2025
rtmsEcho: An Open-Source R Package for Automated Analysis of Acoustic Ejection Mass Spectrometry Data
Rimmer M, Twarog N, Ranathunge T, Wang J, Li Y, Chen T, Shelat A, Yang L. rtmsEcho: An Open-Source R Package for Automated Analysis of Acoustic Ejection Mass Spectrometry Data. Analytical Chemistry 2025, 97: 20444-20452. PMID: 40940023, PMCID: PMC12462762, DOI: 10.1021/acs.analchem.5c03730.Peer-Reviewed Original ResearchConceptsAcoustic Ejection Mass SpectrometryMass spectrometryAnalysis of complex samplesLC-MS systemFull-scan acquisitionQuantitative analysis of complex samplesChromatographic separationHigh-throughput workflowComplex samplesLC-MSDrug discoverySpectrometryTargeted analysisClinical diagnosticsQuantitative analysisHigh-throughput applicationsSpectral analysisMRMPeak detectionSeparationChromatographyReproducibilityUnbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics
Steger M, Nishiguchi G, Wu Q, Schwalb B, Shashikadze B, McGowan K, Actis M, Aggarwal A, Shi Z, Price J, Mayasundari A, Yang L, Bednarz A, Machata S, Graef T, Bartoschek D, Demichev V, Ohmayer U, Yang J, Daub H, Rankovic Z. Unbiased mapping of cereblon neosubstrate landscape by high-throughput proteomics. Nature Communications 2025, 16: 7773. PMID: 40835825, PMCID: PMC12368047, DOI: 10.1038/s41467-025-62829-0.Peer-Reviewed Original ResearchConceptsMolecular glue degradersHigh-throughput proteomic platformsData-independent acquisition mass spectrometryDIA-MSMass spectrometryHigh-throughput proteomicsSmall moleculesDrug discoveryGlue degradersRelationship analysisLabel-freeScreening approachTarget proteinsPhenylNovel degradersImideDegradation of target proteinsProteomics platformUbiquitin-proteasome systemNeosubstratesLigandDegradationSpectrometryMoleculesProteome-wide screening approachA robust multiplex-DIA workflow profiles protein turnover regulations associated with cisplatin resistance and aneuploidy
Salovska B, Li W, Bernhardt O, Germain P, Wang Q, Gandhi T, Reiter L, Liu Y. A robust multiplex-DIA workflow profiles protein turnover regulations associated with cisplatin resistance and aneuploidy. Nature Communications 2025, 16: 5034. PMID: 40447611, PMCID: PMC12125295, DOI: 10.1038/s41467-025-60319-x.Peer-Reviewed Original ResearchConceptsMS platformsMass spectrometryDrug discoveryCisplatin resistanceDegradation kineticsDegradation profileAssociated with cisplatin resistanceProtein turnoverLabeled channelsProtein complex subunitsRespiratory complex IMitochondrial metabolic adaptationRobust workflowProtein degradation profilesCancer cell modelsMeasure protein turnoverProtein turnover regulationProteome dynamicsSpectrometryHigh-throughputComplex ICellular processesComplex subunitsSILAC labelingAneuploid genomesAutomated Quality Assurance Rules for Liquid Chromatography–Mass Spectrometry Testing in a Clinical Laboratory
Cassella-Mclane G, McGowan M, Kodger J, Durant T. Automated Quality Assurance Rules for Liquid Chromatography–Mass Spectrometry Testing in a Clinical Laboratory. Clinics In Laboratory Medicine 2025, 45: 221-232. PMID: 40348434, DOI: 10.1016/j.cll.2025.01.006.Peer-Reviewed Original ResearchConceptsCollege of American PathologistsClinical Laboratory Improvement AmendmentsClinical benefit to patientsTherapeutic drug monitoringBenefits to patientsDrug monitoringLiquid chromatography-tandem mass spectrometryClinical laboratoriesLC-MS/MSChromatography-tandem mass spectrometryAmerican PathologistsDietary monitoringClinicData reviewBiochemical geneticsSpectrometry testCLSIMass spectrometryPatientsReviewEndocrinologyRecent Advances in Mass Spectrometry-Based Bottom-Up Proteomics
Movassaghi C, Sun J, Jiang Y, Turner N, Chang V, Chung N, Chen R, Browne E, Lin C, Schweppe D, Malaker S, Meyer J. Recent Advances in Mass Spectrometry-Based Bottom-Up Proteomics. Analytical Chemistry 2025, 97: 4728-4749. PMID: 40000226, PMCID: PMC12117541, DOI: 10.1021/acs.analchem.4c06750.Peer-Reviewed Original ResearchQuantitative Glycan-Protein Cross-Linking Mass Spectrometry Using Enrichable Linkers Reveals Extensive Glycan-Mediated Protein Interaction Networks
Chen S, Xie Y, Alvarez M, Sheng Y, Bouchibti Y, Chang V, Lebrilla C. Quantitative Glycan-Protein Cross-Linking Mass Spectrometry Using Enrichable Linkers Reveals Extensive Glycan-Mediated Protein Interaction Networks. Analytical Chemistry 2025, 97: 1584-1593. PMID: 39805041, PMCID: PMC11780575, DOI: 10.1021/acs.analchem.4c04134.Peer-Reviewed Original ResearchMeSH KeywordsCell Line, TumorCross-Linking ReagentsGlycopeptidesGlycoproteinsHumansMass SpectrometryPolysaccharidesProtein Interaction MapsConceptsProtein-protein interactionsProtein interaction networkCell surface glycansTerminal sialic acidAbundant membrane proteinProtein pairsCross-linking mass spectrometrySurface glycansAffinity purificationInteraction networkSialylated glycoformsMembrane proteinsLysine residuesProtein networkTarget proteinsSialic acidGlycansBiotin groupPolypeptide moietyProteinInteractomeExtensive interactionsCell membranePeptide pairsPolypeptide
2024
Development of a High-Throughput Platform for Quantitation of Histone Modifications on a New QTOF Instrument
Zahn E, Xie Y, Liu X, Karki R, Searfoss R, de Luna Vitorino F, Lempiäinen J, Gongora J, Lin Z, Zhao C, Yuan Z, Garcia B. Development of a High-Throughput Platform for Quantitation of Histone Modifications on a New QTOF Instrument. Molecular & Cellular Proteomics 2024, 24: 100897. PMID: 39708910, PMCID: PMC11787651, DOI: 10.1016/j.mcpro.2024.100897.Peer-Reviewed Original ResearchConceptsData-independent acquisitionModified histone peptidesLC-MSMass spectrometry (MS)-based approachesMicroflow liquid chromatographyNanoflow LC-MSPost-translational modificationsIsobaric peptidesQTOF instrumentLC gradientSequential window acquisitionHistone post-translational modificationsMass spectrometerHistone peptidesTransforming growth factor beta 1Histone deacetylase inhibitorsHistone samplesWindow acquisitionOrbitrapLow stoichiometryLiquid chromatographyCharacterization of histone PTMsHigh-throughput methodDeacetylase inhibitorsInstrumentation timeUsing in vivo intact structure for system-wide quantitative analysis of changes in proteins
Son A, Kim H, Diedrich J, Bamberger C, McClatchy D, Lipton S, Yates J. Using in vivo intact structure for system-wide quantitative analysis of changes in proteins. Nature Communications 2024, 15: 9310. PMID: 39468068, PMCID: PMC11519357, DOI: 10.1038/s41467-024-53582-x.Peer-Reviewed Original ResearchConceptsAlzheimer's diseaseProtein footprinting methodGlobal expression profilingIn vivo conformationStructural alterations of proteinsCo-expressed proteinsMass spectrometry-based methodsAlterations of proteinsProteostasis dysfunctionSpectrometry-based methodsProtein misfoldingConformation of proteinsStructural changesLysine residuesDynamic structural changesBiological functionsProteomics experimentsDimethyl labelingExpression profilesProtein conformationConformational changesProteinIntact proteinDesign of therapeutic interventionsMeasuring dynamic structural changesImmuneApp for HLA-I epitope prediction and immunopeptidome analysis
Xu H, Hu R, Dong X, Kuang L, Zhang W, Tu C, Li Z, Zhao Z. ImmuneApp for HLA-I epitope prediction and immunopeptidome analysis. Nature Communications 2024, 15: 8926. PMID: 39414796, PMCID: PMC11484853, DOI: 10.1038/s41467-024-53296-0.Peer-Reviewed Original ResearchMeSH KeywordsAllelesComputational BiologyDeep LearningEpitopesHistocompatibility Antigens Class IHumansLigandsMass SpectrometryPeptidesProteomicsAnalysis 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 ResearchTargeted metabolomics-based understanding of the sleep disturbances in drug-naïve patients with schizophrenia
Yan H, Li G, Zhang X, Zhang C, Li M, Qiu Y, Sun W, Dong Y, Li S, Li J. Targeted metabolomics-based understanding of the sleep disturbances in drug-naïve patients with schizophrenia. BMC Psychiatry 2024, 24: 355. PMID: 38741058, PMCID: PMC11089724, DOI: 10.1186/s12888-024-05805-0.Peer-Reviewed Original ResearchConceptsPositive and Negative Symptom ScaleDrug-naive patientsLiquid chromatography-mass spectrometryDrug-naive schizophreniaAssociated with sleep disturbancesOrthogonal partial least squares discriminant analysisSleep disturbancePittsburgh Sleep Quality IndexPartial least-squares discriminant analysisMetabolomics-based approachNegative Symptom ScaleChromatography-mass spectrometryCharacteristic metabolitesSchizophreniaSymptom ScaleMethodsPlasma samplesPotential biological mechanismsSleep Quality IndexClinical symptomsGlycerophospholipid metabolismPartial correlation analysisHealthy controlsMetabolomic analysisPatientsBackgroundSleep disturbanceGlycoproteomics: 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 ResearchBERNN: Enhancing classification of Liquid Chromatography Mass Spectrometry data with batch effect removal neural networks
Pelletier S, Leclercq M, Roux-Dalvai F, de Geus M, Leslie S, Wang W, Lam T, Nairn A, Arnold S, Carlyle B, Precioso F, Droit A. BERNN: Enhancing classification of Liquid Chromatography Mass Spectrometry data with batch effect removal neural networks. Nature Communications 2024, 15: 3777. PMID: 38710683, PMCID: PMC11074280, DOI: 10.1038/s41467-024-48177-5.Peer-Reviewed Original ResearchMeSH KeywordsChromatography, LiquidHumansMass SpectrometryNeural Networks, ComputerReproducibility of ResultsConceptsLC-MS experimentsLC-MSLiquid chromatography mass spectrometry dataComplex biological samplesMass spectrometry dataLiquid chromatography mass spectrometryChromatography mass spectrometryMass spectrometrySpectrometry dataEffective removalBiological samplesExperimental conditionsBatch effect removalSample processing protocolBatch effectsSpectrometryBatch effect correction methodsCorrecting batch effectsRemoval of batch effects
2023
Mass spectrometry in cerebrospinal fluid uncovers association of glycolysis biomarkers with Alzheimer’s disease in a large clinical sample
de Geus M, Leslie S, Lam T, Wang W, Roux-Dalvai F, Droit A, Kivisakk P, Nairn A, Arnold S, Carlyle B. Mass spectrometry in cerebrospinal fluid uncovers association of glycolysis biomarkers with Alzheimer’s disease in a large clinical sample. Scientific Reports 2023, 13: 22406. PMID: 38104170, PMCID: PMC10725469, DOI: 10.1038/s41598-023-49440-3.Peer-Reviewed Original ResearchHuman-specific features and developmental dynamics of the brain N-glycome
Klarić T, Gudelj I, Santpere G, Novokmet M, Vučković F, Ma S, Doll H, Risgaard R, Bathla S, Karger A, Nairn A, Luria V, Bečeheli I, Sherwood C, Ely J, Hof P, Sousa A, Josić D, Lauc G, Sestan N. Human-specific features and developmental dynamics of the brain N-glycome. Science Advances 2023, 9: eadg2615. PMID: 38055821, PMCID: PMC10699788, DOI: 10.1126/sciadv.adg2615.Peer-Reviewed Original ResearchThe SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics
Huang X, Gan Z, Cui H, Lan T, Liu Y, Caron E, Shao W. The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics. Nucleic Acids Research 2023, 52: d1062-d1071. PMID: 38000392, PMCID: PMC10767952, DOI: 10.1093/nar/gkad1068.Peer-Reviewed Original ResearchAnalysis of Cell Glycogen with Quantitation and Determination of Branching Using Liquid Chromatography–Mass Spectrometry
Chen S, Bouchibti Y, Xie Y, Chen Y, Chang V, Lebrilla C. Analysis of Cell Glycogen with Quantitation and Determination of Branching Using Liquid Chromatography–Mass Spectrometry. Analytical Chemistry 2023, 95: 12884-12892. PMID: 37584460, PMCID: PMC11672122, DOI: 10.1021/acs.analchem.3c02230.Peer-Reviewed Original ResearchMeSH KeywordsChromatography, High Pressure LiquidChromatography, LiquidEdaravoneGlucoseGlycogenHumansInsulinsMass SpectrometryConceptsUHPLC/QqQ-MSDegree of branchingUltra-high-performance liquid chromatography/triple quadrupole mass spectrometryLiquid chromatography/triple quadrupole mass spectrometryQuadrupole mass spectrometryLiquid chromatography-mass spectrometryChromatography-mass spectrometryPMP derivatizationStructure determinationMass spectrometryDetermination of branchesHep G2) cellsLinkage analysisGlycogen phenotypeToxic to cellsBiological samplesHuman hepatocellular carcinomaBiological functionsSucrose gradientsEnzyme resultsGlucose residuesEffect of insulinSpectrometryInsulin-resistant statesFunction of glycogenStudying Membrane Protein–Lipid Specificity through Direct Native Mass Spectrometric Analysis from Tunable Proteoliposomes
Panda A, Brown C, Gupta K. Studying Membrane Protein–Lipid Specificity through Direct Native Mass Spectrometric Analysis from Tunable Proteoliposomes. Journal Of The American Society For Mass Spectrometry 2023, 34: 1917-1927. PMID: 37432128, PMCID: PMC10932607, DOI: 10.1021/jasms.3c00110.Peer-Reviewed Original ResearchConceptsIntegral membrane proteinsMembrane proteinsNative mass spectrometryTrafficking pathwaysPlasma membraneEukaryotic integral membrane proteinsEndoplasmic reticulumBiophysical propertiesMembrane protein assemblySynaptic vesiclesCellular trafficking pathwaysOrganellar membranesLipid specificityTransmembrane proteinProtein assembliesMembrane contextMass spectrometric analysisProteinNative mass spectrometric analysesVAMP2Lipid compositionExogenous ligandsLipid membranesIndividual lipidsMembraneUnlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery
Stutzmann C, Peng J, Wu Z, Savoie C, Sirois I, Thibault P, Wheeler A, Caron E. Unlocking the potential of microfluidics in mass spectrometry-based immunopeptidomics for tumor antigen discovery. Cell Reports Methods 2023, 3: 100511. PMID: 37426761, PMCID: PMC10326451, DOI: 10.1016/j.crmeth.2023.100511.Commentaries, Editorials and LettersMeSH KeywordsAntigens, NeoplasmHistocompatibility Antigens Class IHLA AntigensHumansMass SpectrometryMicrofluidicsNeoplasmsConceptsSingle-cell proteomicsMicrofluidic technologyPotential of microfluidicsMass spectrometrySample preparationDroplet microfluidicsDigital microfluidicsMicrofluidic methodPhysical moleculesMicrofluidicsHigh sensitivityReproducible mannerPillar arraysRecent advancesSpectrometryMoleculesImmunopeptidomicsPowerful toolProteomicsPreparationMsPeptidesSolutionDirect determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer
Panda A, Giska F, Duncan A, Welch A, Brown C, McAllister R, Hariharan P, Goder J, Coleman J, Ramakrishnan S, Pincet F, Guan L, Krishnakumar S, Rothman J, Gupta K. Direct determination of oligomeric organization of integral membrane proteins and lipids from intact customizable bilayer. Nature Methods 2023, 20: 891-897. PMID: 37106230, PMCID: PMC10932606, DOI: 10.1038/s41592-023-01864-5.Peer-Reviewed Original ResearchConceptsIntegral membrane proteinsMembrane proteinsOligomeric organizationOligomeric stateNative mass spectrometry analysisFunctional oligomeric stateKey membrane componentMass spectrometry analysisNMS analysisTarget membraneLipid bindingMembrane componentsProteolipid vesiclesMembrane compositionLipid compositionSpectrometry analysisLipid membranesNeurotransmitter releaseProteinMembraneLipidsMembrane propertiesDirect determinationBilayersTransporters
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply