acta Gen Subj 2014; 1850:33-42. [PMID: 25284204 DOI: 10.1016/j.bbagen.2014.09.026] [Citation(s) in RCA: 95] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 09/24/2014] [Accepted: 09/25/2014] [Indexed: 12/13/2022]
Abstract
BACKGROUND Global analyses of proteins and their modifications by mass spectrometry are essential tools in cell biology and biomedical research. Analyses of glycoproteins represent particular challenges and we are only at the beginnings of the glycoproteomic era. Some of the challenges have been overcome with N-glycoproteins and proteome-wide analysis of N-glycosylation sites is accomplishable today but only by sacrificing information of structures at individual glycosites. More recently advances in analysis of O-glycoproteins have been made and proteome-wide analysis of O-glycosylation sites is becoming available as well. SCOPE OF REVIEW Here we discuss the challenges of analysis of O-glycans and new O-glycoproteomics strategies focusing on O-GalNAc and O-Man glycoproteomes. MAJOR CONCLUSIONS A variety of strategies are now available for proteome-wide analysis of O-glycosylation sites enabling functional studies. However, further developments are still needed for complete analysis of glycan structures at individual sites for both N- and O-glycoproteomics strategies. GENERAL SIGNIFICANCE The advances in O-glycoproteomics have led to identification of new biological functions of O-glycosylation and a new understanding of the importance of where O-glycans are positioned on proteins.
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Affiliation(s)
- Steven B Levery
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Catharina Steentoft
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Adnan Halim
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Yoshiki Narimatsu
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Henrik Clausen
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark
| | - Sergey Y Vakhrushev
- Copenhagen Center for Glycomics, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Blegdamsvej 3, DK-2200 Copenhagen N, Denmark.
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198
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Cheng K, Chen R, Seebun D, Ye M, Figeys D, Zou H. Large-scale characterization of intact N-glycopeptides using an automated glycoproteomic method. J Proteomics 2014; 110:145-54. [DOI: 10.1016/j.jprot.2014.08.006] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2014] [Revised: 07/29/2014] [Accepted: 08/12/2014] [Indexed: 02/06/2023]
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199
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Zhang Z, Sun Z, Zhu J, Liu J, Huang G, Ye M, Zou H. High-Throughput Determination of the Site-Specific N-Sialoglycan Occupancy Rates by Differential Oxidation of Glycoproteins Followed with Quantitative Glycoproteomics Analysis. Anal Chem 2014; 86:9830-7. [DOI: 10.1021/ac5024638] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Zhang Zhang
- 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
| | - Zhen Sun
- 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
| | - 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
| | - Guang Huang
- 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
| | - Mingliang Ye
- 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
| | - 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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200
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Song E, Zhu R, Hammoud ZT, Mechref Y. LC-MS/MS quantitation of esophagus disease blood serum glycoproteins by enrichment with hydrazide chemistry and lectin affinity chromatography. J Proteome Res 2014; 13:4808-20. [PMID: 25134008 PMCID: PMC4227547 DOI: 10.1021/pr500570m] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
![]()
Changes
in glycosylation have been shown to have a profound correlation
with development/malignancy in many cancer types. Currently, two major
enrichment techniques have been widely applied in glycoproteomics,
namely, lectin affinity chromatography (LAC)-based and hydrazide chemistry
(HC)-based enrichments. Here we report the LC–MS/MS quantitative
analyses of human blood serum glycoproteins and glycopeptides associated
with esophageal diseases by LAC- and HC-based enrichment. The separate
and complementary qualitative and quantitative data analyses of protein
glycosylation were performed using both enrichment techniques. Chemometric
and statistical evaluations, PCA plots, or ANOVA test, respectively,
were employed to determine and confirm candidate cancer-associated
glycoprotein/glycopeptide biomarkers. Out of 139, 59 common glycoproteins
(42% overlap) were observed in both enrichment techniques. This overlap
is very similar to previously published studies. The quantitation
and evaluation of significantly changed glycoproteins/glycopeptides
are complementary between LAC and HC enrichments. LC–ESI–MS/MS
analyses indicated that 7 glycoproteins enriched by LAC and 11 glycoproteins
enriched by HC showed significantly different abundances between disease-free
and disease cohorts. Multiple reaction monitoring quantitation resulted
in 13 glycopeptides by LAC enrichment and 10 glycosylation sites by
HC enrichment to be statistically different among disease cohorts.
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Affiliation(s)
- Ehwang Song
- Department of Chemistry and Biochemistry, Texas Tech University , Memorial Circle & Boston, Lubbock, Texas 79409, United States
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