{"title":"Qualitative and Quantitative Methods for N-Glycans in N-Glycomics","authors":"S. Ren, Haojie Lu","doi":"10.1201/9781003185833-3","DOIUrl":"https://doi.org/10.1201/9781003185833-3","url":null,"abstract":"","PeriodicalId":302684,"journal":{"name":"Mass Spectrometry–Based Glycoproteomics and Its Clinic Application","volume":"80 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117245936","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Qualitative and Quantitative Analytical Methods for Intact Glycopeptides","authors":"Weiqian Cao, Pengyuan Yang","doi":"10.1201/9781003185833-4","DOIUrl":"https://doi.org/10.1201/9781003185833-4","url":null,"abstract":"This chapter presents an overview of mass spectrometry (MS)-based qualitative and quantitative analytical methods, for intact glycopeptides, that are major drivers and greatly facilitating the analysis of intact glycopeptides. Software tools are also key roles in promoting the intact glycopeptide identification, which are described in Chapter 5.","PeriodicalId":302684,"journal":{"name":"Mass Spectrometry–Based Glycoproteomics and Its Clinic Application","volume":"65 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"125871466","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Analytical Software and Databases in N-Glycoproteomics","authors":"Suideng Qin, Z. Tian","doi":"10.1201/9781003185833-5","DOIUrl":"https://doi.org/10.1201/9781003185833-5","url":null,"abstract":"With the advancement in chromatographic separation and MS detection, high-throughput and deep site- and structure-specific characterization of glycosylation can be and can only be achieved at the intact glycopeptide level. For an intact N-glycopeptide, site-specific information of amino acid sequence and glycosite can be achieved with selective fragmentation of the peptide backbone; and structure-specific information of the N-glycan can be achieved with the corresponding selective fragmentation. Every LC-MS/MS analysis of intact glycopeptides from any complex sample yield a raw dataset containing tens of thousands of MS and MS/MS spectra. For high-throughput interpretation and database search of raw LC-MS/MS datasets, lots of powerful dedicated intact glycopeptide search engines and auxiliary databases have been developed. This chapter provides a general overview of current analytical software and databases in N-glycoproteomics; for each software, the search algorithm and procedure, method of (false discovery rate) FDR control as well as recent applications are mainly covered. Early search engines (including Byonic, GPQuest, etc.) report site-specific information of amino acid sequences, N-glycosites as well as monosaccharide compositions of intact N-glycopeptides; whereas latest GPSeeker reports additional structure-specific information of monosaccharide sequences, part of which are confirmed with structure-diagnostic fragment ions. Additionally, search engines that support O-glycosylation identification are also briefly introduced.","PeriodicalId":302684,"journal":{"name":"Mass Spectrometry–Based Glycoproteomics and Its Clinic Application","volume":"43 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"116063393","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Selective Enrichment Methods for N-Glycosite Containing Peptides in N-Glycoproteomics","authors":"Guoli Wang, Ying Zhang, Hao Lu","doi":"10.1201/9781003185833-1","DOIUrl":"https://doi.org/10.1201/9781003185833-1","url":null,"abstract":"Glycosylation is an essential biochemical process. It is of great significance to detect the glycoproteins sensitively to understand its biological function. While the rapid development of MS-based technologies has considerably promoted the research of glycoproteome, the low abundance and heterogeneity of glycosylation still make the comprehensive analysis of glycoproteome challenging. To analyze the glycoproteome with high selectivity and sensitivity, the enrichment process before mass spectrometry (MS) analysis is particularly critical. In this chapter, current representative methods for glycoproteins/glycopeptides enrichment are summarized with advantages and limitations discussed.","PeriodicalId":302684,"journal":{"name":"Mass Spectrometry–Based Glycoproteomics and Its Clinic Application","volume":"55 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2021-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122662555","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}