SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides

Schulze, Stefan; Oltmanns, Anne; Fufezan, Christian; Krägenbring, Julia; Mormann, Michael; Pohlschröder, Mechthild; Hippler, Michael

doi:10.1101/2020.10.21.349399

Cited by 4 publications

(3 citation statements)

References 52 publications

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“…In order to assign glycopeptides, samples were measured employing In-Source collision induced dissociation (IS-CID) as described previously followed by analysis of data with Ursgal and SugarPy ( Kremer et al, 2016 ; Oltmanns et al, 2019 ; Schulze et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Altered N-glycan composition impacts flagella-mediated adhesion in Chlamydomonas reinhardtii

Oltmanns

Zhao

et al. 2020

eLife

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For the unicellular alga Chlamydomonas reinhardtii, the presence of N-glycosylated proteins on the surface of two flagella is crucial for both cell-cell interaction during mating and flagellar surface adhesion. However, it is not known whether only the presence or also the composition of N-glycans attached to respective proteins is important for these processes. To this end, we tested several C. reinhardtii insertional mutants and a CRISPR/Cas9 knockout mutant of xylosyltransferase 1A, all possessing altered N-glycan compositions. Taking advantage of atomic force microscopy and micropipette force measurements, our data revealed that reduction in N-glycan complexity impedes the adhesion force required for binding the flagella to surfaces. This results in impaired polystyrene bead binding and transport but not gliding of cells on solid surfaces. Notably, assembly, intraflagellar transport, and protein import into flagella are not affected by altered N-glycosylation. Thus, we conclude that proper N-glycosylation of flagellar proteins is crucial for adhering C. reinhardtii cells onto surfaces, indicating that N-glycans mediate surface adhesion via direct surface contact.

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Section: Methodsmentioning

confidence: 99%

Altered N-glycan composition impacts flagella-mediated adhesion in Chlamydomonas reinhardtii

Oltmanns

Zhao

et al. 2020

eLife

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“…Several groups have developed automated EIC extraction methods to increase the throughput of data analysis. SugarPy takes identified glycopeptides and scans through raw MS1 spectra for predicted isotopic peaks (Schulze et al, 2020). GlycReSoft, deconvolves all MS1 peaks first before extracting chromatograms, and then connects these extracted chromatograms to identified glycopeptides (J.A.…”

Section: The Strengths and Weakness Of Bottom‐up Ms For Complete And ...mentioning

confidence: 99%

Methods to improve quantitative glycoprotein coverage from bottom‐up LC‐MS data

Chang

Zaia

2021

Mass Spectrometry Reviews

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Advances in mass spectrometry instrumentation, methods development, and bioinformatics have greatly improved the ease and accuracy of site-specific, quantitative glycoproteomics analysis. Data-dependent acquisition is the most popular method for identification and quantification of glycopeptides; however, complete coverage of glycosylation site glycoforms remains elusive with this method. Targeted acquisition methods improve the precision and accuracy of quantification, but at the cost of throughput and discoverability. Dataindependent acquisition (DIA) holds great promise for more complete and highly quantitative site-specific glycoproteomics analysis, while maintaining the ability to discover novel glycopeptides without prior knowledge. We review additional features that can be used to increase selectivity and coverage to the DIA workflow: retention time modeling, which would simplify the interpretation of complex tandem mass spectra, and ion mobility separation, which would maximize the sampling of all precursors at a giving chromatographic retention time.The instrumentation and bioinformatics to incorporate these features into glycoproteomics analysis exist. These improvements in quantitative, site-specific analysis will enable researchers to assess glycosylation similarity in related biological systems, answering new questions about the interplay between glycosylation state and biological function.

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“…The software aims at matching these factors with the reference values in glycan repositories. The currently preferred softwares for glyco-peptide and/or released glycan analysis, such as Byonic™ [10], Sug-arQb [11], and pGlyco [12], typically rely on built-in glycan database dependent search algorithms [13].…”

Section: Introductionmentioning

confidence: 99%

Mass spectrometry‐based glycoprofiling of biopharmaceuticals by using an automated data processing tool: SimGlycan^®

Puranik

Goswami²,

Sutar³

et al. 2022

J of Separation Science

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The therapeutic and immunological properties of biopharmaceuticals are governed by the glycoforms contained in them. Thus, bioinformatics tools capable of performing comprehensive characterization of glycans are significantly important to the biopharma industry. The primary structural elucidation of glycans using mass spectrometry is tricky and tedious in terms of spectral interpretation. In this study, the biosimilars of a therapeutic monoclonal antibody and an Fc‐fusion protein with moderate and heavy glycosylation, respectively, were employed as representative biopharmaceuticals for released glycan analysis using liquid chromatography–tandem mass spectrometry instead of conventional mass spectrometry‐based analysis. SimGlycan® is a software with proven ability to process tandem MS data for released glycans could identify eight additional glycoforms in Fc‐fusion protein biosimilar, which were not detected during mass spectrometry analysis of released glycans or glyco‐peptide mapping of the same molecule. Thus, liquid chromatography–tandem mass spectrometry analysis of released glycans not only complements conventional liquid chromatography–mass spectrometry‐based glycan profiling but can also identify additional glycan structures that may otherwise be omitted during conventional liquid chromatography–tandem mass spectrometry based analysis of mAbs. The mass spectrometry data processing tools, such as PMI Byos™, SimGlycan®, etc., can display pivotal analytical capabilities in automated liquid chromatography–mass spectrometry and liquid chromatography–tandem mass spectrometry‐based glycan analysis workflows, especially for high‐throughput structural characterization of glycoforms in biopharmaceuticals.

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SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides

Cited by 4 publications

References 52 publications

Altered N-glycan composition impacts flagella-mediated adhesion in Chlamydomonas reinhardtii

Altered N-glycan composition impacts flagella-mediated adhesion in Chlamydomonas reinhardtii

Methods to improve quantitative glycoprotein coverage from bottom‐up LC‐MS data

Mass spectrometry‐based glycoprofiling of biopharmaceuticals by using an automated data processing tool: SimGlycan^®

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SugarPy facilitates the universal, discovery-driven analysis of intact glycopeptides

Cited by 4 publications

References 52 publications

Altered N-glycan composition impacts flagella-mediated adhesion in Chlamydomonas reinhardtii

Altered N-glycan composition impacts flagella-mediated adhesion in Chlamydomonas reinhardtii

Methods to improve quantitative glycoprotein coverage from bottom‐up LC‐MS data

Mass spectrometry‐based glycoprofiling of biopharmaceuticals by using an automated data processing tool: SimGlycan®

Contact Info

Product

Resources

About

Mass spectrometry‐based glycoprofiling of biopharmaceuticals by using an automated data processing tool: SimGlycan^®