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Molnarova K, Cokrtova K, Tomnikova A, Krizek T, Kozlik P. Liquid chromatography and capillary electrophoresis in glycomic and glycoproteomic analysis. MONATSHEFTE FUR CHEMIE 2022; 153:659-686. [PMID: 35754790 PMCID: PMC9212196 DOI: 10.1007/s00706-022-02938-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Accepted: 05/29/2022] [Indexed: 11/28/2022]
Abstract
Glycosylation is one of the most significant and abundant post-translational modifications in cells. Glycomic and glycoproteomic analyses involve the characterization of oligosaccharides (glycans) conjugated to proteins. Glycomic and glycoproteomic analysis is highly challenging because of the large diversity of structures, low abundance, site-specific heterogeneity, and poor ionization efficiency of glycans and glycopeptides in mass spectrometry (MS). MS is a key tool for characterization of glycans and glycopeptides. However, MS alone does not always provide full structural and quantitative information for many reasons, and thus MS is combined with some separation technique. This review focuses on the role of separation techniques used in glycomic and glycoproteomic analyses, liquid chromatography and capillary electrophoresis. The most important separation conditions and results are presented and discussed. Graphical abstract
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Affiliation(s)
- Katarina Molnarova
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Katerina Cokrtova
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Alice Tomnikova
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tomas Krizek
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
| | - Petr Kozlik
- Department of Analytical Chemistry, Faculty of Science, Charles University, Prague, Czech Republic
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Jennings ME, Silveira JR, Treier KM, Tracy PB, Matthews DE. Total Retention Liquid Chromatography-Mass Spectrometry to Achieve Maximum Protein Sequence Coverage. Anal Chem 2021; 93:5054-5060. [PMID: 33724001 DOI: 10.1021/acs.analchem.0c04292] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Peptide identification by liquid chromatography-mass spectrometry (LC-MS) requires retention and elution of peptides from the LC column. Although medium and hydrophobic peptides are readily retained by the C18 columns that are commonly used in proteomics, short and hydrophilic peptides are not retained nor measured by MS due to their elution in the void volume after sample injection. These nonretained peptides can possess important post-translational modifications, such as glycosylation or phosphorylation. We describe a total retention LC-MS method that employs a reverse phase C18 column and porous graphitic carbon (PGC) column to retain both hydrophobic and hydrophilic peptides for LC-MS analysis. Our setup uses a single valve with a trapping column and two LC pumps run at low microliter/minute flow rates to deliver separate gradients to parallel capillary C18 and PGC columns. Our capillary LC system balances the need for high sensitivity with ease of implementation as compared to other 2D LC systems that use nanocolumns with multiple trapping columns and multiport valves. We demonstrate the utility of the method identifying hydrophilic peptides that went undetected when only a C18 nanocolumn was used. These missed hydrophilic peptides include tripeptides and N-glycosylated species.
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Petrović T, Trbojević-Akmačić I. Lectin and Liquid Chromatography-Based Methods for Immunoglobulin (G) Glycosylation Analysis. EXPERIENTIA SUPPLEMENTUM (2012) 2021; 112:29-72. [PMID: 34687007 DOI: 10.1007/978-3-030-76912-3_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Immunoglobulin (Ig) glycosylation has been shown to dramatically affect its structure and effector functions. Ig glycosylation changes have been associated with different diseases and show a promising biomarker potential for diagnosis and prognosis of disease advancement. On the other hand, therapeutic biomolecules based on structural and functional features of Igs demand stringent quality control during the production process to ensure their safety and efficacy. Liquid chromatography (LC) and lectin-based methods are routinely used in Ig glycosylation analysis complementary to other analytical methods, e.g., mass spectrometry and capillary electrophoresis. This chapter covers analytical approaches based on LC and lectins used in low- and high-throughput N- and O-glycosylation analysis of Igs, with the focus on immunoglobulin G (IgG) applications. General principles and practical examples of the most often used LC methods for Ig purification are described, together with typical workflows for N- and O-glycan analysis on the level of free glycans, glycopeptides, subunits, or intact Igs. Lectin chromatography is a historical approach for the analysis of lectin-carbohydrate interactions and glycoprotein purification but is still being used as a valuable tool in Igs purification and glycan analysis. On the other hand, lectin microarrays have found their application in the rapid screening of glycan profiles on intact proteins.
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Affiliation(s)
- Tea Petrović
- Glycoscience Research Laboratory, Genos Ltd., Zagreb, Croatia
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Integrated omics dissection of proteome dynamics during cardiac remodeling. Nat Commun 2018; 9:120. [PMID: 29317621 PMCID: PMC5760723 DOI: 10.1038/s41467-017-02467-3] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Accepted: 11/29/2017] [Indexed: 11/08/2022] Open
Abstract
Transcript abundance and protein abundance show modest correlation in many biological models, but how this impacts disease signature discovery in omics experiments is rarely explored. Here we report an integrated omics approach, incorporating measurements of transcript abundance, protein abundance, and protein turnover to map the landscape of proteome remodeling in a mouse model of pathological cardiac hypertrophy. Analyzing the hypertrophy signatures that are reproducibly discovered from each omics data type across six genetic strains of mice, we find that the integration of transcript abundance, protein abundance, and protein turnover data leads to 75% gain in discovered disease gene candidates. Moreover, the inclusion of protein turnover measurements allows discovery of post-transcriptional regulations across diverse pathways, and implicates distinct disease proteins not found in steady-state transcript and protein abundance data. Our results suggest that multi-omics investigations of proteome dynamics provide important insights into disease pathogenesis in vivo.
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Szklanna PB, Wynne K, Nolan M, Egan K, Áinle FN, Maguire PB. Comparative proteomic analysis of trophoblast cell models reveals their differential phenotypes, potential uses, and limitations. Proteomics 2017; 17:e1700037. [PMID: 28317260 DOI: 10.1002/pmic.201700037] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Revised: 03/09/2017] [Accepted: 03/15/2017] [Indexed: 12/13/2022]
Abstract
Trophoblastic cell lines are widely used in in vitro studies of placental function as a surrogate for primary trophoblasts. To date, no reference proteomics dataset exists to directly compare the shared and unique characteristics of these cells. Here, we performed comparative proteomic profiling of the BeWo and HTR8/SVneo cell lines using label-free quantitative MS. A total of 1557 proteins were identified, which included 338 uniquely attributed to BeWo cells, and a further 304 specifically identified in HTR8/SVneo cells. Raw data are available via ProteomeXchange, identifier PDX005045. Of the 915 proteins expressed by both cell lines, 105 were of higher abundance in BeWo cells, while 199 proteins had a significantly higher expression in HTR8/SVneo cells. Comparative GO of unique and upregulated proteins revealed principal differences in cell junction/adhesion, catenin complex, spindle and microtubule associated complex, as well as cell differentiation. Our data indicate that BeWo cells express an epithelial proteome more characteristic of villous trophoblasts, whereas HTR8/SVneo cells embrace a mesenchymal phenotype, more characteristic of extravillous trophoblasts. This novel comparative proteomic profiling of these trophoblastic cell lines provides a useful platform for future investigations of placental function.
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Affiliation(s)
- Paulina B Szklanna
- UCD Conway Institute SPHERE Research Group, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Kieran Wynne
- UCD Conway Institute Proteomics Core, University College Dublin, Belfield, Dublin, Ireland
| | - Marie Nolan
- UCD Conway Institute SPHERE Research Group, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
| | - Karl Egan
- UCD Conway Institute SPHERE Research Group, School of Medicine and Medical Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - Fionnuala Ní Áinle
- UCD Conway Institute SPHERE Research Group, School of Medicine and Medical Sciences, University College Dublin, Belfield, Dublin, Ireland
| | - Patricia B Maguire
- UCD Conway Institute SPHERE Research Group, School of Biomolecular and Biomedical Science, University College Dublin, Belfield, Dublin, Ireland
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Abstract
Protein glycosylation is one of the most important posttranslational modifications. Numerous biological functions are related to protein glycosylation. However, analytical challenges remain in the glycoprotein analysis. To overcome the challenges associated with glycoprotein analysis, many analytical techniques were developed in recent years. Enrichment methods were used to improve the sensitivity of detection, while HPLC and mass spectrometry methods were developed to facilitate the separation of glycopeptides/proteins and enhance detection, respectively. Fragmentation techniques applied in modern mass spectrometers allow the structural interpretation of glycopeptides/proteins, while automated software tools started replacing manual processing to improve the reliability and throughput of the analysis. In this chapter, the current methodologies of glycoprotein analysis were discussed. Multiple analytical techniques are compared, and advantages and disadvantages of each technique are highlighted.
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Stine KJ. Application of Porous Materials to Carbohydrate Chemistry and Glycoscience. Adv Carbohydr Chem Biochem 2017; 74:61-136. [PMID: 29173727 DOI: 10.1016/bs.accb.2017.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
There is a growing interest in using a range of porous materials to meet research needs in carbohydrate chemistry and glycoscience in general. Among the applications of porous materials reviewed in this chapter, enrichment of glycans from biological samples prior to separation and analysis by mass spectrometry is a major emphasis. Porous materials offer high surface area, adjustable pore sizes, and tunable surface chemistry for interacting with glycans, by boronate affinity, hydrophilic interactions, molecular imprinting, and polar interactions. Among the materials covered in this review are mesoporous silica and related materials, porous graphitic carbon, mesoporous carbon, porous polymers, and nanoporous gold. In some applications, glycans are enzymatically or chemically released from glycoproteins or glycopeptides, and the porous materials have the advantage of size selectivity admitting only the glycans into the pores and excluding proteins. Immobilization of lectins onto porous materials of suitable pore size allows for the use of lectin-carbohydrate interactions in capture or separation of glycoproteins. Porous material surfaces modified with carbohydrates can be used for the selective capture of lectins. Controlled release of therapeutics from porous materials mediated by glycans has been reported, and so has therapeutic targeting using carbohydrate-modified porous particles. Additional applications of porous materials in glycoscience include their use in the supported synthesis of oligosaccharides and in the development of biosensors for glycans.
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Lau E, Cao Q, Ng DCM, Bleakley BJ, Dincer TU, Bot BM, Wang D, Liem DA, Lam MPY, Ge J, Ping P. A large dataset of protein dynamics in the mammalian heart proteome. Sci Data 2016; 3:160015. [PMID: 26977904 PMCID: PMC4792174 DOI: 10.1038/sdata.2016.15] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/12/2016] [Indexed: 01/03/2023] Open
Abstract
Protein stability is a major regulatory principle of protein function and cellular homeostasis. Despite limited understanding on mechanisms, disruption of protein turnover is widely implicated in diverse pathologies from heart failure to neurodegenerations. Information on global protein dynamics therefore has the potential to expand the depth and scope of disease phenotyping and therapeutic strategies. Using an integrated platform of metabolic labeling, high-resolution mass spectrometry and computational analysis, we report here a comprehensive dataset of the in vivo half-life of 3,228 and the expression of 8,064 cardiac proteins, quantified under healthy and hypertrophic conditions across six mouse genetic strains commonly employed in biomedical research. We anticipate these data will aid in understanding key mitochondrial and metabolic pathways in heart diseases, and further serve as a reference for methodology development in dynamics studies in multiple organ systems.
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Affiliation(s)
- Edward Lau
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Quan Cao
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Dominic C M Ng
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Brian J Bleakley
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - T Umut Dincer
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Bioinformatics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Brian M Bot
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Sage Bionetworks, Seattle, Washignton 98109, USA
| | - Ding Wang
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - David A Liem
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Maggie P Y Lam
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Bioinformatics, University of California at Los Angeles, Los Angeles, California 90095, USA
| | - Junbo Ge
- Department of Shanghai Institute of Cardiovascular Diseases, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Peipei Ping
- The NIH Big Data to Knowledge (BD2K) Center of Excellence in Biomedical Computing at UCLA, Los Angeles, California 90095, USA.,Department of Physiology, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Bioinformatics, University of California at Los Angeles, Los Angeles, California 90095, USA.,Department of Medicine,University of California at Los Angeles, Los Angeles, California 90095, USA
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Lee CL, Lam KKW, Vijayan M, Koistinen H, Seppala M, Ng EHY, Yeung WSB, Chiu PCN. The Pleiotropic Effect of Glycodelin-A in Early Pregnancy. Am J Reprod Immunol 2016; 75:290-7. [DOI: 10.1111/aji.12471] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 12/02/2015] [Indexed: 11/28/2022] Open
Affiliation(s)
- Cheuk-Lun Lee
- Department of Obstetrics and Gynaecology; LKS Faculty of Medicine; The University of Hong Kong; Hong Kong Hong Kong
- Centre for Reproduction, Development and Growth; LKS Faculty of Medicine; The University of Hong Kong; Hong Kong Hong Kong
- Shenzhen Key Laboratory of Fertility Regulation; Department of Obstetrics and Gynecology; The University of Hong Kong-Shenzhen Hospital; Hong Kong Hong Kong
| | - Kevin K. W. Lam
- Department of Obstetrics and Gynaecology; LKS Faculty of Medicine; The University of Hong Kong; Hong Kong Hong Kong
- Shenzhen Key Laboratory of Fertility Regulation; Department of Obstetrics and Gynecology; The University of Hong Kong-Shenzhen Hospital; Hong Kong Hong Kong
| | - Madhavi Vijayan
- Department of Obstetrics and Gynaecology; LKS Faculty of Medicine; The University of Hong Kong; Hong Kong Hong Kong
| | - Hannu Koistinen
- Department of Clinical Chemistry and Obstetrics and Gynecology; University of Helsinki and Helsinki University Central Hospital; Helsinki Finland
| | - Markku Seppala
- Department of Clinical Chemistry and Obstetrics and Gynecology; University of Helsinki and Helsinki University Central Hospital; Helsinki Finland
| | - Ernest H. Y. Ng
- Department of Obstetrics and Gynaecology; LKS Faculty of Medicine; The University of Hong Kong; Hong Kong Hong Kong
- Centre for Reproduction, Development and Growth; LKS Faculty of Medicine; The University of Hong Kong; Hong Kong Hong Kong
- Shenzhen Key Laboratory of Fertility Regulation; Department of Obstetrics and Gynecology; The University of Hong Kong-Shenzhen Hospital; Hong Kong Hong Kong
| | - William S. B. Yeung
- Department of Obstetrics and Gynaecology; LKS Faculty of Medicine; The University of Hong Kong; Hong Kong Hong Kong
- Centre for Reproduction, Development and Growth; LKS Faculty of Medicine; The University of Hong Kong; Hong Kong Hong Kong
- Shenzhen Key Laboratory of Fertility Regulation; Department of Obstetrics and Gynecology; The University of Hong Kong-Shenzhen Hospital; Hong Kong Hong Kong
| | - Philip C. N. Chiu
- Department of Obstetrics and Gynaecology; LKS Faculty of Medicine; The University of Hong Kong; Hong Kong Hong Kong
- Centre for Reproduction, Development and Growth; LKS Faculty of Medicine; The University of Hong Kong; Hong Kong Hong Kong
- Shenzhen Key Laboratory of Fertility Regulation; Department of Obstetrics and Gynecology; The University of Hong Kong-Shenzhen Hospital; Hong Kong Hong Kong
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Stavenhagen K, Plomp R, Wuhrer M. Site-Specific Protein N- and O-Glycosylation Analysis by a C18-Porous Graphitized Carbon–Liquid Chromatography-Electrospray Ionization Mass Spectrometry Approach Using Pronase Treated Glycopeptides. Anal Chem 2015; 87:11691-9. [DOI: 10.1021/acs.analchem.5b02366] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Kathrin Stavenhagen
- Division
of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
| | - Rosina Plomp
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
| | - Manfred Wuhrer
- Division
of BioAnalytical Chemistry, VU University Amsterdam, De Boelelaan
1083, 1081 HV Amsterdam, The Netherlands
- Center
for Proteomics and Metabolomics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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Zhao Y, Law HC, Zhang Z, Lam HC, Quan Q, Li G, Chu IK. Online coupling of hydrophilic interaction/strong cation exchange/reversed-phase liquid chromatography with porous graphitic carbon liquid chromatography for simultaneous proteomics and N-glycomics analysis. J Chromatogr A 2015; 1415:57-66. [DOI: 10.1016/j.chroma.2015.08.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2014] [Revised: 07/20/2015] [Accepted: 08/10/2015] [Indexed: 11/25/2022]
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12
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Pagel O, Loroch S, Sickmann A, Zahedi RP. Current strategies and findings in clinically relevant post-translational modification-specific proteomics. Expert Rev Proteomics 2015; 12:235-53. [PMID: 25955281 PMCID: PMC4487610 DOI: 10.1586/14789450.2015.1042867] [Citation(s) in RCA: 122] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Mass spectrometry-based proteomics has considerably extended our knowledge about the occurrence and dynamics of protein post-translational modifications (PTMs). So far, quantitative proteomics has been mainly used to study PTM regulation in cell culture models, providing new insights into the role of aberrant PTM patterns in human disease. However, continuous technological and methodical developments have paved the way for an increasing number of PTM-specific proteomic studies using clinical samples, often limited in sample amount. Thus, quantitative proteomics holds a great potential to discover, validate and accurately quantify biomarkers in body fluids and primary tissues. A major effort will be to improve the complete integration of robust but sensitive proteomics technology to clinical environments. Here, we discuss PTMs that are relevant for clinical research, with a focus on phosphorylation, glycosylation and proteolytic cleavage; furthermore, we give an overview on the current developments and novel findings in mass spectrometry-based PTM research.
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Affiliation(s)
- Oliver Pagel
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
| | - Stefan Loroch
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
| | | | - René P Zahedi
- Leibniz-Institut für Analytische Wissenschaften – ISAS – e.V., Otto-Hahn-Straße 6b, 44227 Dortmund, Germany
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Wang D, Liem DA, Lau E, Ng DCM, Bleakley BJ, Cadeiras M, Deng MC, Lam MPY, Ping P. Characterization of human plasma proteome dynamics using deuterium oxide. Proteomics Clin Appl 2015; 8:610-9. [PMID: 24946186 DOI: 10.1002/prca.201400038] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2014] [Revised: 05/23/2014] [Accepted: 06/11/2014] [Indexed: 11/06/2022]
Abstract
PURPOSE High-throughput quantification of human protein turnover via in vivo administration of deuterium oxide ((2) H2 O) is a powerful new approach to examine potential disease mechanisms. Its immediate clinical translation is contingent upon characterizations of the safety and hemodynamic effects of in vivo administration of (2) H2 O to human subjects. EXPERIMENTAL DESIGN We recruited ten healthy human subjects with a broad demographic variety to evaluate the safety, feasibility, efficacy, and reproducibility of (2) H2 O intake for studying protein dynamics. We designed a protocol where each subject orally consumed weight-adjusted doses of 70% (2) H2 O daily for 14 days to enrich body water and proteins with deuterium. Plasma proteome dynamics was measured using a high-resolution MS method we recently developed. RESULTS This protocol was successfully applied in ten human subjects to characterize the endogenous turnover rates of 542 human plasma proteins, the largest such human dataset to-date. Throughout the study, we did not detect physiological effects or signs of discomfort from (2) H2 O consumption. CONCLUSIONS AND CLINICAL RELEVANCE Our investigation supports the utility of a (2) H2 O intake protocol that is safe, accessible, and effective for clinical investigations of large-scale human protein turnover dynamics. This workflow shows promising clinical translational value for examining plasma protein dynamics in human diseases.
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Affiliation(s)
- Ding Wang
- The NHLBI Proteomics Center at UCLA, Los Angeles, CA, USA; Department of Physiology, David Geffen School of Medicine at UCLA, Los Angeles, CA, USA
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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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15
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Marriott AS, António C, Thomas-Oates J. Application of Carbonaceous Materials in Separation Science. POROUS CARBON MATERIALS FROM SUSTAINABLE PRECURSORS 2015. [DOI: 10.1039/9781782622277-00103] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Porous carbons in the separation sciences occupy an important niche owing to their unique retention characteristics, chemical stability and the ability to control pore structure through template strategies. However, these same synthetic processes utilise oil-based carbonising resins and high temperature, energy-intensive pyrolysis steps to ensure the carbon product has pore-size regularity, minimal micropore content and homogeneous surface chemistry. This chapter will primarily focus on the development of porous carbons for application as chromatographic stationary phases. Discussion will cover the unique characteristics of the porous carbon retention mechanism and its application in separating a broad range of analyte classes. The chapter then moves on to describe the current disadvantages in the manufacture of commercially available carbon phase and then highlight recent efforts aimed at the development of alternative porous carbon stationary phases derived from sustainable carbon precursors.
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Affiliation(s)
| | - Carla António
- Plant Metabolomics Laboratory, Instituto de Tecnologia Química e Biológica António Xavier-Universidade Nova de Lisboa (ITQB-UNL) Av. República 2780-157 Oeiras Portugal
| | - Jane Thomas-Oates
- Department of Chemistry, University of York York YO10 5DD UK
- Centre of Excellence in Mass Spectrometry, University of York York YO10 5DD UK
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16
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Zhao Y, Szeto SSW, Kong RPW, Law CH, Li G, Quan Q, Zhang Z, Wang Y, Chu IK. Online two-dimensional porous graphitic carbon/reversed phase liquid chromatography platform applied to shotgun proteomics and glycoproteomics. Anal Chem 2014; 86:12172-9. [PMID: 25393709 DOI: 10.1021/ac503254t] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
A novel fully automatable two-dimensional liquid chromatography (2DLC) platform has been integrated into a modified commercial off-the-shelf LC instrument, incorporating porous graphitic carbon (PGC) separation and conventional low-pH reversed-phase (RP) separation for both proteomics and N-glycomics analyses; the dual-trap column configuration of this platform offers desirable high-throughput analyses with almost no idle time, in addition to a miniaturized setup and simplified operation. The total run time per analysis was only 19 h when using eight PGC fractions for unattended large-scale qualitative and quantitative proteomic analyses; the identification of 2678 nonredundant proteins and 11,984 unique peptides provided one of the most comprehensive proteome data sets for primary cerebellar granule neurons (CGNs). The effect of pH on the PGC column was investigated for the first time to improve the hydrophobic peptide coverage; the performance of the optimized system was first benchmarked using tryptic digests of Saccharomyces cerevisiae cell lysates and then evaluated through duplicate analyses of Macaca fascicularis cerebral cortex lysates using isobaric tags for relative and absolute quantitation (iTRAQ) technology. An additional plug-and-play PGC module functioned in a complementary manner to recover unretained hydrophilic solutes from the low-pH RP column; synchronization of the fractionations between the PGC-RP system and the PGC module facilitated simultaneous analyses of hydrophobic and hydrophilic compounds from a single sample injection event. This methodology was applied to perform, for the first time, detailed glycomics analyses of Macaca fascicularis plasma, resulting in the identification of a total 130 N-glycosylated plasma proteins, 705 N-glycopeptides, and 254 N-glycosylation sites.
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Affiliation(s)
- Yun Zhao
- Department of Chemistry, The University of Hong Kong , Hong Kong, China
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Sun B, Hood L. Protein-centric N-glycoproteomics analysis of membrane and plasma membrane proteins. J Proteome Res 2014; 13:2705-14. [PMID: 24754784 PMCID: PMC4053080 DOI: 10.1021/pr500187g] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
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The advent of proteomics technology
has transformed our understanding
of biological membranes. The challenges for studying membrane proteins
have inspired the development of many analytical and bioanalytical
tools, and the techniques of glycoproteomics have emerged as an effective
means to enrich and characterize membrane and plasma-membrane proteomes.
This Review summarizes the development of various glycoproteomics
techniques to overcome the hurdles formed by the unique structures
and behaviors of membrane proteins with a focus on N-glycoproteomics.
Example contributions of N-glycoproteomics to the understanding of
membrane biology are provided, and the areas that require future technical
breakthroughs are discussed.
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Affiliation(s)
- Bingyun Sun
- Department of Chemistry, Simon Fraser University , 8888 University Drive, Burnaby, British Columbia V5A1S6, Canada
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Liu J, Wang F, Zhu J, Mao J, Liu Z, Cheng K, Qin H, Zou H. Highly efficient N-glycoproteomic sample preparation by combining C18 and graphitized carbon adsorbents. Anal Bioanal Chem 2014; 406:3103-9. [DOI: 10.1007/s00216-014-7716-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Revised: 02/17/2014] [Accepted: 02/20/2014] [Indexed: 01/07/2023]
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Lee CL, Lam MPY, Lam KKW, Leung CON, Pang RTK, Chu IK, Wan THL, Chai J, Yeung WSB, Chiu PCN. Identification of CD147 (basigin) as a mediator of trophoblast functions. Hum Reprod 2013; 28:2920-9. [PMID: 24014600 DOI: 10.1093/humrep/det355] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
STUDY QUESTION Does CD147 regulate trophoblast functions in vitro? SUMMARY ANSWER CD147 exists as a receptor complex on human trophoblast and regulates the implantation, invasion and differentiation of trophoblast. WHAT IS KNOWN ALREADY CD147 is a membrane protein implicated in a variety of physiological and pathological conditions due to its regulation of cell-cell recognition, cell differentiation and tissue remodeling. Reduced placental CD147 expression is associated with pre-eclampsia, but the mechanism of actions remains unclear. STUDY DESIGN, SIZE, DURATION A loss of function approach or functional blocking antibody was used to study the function of CD147 in primary human cytotrophoblasts isolated from first trimester termination of pregnancy and/or in the BeWo cell line, which possesses characteristics of human cytotrophoblasts. PARTICIPANTS/MATERIALS, SETTING METHODS CD147 expression was analyzed by immunofluorescence staining and western blotting. CD147-associated protein complex on plasma membrane were separated by blue native gel electrophoresis and identified by reversed-phase liquid chromatography coupled with quadrupole time-of-flight hybrid mass spectrometer. Cell proliferation and invasion were determined by fluorometric cell proliferation assays and transwell invasion assays, respectively. Matrix metalloproteinases (MMPs) and urokinase plasminogen activator (uPA) activities were measured by gelatin gel zymography and uPA assay kits, respectively. Cell migration was determined by wound-healing assays. Cell fusion was analyzed by immunocytochemistry staining of E-cadherin and 4',6-diamidino-2-phenylindole. The transcripts of matrix proteinases and trophoblast lineage markers were measured by quantitative PCR. Extracellular signal-regulated kinase (ERK) activation was analyzed by western blot using antibodies against ERKs. MAIN RESULTS AND THE ROLE OF CHANCE CD147 exists as protein complexes on the plasma membrane of primary human cytotrophoblasts and BeWo cells. Several known CD147-interacting partners, including integrin β1 and monocarboxylate transporter-1, were identified. Suppression of CD147 by siRNA significantly (P < 0.05) reduced trophoblast-endometrial cell interaction, cell invasion, syncytialization, differentiation and ERK activation of BeWo cells. Consistently, anti-CD147 functional blocking antibody suppressed the invasiveness of primary human cytotrophoblasts. The reduced invasiveness was probably due to the restrained (P < 0.05) enzyme activities of MMP-2, MMP-9 and uPA. LIMITATIONS, REASONS FOR CAUTION Most of the above findings are based on BeWo cell lines. These results need to be confirmed with human first trimester primary cytotrophoblast. WIDER IMPLICATIONS OF THE FINDINGS This is the first study on the role of CD147 in trophoblast function. Further investigation on the function of CD147 and its associated protein complexes will enhance our understanding on human placentation. STUDY FUNDING/COMPETING INTEREST(S) This work was supported in part by the University of Hong Kong Grant 201011159200. The authors have no competing interests to declare.
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Affiliation(s)
- Cheuk-Lun Lee
- Department of Obstetrics and Gynaecology, University of Hong Kong, Pokfulam Road, Hong Kong, China
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Ueda K. Glycoproteomic strategies: From discovery to clinical application of cancer carbohydrate biomarkers. Proteomics Clin Appl 2013; 7:607-17. [PMID: 23640819 DOI: 10.1002/prca.201200123] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 12/27/2012] [Indexed: 12/15/2022]
Abstract
Carbohydrate antigens are the most frequently and traditionally used biomarkers for cancer, such as CA19-9, CA125, DUPAN-II, AFP-L3, and many others. The diagnostic potential of them was simply based on the cancer-specific alterations of glycan structures on particular glycoproteins in serum/plasma. In spite of the facts that glycosylation disorders are feasible for cancer biomarkers and glycomic analysis technologies to explore them have been rapidly developed, it remains difficult to sensitively screen glycan structure changes on cancer-associated glycoproteins from clinical specimens. Moreover, a lot of additional issues should be appropriately addressed for the clinical application of newly identified glycosylation biomarkers, including analytical throughput, quantitative confirmation of structural changes, and biological explanation for the alterations. In the last decade, significant improvement of mass spectrometric techniques is being made in the aspects of both hardware spec and preanalytical purification procedures for glycoprotein analysis. Here we review potential approaches to perform comprehensive analysis of glycoproteomic biomarker screening from serum/plasma and to realize high-throughput validation of site-specific oligosaccharide variations. The power and problems of mass spectrometric applications on the clinical use of carbohydrate biomarkers are also discussed in this review.
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Affiliation(s)
- Koji Ueda
- Laboratory for Biomarker Development, Center for Genomic Medicine, RIKEN, Minato-ku, Tokyo, Japan.
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22
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Tian Y, Zhang H. Characterization of disease-associated N-linked glycoproteins. Proteomics 2013; 13:504-11. [PMID: 23255236 DOI: 10.1002/pmic.201200333] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 09/20/2012] [Accepted: 10/13/2012] [Indexed: 12/14/2022]
Abstract
N-linked glycoproteins play important roles in biological processes, including cell-to-cell recognition, growth, differentiation, and programmed cell death. Specific N-linked glycoprotein changes are associated with disease progression and identification of these N-linked glycoproteins has potential for use in disease diagnosis, prognosis, and prediction of treatments. In this review, we summarize common strategies for N-linked glycoprotein characterization and applications of these strategies to identification of glycoprotein changes associated with disease states. We also review the N-linked glycoproteins altered in diseases such as breast cancer, lung cancer, and prostate cancer. Although assays for these glycoproteins have potential clinical utility, research is needed to translate these glycoproteins to clinical biomarkers.
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Affiliation(s)
- Yuan Tian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
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Zhao X, Ma C, Han H, Jiang J, Tian F, Wang J, Ying W, Qian X. Comparison and optimization of strategies for a more profound profiling of the sialylated N-glycoproteomics in human plasma using metal oxide enrichment. Anal Bioanal Chem 2013; 405:5519-29. [DOI: 10.1007/s00216-013-6971-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2013] [Revised: 04/02/2013] [Accepted: 04/03/2013] [Indexed: 11/28/2022]
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Abstract
New analytical platforms have been developed in response to the need for attaining increased peak capacity for multicomponent complex analysis with higher sensitivity and characterization of the analytes, and high-throughput capabilities. This review outlines the fundamental principles of target and comprehensive 2D LC method development and encompasses applications of LC–LC and LC × LC coupled to MS in bioanalysis using a variety of online analytical procedures. It also provides a rationale for the usage of the most employed mass analyzers and ionization sources on these platforms.
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