Dataset Information

GlyXtoolMS Example Data Sets - glyXtoolMS: An Open-Source Pipeline for Semiautomated Analysis of Glycopeptide Mass Spectrometry Data

ABSTRACT: The data sets of human IgG and human fibrinogen are used as test data for the publication of glyXtoolMS (https://github.com/glyXera/glyXtoolMS). GlyXtoolMS is an open-source analysis software for the (semi)automated targeted analysis of glycopeptide mass spectrometry data using OpenMS/TOPPAS as a framework and pipeline engine. The proteins were selected to show the successful analysis of both N-glycopeptide and O-glycopeptide samples. The samples were measured by nano reversed phase liquid chromatography coupled online to an electrospray ionization orbitrap mass spectrometer (nano RP-LC ESI- OT-MS/MS; LTQ Orbitrap Elite, Thermo Scientific, Waltham, MA, USA) with HCD fragmentation.

INSTRUMENT(S): LTQ Orbitrap Elite

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Blood Plasma

SUBMITTER: Markus Pioch

LAB HEAD: Erdmann Rapp

PROVIDER: PXD009716 | Pride | 2018-09-24

REPOSITORIES: Pride

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glyXtool<sup>MS</sup>: An Open-Source Pipeline for Semiautomated Analysis of Glycopeptide Mass Spectrometry Data.

Pioch Markus M Hoffmann Marcus M Pralow Alexander A Reichl Udo U Rapp Erdmann E

Analytical chemistry 20180925 20

For glycoproteomic analyses several web tools and standalone software packages have been developed over the recent years. These tools support or replace the time-consuming, cumbersome, and error-prone manual spectra analysis and glycopeptide identification. However, existing software tools are usually tailored to one fragmentation technique and only present the final analysis results. This makes manual inspection and correction of intermediate results difficult or even impossible. We solved this ...[more]

PMID: 30252445

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Project description:Human noroviruses, globally the main cause of viral gastroenteritis, show strain specific affinity for histo-blood group antigens (HBGA) and can successfully be propagated ex vivo in human intestinal enteroids (HIEs). HIEs established from jejunal stem cells of individuals with different ABO, Lewis and secretor geno- and phenotypes, show varying susceptibility to such infections. Using bottom-up glycoproteomic approaches we have defined and compared the N-linked glycans of glycoproteins of seven jejunal HIEs. Membrane proteins were extracted, trypsin digested, and glycopeptides enriched by hydrophilic interaction liquid chromatography and analyzed by nanoLC-MS/MS. The Byonic software was used for glycopeptide identification followed by hands-on verifications and interpretations. Glycan structures and attachment sites were identified from MS 2 spectra obtained by higher-energy collision dissociation through analysis of diagnostic saccharide oxonium ions (B-ions), stepwise glycosidic fragmentation of the glycans (Y-ions), and peptide sequence ions (b- and y-ions). Altogether 694 unique glycopeptides from 93 glycoproteins were identified. The N-glycans encompassed pauci- and oligomannose, hybrid- and complex-type structures. Notably, polyfucosylated HBGA-containing glycopeptides of the four glycoproteins tetraspanin-8, carcinoembryonic antigen-related cell adhesion molecule 5, sucrose-isomaltase and aminopeptidase N were especially prominent and were characterized in detail and related to donor ABO, Lewis and secretor types of each HIE. Virtually no sialylated N-glycans were identified for these glycoproteins suggesting that terminal sialylation was infrequent compared to fucosylation and HBGA biosynthesis. This approach gives unique site-specific information on the structural complexity of N-linked glycans of glycoproteins of human HIEs and provides a platform for future studies on the role of host glycoproteins in gastrointestinal infectious diseases.

Dataset Information

GlyXtoolMS Example Data Sets - glyXtoolMS: An Open-Source Pipeline for Semiautomated Analysis of Glycopeptide Mass Spectrometry Data

Publications

glyXtool<sup>MS</sup>: An Open-Source Pipeline for Semiautomated Analysis of Glycopeptide Mass Spectrometry Data.

Similar Datasets

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