Validation of the curation pipeline of UniCarb-DB: Building a global glycan reference MS/MS repository

Campbell, Matthew P.; Nguyen-Khuong, Terry; Hayes, Catherine A.; Flowers, Sarah A.; Alagesan, Kathirvel; Kolarich, Daniel; Packer, Nicolle H.; Karlsson, Niclas G.

doi:10.1016/j.bbapap.2013.04.018

Cited by 61 publications

(53 citation statements)

References 35 publications

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“…This mode gives much more informative spectra of N ‐glycans than most of the common positive ion spectra. A dot product score was calculated for each spectrum from the three sets of data and the effects of charge state, de‐ isotoping and threshold levels on the quality of the input data are shown in the database (Campbell et al, ).…”

Section: Computer Analysis Of Spectramentioning

confidence: 99%

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2013–2014

Harvey

2018

Mass Spectrometry Reviews

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This review is the eighth update of the original article published in 1999 on the application of Matrix-assisted laser desorption/ionization mass spectrometry (MALDI) mass spectrometry to the analysis of carbohydrates and glycoconjugates and brings coverage of the literature to the end of 2014. Topics covered in the first part of the review include general aspects such as theory of the MALDI process, matrices, derivatization, MALDI imaging, fragmentation, and arrays. The second part of the review is devoted to applications to various structural types such as oligo- and poly- saccharides, glycoproteins, glycolipids, glycosides, and biopharmaceuticals. Much of this material is presented in tabular form. The third part of the review covers medical and industrial applications of the technique, studies of enzyme reactions, and applications to chemical synthesis. © 2018 Wiley Periodicals, Inc. Mass Spec Rev 37:353-491, 2018.

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Section: Computer Analysis Of Spectramentioning

confidence: 99%

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2013–2014

Harvey

2018

Mass Spectrometry Reviews

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“…Glycan structures were identified based on manual annotation of tandem MS fragmentation spectra and further characterized with the aid of software-generated mass fragments using GlycoWorkBench (Ceroni et al, 2008). Verification of the proposed structures was also carried out using UniCarb DB (Campbell et al, 2014b;Hayes et al, 2011), a web-based LC-MS/MS database containing fragmentation and retention times of previously reported N-and O-glycans (Campbell et al, 2014a).…”

Section: Mass Spectrometric Analysis Of N-and Oglycansmentioning

confidence: 99%

Tissue glycomics distinguish tumour sites in women with advanced serous adenocarcinoma

et al. 2017

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In the era of precision medicine, the tailoring of cancer treatment is increasingly important as we transition from organ‐based diagnosis towards a more comprehensive and patient‐centric molecular diagnosis. This is particularly the case for high‐grade serous adenocarcinomas of the ovary and peritoneum, which are commonly diagnosed at an advanced stage, and collectively treated and managed similarly. We characterized the N‐ and O‐glycome of serous ovarian (OC) and peritoneal cancer (PC) tissues using PGC‐LC‐ESI‐IT‐MS/MS profiling and validated the discriminatory glycans and their corresponding glyco‐gene expression levels using cell lines and transcriptomic data from 232 patients. Overall, the N‐ and O‐glycan repertoires of both cancer types were found to comprise mostly of α2,6‐sialylated glycan structures, with the majority of N‐glycans displaying the biantennary mono‐ and disialylation as well as bisecting‐type biantennary glycans. The MS profiling by PGC‐LC also revealed several glycan structural isomers that corresponded to LacdiNAc‐type (GalNAcβ1‐4GlcNAc) motifs that were unique to the serous ovarian cancers and that correlated with elevated gene expression of B4GALNT3 and B4GALNT4 in patients with serous cancer. Statistical evaluation of the discriminatory glycans also revealed 13 N‐ and 3 O‐glycans (P < 0.05) that significantly discriminated tumour‐sampling sites, with LacdiNAc‐type N‐glycans (m/z 1205.02− and m/z 1059.42−) being associated with ovarian‐derived cancer tissue and bisecting GlcNAc‐type (m/z 994.92−) and branched N‐glycans (m/z 1294.02− and m/z 1148.42−) upregulated at the metastatic sites. Hence, we demonstrate for the first time that OC and PC display distinct molecular signatures at both their glycomic and transcriptomic levels. These signatures may have potential utility for the development of accurate diagnosis and personalized treatments.

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“…Unfortunately, these essential cross-ring fragments are only observed in smaller oligomers, where effective collision energies are higher. On this single constraint glycan sequencing efforts have stalled, encouraging a culture of accepting biological inference data in publications [3] and a growing use of meta data [4] for assigning the details of structure. To this specific problem the ion trap delivers a solution.…”

Section: Introductionmentioning

confidence: 99%

Structural Documentation of Glycan Epitopes: Sequential Mass Spectrometry and Spectral Matching

Ashline

Hanneman

Zhang

et al. 2014

J. Am. Soc. Mass Spectrom.

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Documenting mass spectral data is a fundamental aspect of accepted protocols. In this report we contrast MSn sequential disassembly spectra obtained from natural and synthetic glycan epitopes. The epitopes considered are clusters found on conjugate termini of lipids and N-, and O-glycans of proteins. The latter are most frequently pendant through a CID-labile HexNAc glycosidic linkage. The synthetic samples were supplied by collaborating colleagues and commercial sources and usually possessed a readily released reducing-end linker, a by-product of synthesis. All samples were comparably methylated, extracted, and MSn disassembled to compare their linkage and branching spectral details. Both sample types provide B-ion type fragments early in a disassembly pathway and their compositions are a suggestion of structure. Further steps of disassembly are necessary to confirm the details of linkage and branching. Included in this study were various Lewis and H antigens, 3- and 6-linked sialyl-lactosamine, NeuAc-2,8-NeuAc dimer, and Galα1,3Gal. Sample infusion provided high quality spectral data while disassembly to small fragments generates reproducible high signal/noise spectra for spectral matching. All samples were analyzed as sodium adducted positive ions. This study includes comparability statistics and evaluations on several mass spectrometers.

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Validation of the curation pipeline of UniCarb-DB: Building a global glycan reference MS/MS repository

Cited by 61 publications

References 35 publications

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2013–2014

Analysis of carbohydrates and glycoconjugates by matrix‐assisted laser desorption/ionization mass spectrometry: An update for 2013–2014

Tissue glycomics distinguish tumour sites in women with advanced serous adenocarcinoma

Structural Documentation of Glycan Epitopes: Sequential Mass Spectrometry and Spectral Matching

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