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Glycoprotein Enrichment Analytical Techniques [chapter]

R. Zhu, L. Zacharias, K.M. Wooding, W. Peng, Y. Mechref
2017 Methods in Enzymology  
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  ...  Protein glycosylation is one of the most important posttranslational modifications. Numerous biological functions are related to protein glycosylation.  ...  Acknowledgments This work was supported by a grant from the Cancer Prevention Institute of Texas (CPRIT, RP130624) and partially by an NIH grant (1R01GM112490).  ... 
doi:10.1016/bs.mie.2016.11.009 pmid:28109440 pmcid:PMC5708143 fatcat:o2qj3vzltjeb5a7g75c5ihzlze

Lipidomics: A Promising area in "OMICS" Research

Kadambini Tripathy
2012 Journal of computer science and systems biology  
In this review, we will discuss the technical developments in the field of lipidomics and overview the current state of the lipid bioinformatics field as well as suggest few potential new areas of research  ...  The role of bioinformatics in the development of lipidomics will also be discussed.  ...  Novel tools for lipid research [8] • Structure-drawing tools • MS prediction tools Technical Developments of Lipidomics Lipidomics mass spectrometry Mass spectrometry has emerged as a powerful tool  ... 
doi:10.4172/jcsb.1000082 fatcat:orug62dvnrclrcxxcicelq7yi4

Recent advances in the MS analysis of glycoproteins: Capillary and microfluidic workflows

Diego F. Cortes, Jarod L. Kabulski, Alexandru C. Lazar, Iulia M. Lazar
2010 Electrophoresis  
This review describes the progress achieved in the characterization of protein glycosylation by using advanced capillary and microfluidic-MS technologies.  ...  In addition, quantitative analysis strategies are assessed, and the bioinformatics aspects of glycoproteomic data processing are summarized.  ...  Acknowledgments This work was supported in part by grants from NSF (Career BES-0448840) and NIH/NCI (R21CA126669).  ... 
doi:10.1002/elps.201000394 pmid:21171110 pmcid:PMC3717299 fatcat:mlplmowddrchzlgskfjrmwqzdq

Developments in the Identification of Glycan Biomarkers for the Detection of Cancer

L. Renee Ruhaak, Suzanne Miyamoto, Carlito B. Lebrilla
2013 Molecular & Cellular Proteomics  
Thanks to recent advances in the development of analytical techniques and instrumentation, especially in mass spectrometry, it is now possible to identify blood-derived glycan-based biomarkers using glycomics  ...  It is anticipated that the progressing instrumental and bioinformatics developments will allow the identification of relevant glycan biomarkers for the diagnosis, early detection, and monitoring of cancer  ...  Acknowledgments-The authors are thankful for the funding provided by the National Institutes of Health, the Department of Defense, the Tobacco Related Disease Research Program and the LUNGevity Foundation  ... 
doi:10.1074/mcp.r112.026799 pmid:23365456 pmcid:PMC3617331 fatcat:2mydacsfrrbfrjxm5vdbajcqcy

Recent advances in mass spectrometric analysis of glycoproteins

Alireza Banazadeh, Lucas Veillon, Kerry M. Wooding, Masoud Zabet-moghaddam, Yehia Mechref
2016 Electrophoresis  
Mass spectrometry in conjugation with different separation methods, such as capillary electrophoresis, ion mobility, and high performance liquid chromatography, has become a popular tool for glycoprotein  ...  Over the past decade, mass spectrometry (MS) techniques such as high-performance liquid chromatography-electrospray tandem mass spectrometry (LC-ESI-MS/MS) and matrixassisted laser desorption/ionization  ...  Acknowledgments This work was supported by an NIH grant (1R01GM112490-01) and a grant from the Cancer Prevention and Research Institute of Texas (RP130624).  ... 
doi:10.1002/elps.201600357 pmid:27757981 pmcid:PMC5221507 fatcat:hqqzt6kqjna4rcsjju5w2zkzcq

Current Insights in Mammalian Glycosylation: Implication of Glycoproteomics as Next-Generation Biomarkers in Diabetes Mellitus

Alok Raghav, Jamal Ahmad, Zeeshan Ahmad Khan, Brijesh Kumar Mishra, Rai Pawankumar Anirudh
2017 Journal of Glycobiology  
Glycosylation, an enzyme-directed, site-specific process is one of the major co-translational and post-translational modifications in proteins.  ...  This tool can unreveal the secrets of the patterned expression of glycoproteins in healthy and patients with diabetes with secondary complications.  ...  liquid chromatography mass spectroscopy (LC-MS) may contribute in the validation and identification of novel glycopeptides biomarkers in diabetes and its associated complications.  ... 
doi:10.4172/2168-958x.1000125 fatcat:wdu26d7lffh4bpvot5eaco2ose

Databases and Bioinformatic Tools for Glycobiology and Glycoproteomics

Xing Li, Zhijue Xu, Xiaokun Hong, Yan Zhang, Xia Zou
2020 International Journal of Molecular Sciences  
In this study, the representative databases of glycan structure, glycoprotein, glycan–protein interactions, glycogenes, and the newly developed bioinformatic tools and integrated portal for glycoproteomics  ...  However, these databases and tools are not well known or widely used by the public, including clinicians and other researchers who are not in the field of glycobiology, but are interested in glycoproteins  ...  Software Tools for Glycan and Intact Glycopeptide Analysis Mass spectrometry (MS) has long been considered as one of the most powerful techniques for glycomic and glycoproteomic study.  ... 
doi:10.3390/ijms21186727 pmid:32937895 fatcat:cqhmegyfebdtfbeqgu2yrdzv7y

Systems Glycobiology: Past, Present, and Future [chapter]

Songül Yaşar Yıldız
2020 Computational Biology and Chemistry [Working Title]  
The chapter provides basic knowledge both for glycobiologists interested in the application of bioinformatics tools and scientists of computational biology interested in studying the glycome.  ...  This chapter will summarize the up-to-date leading edge in the use of bioinformatics tools in the field of glycobiology.  ...  As a consequence, liquid chromatography-mass spectrometry (LC-MS) in a number of forms is in general necessary since glycans with low abundancy or poor ionization capacity can be suppressed in the case  ... 
doi:10.5772/intechopen.92267 fatcat:52dnyiusu5bpvbiluegofjlgpm

Mass Spectrometry Based Glycoproteomics—From a Proteomics Perspective

Sheng Pan, Ru Chen, Ruedi Aebersold, Teresa A. Brentnall
2010 Molecular & Cellular Proteomics  
This report provides an overview of the recent advances in mass spectrometry based glycoproteomic methods and technology, in the context of biomarker discovery and clinical application.  ...  Glycosylation is one of the most important and common forms of protein post-translational modification that is involved in many physiological functions and biological pathways.  ...  It is notable that the reliable analysis of mass spectrometric data in glycoproteomic studies largely relies on bioinformatic tools and glycorelated databases that are available.  ... 
doi:10.1074/mcp.r110.003251 pmid:20736408 pmcid:PMC3013464 fatcat:5woh3heas5h7hcvd75vartdc5u

Advances in Proteomics and Bioinformatics in Agriculture Research and Crop Improvement

Keyura Katam Khoranhlai
2015 Journal of Proteomics & Bioinformatics  
Acknowledgement The author Keyura Katam acknowledges NSF for providing summer research opportunity and financial support.  ...  Isolation and Characterization of Plant Protein Complexes by Mass Spectrometry Even though high-resolution LC-MS (Liquid chromatographymass spectrometry) strategies have resolved some of the issues with  ...  Multidimensional protein identification technology (MudPIT) uses a combination of liquid chromatography (LC-MS/MS) and high performance liquid chromatography (HPLC), enhances the separation of peptide  ... 
doi:10.4172/jpb.1000351 fatcat:imju7v737rhivkqgobptas4gce

Combining various strategies to increase the coverage of the plant cell wall glycoproteome

Yu Zhang, Aurélie Giboulot, Michel Zivy, Benoît Valot, Elisabeth Jamet, Cécile Albenne
2011 Phytochemistry  
The first part of this paper consists of a mini-review on the strategies used in glycoproteomics, namely methods for enrichment in glycoproteins and mass spectrometry (MS) techniques currently used.  ...  PNA, ConA and WGA lectins) and subsequent identification of glycoproteins by MALDI-TOF MS and LC-MS/MS; (iii) boronic acid chromatography followed by identification of glycoproteins by MALDI-TOF MS.  ...  ACKNOWLEDGEMENTS This study was funded by the Université Paul Sabatier in Toulouse and the Centre National de la Recherche Scientifique (France).  ... 
doi:10.1016/j.phytochem.2010.10.019 pmid:21109274 fatcat:ik2zbmzgxfelpambhhx5uwocou

Post-translational modifications and their applications in eye research

Bing-Jie Chen, Thomas Chuen Lam, Long-Qian Liu, Chi-Ho To
2017 Molecular Medicine Reports  
The study of protein expression and PTMs has attracted attention in the post-genomic era.  ...  The introduction of effective protein separation methods, specific PTM purification strategies and advanced mass spectrometers has enabled the global profiling of PTMs and the identification of a targeted  ...  Rivier L: Criteria for the identification of compounds by liquid chromatography-mass spectrometry and liquid chromatography-multiple mass spectrometry in forensic toxicology and doping analysis.  ... 
doi:10.3892/mmr.2017.6529 pmid:28487982 fatcat:xhhspflk2rfc5kf24t7omp4z6a

Proteomics and Opportunities for Clinical Translation in Urological Disease

Ali R. Vaezzadeh, Hanno Steen, Michael R. Freeman, Richard S. Lee
2009 Journal of Urology  
Proteomics approaches consist of a combination of powerful technologies: protein/peptide separation, identification and bioinformatic detection and quantitation based on powerful computational data processing  ...  tools.  ...  Acknowledgments This study was supported by NIH P50DK65298 (MRF), NIH K08DK077836 (RSL), and a Children's Hospital Boston Career Development Fellowship (RSL).  ... 
doi:10.1016/j.juro.2009.05.001 pmid:19616261 pmcid:PMC4370209 fatcat:c5sil3u7cbbetgiadahj3r3kry

Integration of Bioinformatics Tools for Proteomics Research

Tushar Nanda, Kadambini Tripathy
2011 Journal of computer science and systems biology  
An emerging field for the analysis of biological systems is the study of the complete protein complement of the genome, the 'proteome'.  ...  Bioinformatics is an integral part of proteomics research.  ...  Finally, mass spectrometry, possibly the most important proteomics tool to date, generates vast quantities of data through large-scale liquid chromatography (LC), tandem mass spectrometry (MS/MS) for identification  ... 
doi:10.4172/jcsb.s13-002 fatcat:k3d5kuw3vbcxzi5a3dopmmnlwq

Proteomics - The Future of Periodontal Diagnostics

Nisha KJ
2017 Biomedical Journal of Scientific & Technical Research  
Identifying unique patterns of protein expression, or biomarkers, associated with specific diseases is one of the most promising areas of clinical proteomics.  ...  Advances in proteomic technologies have enabled comprehensive profiling of protein expression in cells, tissue, and body fluids.  ...  Proteomic studies conducted on human saliva using a combination of liquid chromatography, electro spray tandem mass spectrometry and 2D-electrophoresis have led to the identification of 309 separate proteins  ... 
doi:10.26717/bjstr.2017.01.000447 fatcat:ko3pognjcjebxgvni57mwtdnpy
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