2024
Analysis of Mucin‐Domain Glycoproteins Using Mass Spectrometry
Mahoney K, Malaker S. Analysis of Mucin‐Domain Glycoproteins Using Mass Spectrometry. Current Protocols 2024, 4: e1100. PMID: 38984456, PMCID: PMC11239139, DOI: 10.1002/cpz1.1100.Peer-Reviewed Original ResearchGlycoproteomics: Charting new territory in mass spectrometry and glycobiology
Malaker S. Glycoproteomics: Charting new territory in mass spectrometry and glycobiology. Journal Of Mass Spectrometry 2024, 59: e5034. PMID: 38726698, DOI: 10.1002/jms.5034.Peer-Reviewed Original Research
2022
Current strategies for characterization of mucin-domain glycoproteins
Ince D, Lucas TM, Malaker SA. Current strategies for characterization of mucin-domain glycoproteins. Current Opinion In Chemical Biology 2022, 69: 102174. PMID: 35752002, DOI: 10.1016/j.cbpa.2022.102174.Peer-Reviewed Original ResearchConceptsGlycopeptide mimeticsPost-translational modificationsCurrent characterization techniquesCellular glycosylation pathwaysSynthetic methodCharacterization techniquesGlycosylation pathwayMucin domainO-glycosylationBiological functionsGlycoproteomic workflowGlycosylationGlycoproteinExciting avenuesRecent breakthroughsMucin glycoproteinsRecent developmentsRevealing the human mucinome
Malaker SA, Riley NM, Shon DJ, Pedram K, Krishnan V, Dorigo O, Bertozzi CR. Revealing the human mucinome. Nature Communications 2022, 13: 3542. PMID: 35725833, PMCID: PMC9209528, DOI: 10.1038/s41467-022-31062-4.Peer-Reviewed Original ResearchConceptsModular protein domainsKey molecular signaturesProtein domainsTransmembrane proteinDetection of hundredsMucin domainGlycoprotein identificationHuman diseasesMolecular signaturesCell lysatesEnrichment strategyGlycoproteinVivo sourceOverlapping populationsImportant roleDomainStcEProteinLysatesOvarian cancer patientsComplex samples
2021
Novel Antibodies for the Simple and Efficient Enrichment of Native O-GlcNAc Modified Peptides
Burt RA, Dejanovic B, Peckham HJ, Lee KA, Li X, Ounadjela JR, Rao A, Malaker SA, Carr SA, Myers SA. Novel Antibodies for the Simple and Efficient Enrichment of Native O-GlcNAc Modified Peptides. Molecular & Cellular Proteomics 2021, 20: 100167. PMID: 34678516, PMCID: PMC8605273, DOI: 10.1016/j.mcpro.2021.100167.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsAntibodies, MonoclonalBrainGlycopeptidesMiceMouse Embryonic Stem CellsN-AcetylglucosaminyltransferasesConceptsO-GlcNAc-modified peptidesPosttranslational modificationsNumerous biological processesUbiquitin remnantsMouse brain tissue samplesGlcNAc signalingThreonine residuesLysine acetylationGlcNAc transferaseO-GlcNAcylationGlcNAc antibodiesBiological processesO-GalNAcExtended glycansN-acetylglucosamineEnrichment strategyFundamental roleDisease statesPeptidesInstrument timeModified peptidePhosphotyrosineNovel antibodyBrain tissue samplesImmunoprecipitationBenefits of Chemical Sugar Modifications Introduced by Click Chemistry for Glycoproteomic Analyses
Calle B, Bineva-Todd G, Marchesi A, Flynn H, Ghirardello M, Tastan OY, Roustan C, Choi J, Galan MC, Schumann B, Malaker SA. Benefits of Chemical Sugar Modifications Introduced by Click Chemistry for Glycoproteomic Analyses. Journal Of The American Society For Mass Spectrometry 2021, 32: 2366-2375. PMID: 33871988, PMCID: PMC7611619, DOI: 10.1021/jasms.1c00084.Peer-Reviewed Original ResearchConceptsMass spectrometryCharge densityMass spectrometric signatureLow charge densityIntact O-glycopeptidesHigh charge densityTandem mass spectrometryClick chemistryChemical methodsChemical modificationO-glycopeptidesETD fragmentationFragmentation behaviorMonosaccharide analoguesSpectrometric signaturesMucin-type O-glycansGlycoproteomic analysisCharge stateComplex post-translational modificationsRight analytical toolsGlycan structuresO-glycosylationSugar modificationsGlycopeptidesSpectrometryGenome-wide CRISPR screens reveal a specific ligand for the glycan-binding immune checkpoint receptor Siglec-7
Wisnovsky S, Möckl L, Malaker SA, Pedram K, Hess GT, Riley NM, Gray MA, Smith BAH, Bassik MC, Moerner WE, Bertozzi CR. Genome-wide CRISPR screens reveal a specific ligand for the glycan-binding immune checkpoint receptor Siglec-7. Proceedings Of The National Academy Of Sciences Of The United States Of America 2021, 118: e2015024118. PMID: 33495350, PMCID: PMC7865165, DOI: 10.1073/pnas.2015024118.Peer-Reviewed Original Research
2020
Electron-Based Dissociation Is Needed for O‑Glycopeptides Derived from OpeRATOR Proteolysis
Riley NM, Malaker SA, Bertozzi CR. Electron-Based Dissociation Is Needed for O‑Glycopeptides Derived from OpeRATOR Proteolysis. Analytical Chemistry 2020, 92: 14878-14884. PMID: 33125225, PMCID: PMC8329938, DOI: 10.1021/acs.analchem.0c02950.Peer-Reviewed Original ResearchMeSH KeywordsAkkermansiaAmino Acid SequenceElectronsGlycopeptidesPeptide HydrolasesProteolysisTandem Mass SpectrometryConceptsO-glycopeptidesElectron-based fragmentationElectron-driven dissociationMS/MS spectraO-glycositesTandem mass spectrometryMS spectraMass spectrometryGlycoproteomic methodsOrthogonal cleavageDissociation methodO-glycoproteomicsPeptide fragmentsCombined digestionN-terminal residuesThreonine residuesBacterial enzymesO-glycoproteinsDissociationN-terminusExciting opportunitiesO-glycansCanonical proteasesElectronsSpectrometryOptimal Dissociation Methods Differ for N- and O‑Glycopeptides
Riley NM, Malaker SA, Driessen MD, Bertozzi CR. Optimal Dissociation Methods Differ for N- and O‑Glycopeptides. Journal Of Proteome Research 2020, 19: 3286-3301. PMID: 32500713, PMCID: PMC7425838, DOI: 10.1021/acs.jproteome.0c00218.Peer-Reviewed Original Research
2019
Mass Spectrometric Identification and Molecular Modeling of Glycopeptides Presented by MHC Class I and II Processing Pathways
Malaker SA, Ferracane MJ. Mass Spectrometric Identification and Molecular Modeling of Glycopeptides Presented by MHC Class I and II Processing Pathways. Methods In Molecular Biology 2019, 2024: 269-285. PMID: 31364056, DOI: 10.1007/978-1-4939-9597-4_17.Chapters
2017
Identification of Glycopeptides as Posttranslationally Modified Neoantigens in Leukemia
Malaker SA, Penny SA, Steadman LG, Myers PT, Loke JC, Raghavan M, Bai DL, Shabanowitz J, Hunt DF, Cobbold M. Identification of Glycopeptides as Posttranslationally Modified Neoantigens in Leukemia. Cancer Immunology Research 2017, 5: 376-384. PMID: 28314751, PMCID: PMC5508727, DOI: 10.1158/2326-6066.cir-16-0280.Peer-Reviewed Original Research
2016
Identification and Characterization of Complex Glycosylated Peptides Presented by the MHC Class II Processing Pathway in Melanoma
Malaker SA, Ferracane MJ, Depontieu FR, Zarling AL, Shabanowitz J, Bai DL, Topalian SL, Engelhard VH, Hunt DF. Identification and Characterization of Complex Glycosylated Peptides Presented by the MHC Class II Processing Pathway in Melanoma. Journal Of Proteome Research 2016, 16: 228-237. PMID: 27550523, PMCID: PMC5218890, DOI: 10.1021/acs.jproteome.6b00496.Peer-Reviewed Original ResearchAmino Acid SequenceBinding SitesCarbohydrate SequenceCell Line, TumorComplementarity Determining RegionsCrystallography, X-RayDisulfidesGlycopeptidesGlycosylationHLA-DR AntigensHumansMelanocytesModels, MolecularProtein BindingProtein Conformation, alpha-HelicalProtein Conformation, beta-StrandProtein Interaction Domains and MotifsThermodynamics