2025
Evaluation of dried blood spot with inductively coupled plasma mass spectrometry for trace toxic elements measurement in human biomonitoring
Sun Q, Wang Y, Cui W, Yu X, Bai X, Qiu T, Lu Y, Shi X. Evaluation of dried blood spot with inductively coupled plasma mass spectrometry for trace toxic elements measurement in human biomonitoring. Microchemical Journal 2025, 217: 115100. DOI: 10.1016/j.microc.2025.115100.Peer-Reviewed Original ResearchMass spectrometryInductively coupled plasma mass spectrometryInter-batch precisionLow detection limitPlasma mass spectrometryMatrix-matched calibrationDried Blood SpotsICP-MSMatrix effectsSample extraction methodMatrix interferencesDetection limitSatisfactory intra-Excellent linearityInternal standardWorking curveHuman biomonitoringTrace element determinationHuman whole bloodSpectrometryBlood spotsNational human biomonitoring programElement determinationHuman biomonitoring programsField-deployable methodrtmsEcho: 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 approachIn-depth analysis of the tear fluid glycoproteome reveals diverse lacritin glycosylation and spliceoforms
Chang V, Mahoney K, Lian I, Chen R, Chung N, Utheim T, Karlsson N, Malaker S. In-depth analysis of the tear fluid glycoproteome reveals diverse lacritin glycosylation and spliceoforms. Journal Of Biological Chemistry 2025, 301: 110580. PMID: 40784456, PMCID: PMC12450620, DOI: 10.1016/j.jbc.2025.110580.Peer-Reviewed Original ResearchO-glycoproteomics studiesMass spectrometryGlycan structuresDownstream biological processesProtein-level evidenceBackbone rigidityDiverse groupProtein foldingO-glycosylationExtracellular glycoproteinBiological processesGlycosylation profileO-glycositesBiochemical investigationsGlycansGlycosylationMolecular weightSpectrometrySpliceoformsAntimicrobial activityGlycoproteomicsGlycoproteinProteinComprehensive characterizationLacritinAssociations between fluid biomarkers and PET imaging ([11C]UCB‐J) of synaptic pathology in Alzheimer's disease
Nilsson J, Mecca A, Ashton N, Salardini E, O'Dell R, Carson R, Benedet A, Blennow K, Zetterberg H, van Dyck C, Brinkmalm A. Associations between fluid biomarkers and PET imaging ([11C]UCB‐J) of synaptic pathology in Alzheimer's disease. Alzheimer's & Dementia 2025, 21: e70403. PMID: 40878905, PMCID: PMC12245979, DOI: 10.1002/alz.70403.Peer-Reviewed Original ResearchConceptsPositron emission tomographySynaptic densitySynaptic proteinsMass spectrometryC]UCB-J positron emission tomographyLevels of synaptic proteinsAlzheimer's diseaseReduction of synaptic densityCerebrospinal fluidSynaptic vesicle glycoprotein 2AAssociated with higher levelsSyntaxin 7PEBP-1CN participantsAD groupEarly ADAD patientsSynaptic pathologyPositron emission tomography imagingEmission tomographySV2A positron emission tomographyNeuronal pentraxinsSpectrometryGDI-1Syntaxin 1BKey challenges and recommendations for defining organelle membrane contact sites
Calì T, Bayer E, Eden E, Hajnóczky G, Kornmann B, Lackner L, Liou J, Reinisch K, Rhee H, Rizzuto R, Scorrano L, Brini M. Key challenges and recommendations for defining organelle membrane contact sites. Nature Reviews Molecular Cell Biology 2025, 26: 776-796. PMID: 40550870, DOI: 10.1038/s41580-025-00864-x.Peer-Reviewed Original ResearchMembrane contact sitesContact sitesContact site formationMembrane-bound compartmentsOrganelle interactionsTethering proteinsExtracellular stimuliCellular functionsCellular signalingSuper-resolution microscopyProteomic approachReporter constructsMolecular playersSite dynamicsOrganellesSite formationProteinPhysiological conditionsElectron tomographyExperimental approachExchange of ionsSitesPathological conditionsGeneticsMass spectrometryA 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 genomesDesigning Ultraporous Mesostructured Silica Nanoparticles for the Remediation of Per- and Polyfluoroalkyl Substances
Huang C, Lewis R, Thomas S, Tang Z, Jones J, Nason S, Zuverza-Mena N, Piskulich Z, O’Keefe T, Tuga B, Paredes-Beaulieu A, Vasiliou V, Cui Q, Dalluge J, White J, Haynes C. Designing Ultraporous Mesostructured Silica Nanoparticles for the Remediation of Per- and Polyfluoroalkyl Substances. ACS Nano 2025, 19: 19777-19789. PMID: 40402145, DOI: 10.1021/acsnano.5c02008.Peer-Reviewed Original ResearchConceptsMesostructured silica nanoparticlesPFAS moleculesMolecular dynamics simulationsPolyfluoroalkyl substancesLiquid chromatography-tandem mass spectrometryChromatography-tandem mass spectrometrySilica nanoparticlesNitrogen physisorptionDynamic light scatteringSilica surfaceMass spectrometryDynamics simulationsFunctional groupsUptake of PFASsElectrostatic interactionsChain lengthRemediation of per-PFAS uptakeLC-MS/MSMultiple PFASLight scatteringPromote phytoremediationRemediation strategiesEnvironmental matricesNanoparticlesNative Top–Down Analysis of Membrane Protein Complexes Directly From In Vitro and Native Membranes
Jung W, Panda A, Lee J, Ghosh S, Shaw J, Gupta K. Native Top–Down Analysis of Membrane Protein Complexes Directly From In Vitro and Native Membranes. Molecular & Cellular Proteomics 2025, 24: 100993. PMID: 40378922, PMCID: PMC12305242, DOI: 10.1016/j.mcpro.2025.100993.Peer-Reviewed Original ResearchNative mass spectrometryProtein complexesMembrane proteinsBAM complexTop-down MS/MSAnalysis of membrane protein complexesMembrane-associated protein complexesTarget membrane proteinsNative membranesIntegral membrane proteinsTop-down identificationMembrane protein complexesCell-derived membrane vesiclesMass spectrometryMembrane vesiclesOrganization of proteinsDestabilize lipid bilayersAntibiotic targetsProtein-lipid complexesHeteromeric natureSynthetic liposomesCellular membranesCo-factorNative membrane vesiclesTotal membranesOnline Alkaline-pH Reversed-Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Traditional Phosphoproteomic Analysis via Influencing Charge State Distribution of Phosphopeptides
Wang Y, Gao J, Xie W, Tang M, Chen X, Chen L, Chen H, Yang Z, Gao Q, Liu Y, Zhou H. Online Alkaline-pH Reversed-Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Traditional Phosphoproteomic Analysis via Influencing Charge State Distribution of Phosphopeptides. Journal Of Proteome Research 2025, 24: 2443-2453. PMID: 40205994, DOI: 10.1021/acs.jproteome.4c01091.Peer-Reviewed Original ResearchConceptsNanoelectrospray tandem mass spectrometryPhosphopeptide enrichment techniquesNanoelectrospray ionizationTandem MSMass spectrometerC18 columnNormal adjacent tissuesMass spectrometryPairs of hepatocellular carcinomaPhosphorylated peptidesLiquid chromatography fractionationPhosphopeptidesHigh pHActual polarizationBiological functionsPhosphoproteomic analysisChromatography fractionsIonizationSpectrometryLow pHEnrichment techniquesHepatocellular carcinomaSpectrometerAdjacent tissuesGlobal phosphorylationFluoroMatch IM: An Interactive Software for PFAS Analysis by Ion Mobility Spectrometry
Smolinski R, Koelmel J, Stelben P, Weil D, Godri D, Schiessel D, Kummer M, Stow S, Mohsin S, Royer L, McKenzie-Coe A, Lubinsky T, DeBord D, Chevallier O, Rennie E, Pollitt K, McDonough C. FluoroMatch IM: An Interactive Software for PFAS Analysis by Ion Mobility Spectrometry. Environmental Science And Technology 2025, 59: 6636-6648. PMID: 40133053, PMCID: PMC11984190, DOI: 10.1021/acs.est.4c13846.Peer-Reviewed Original ResearchConceptsCollision cross-sectionsNontargeted analysisAccurate mass matchingMass defect filteringIon mobility spectrometryHigh-resolution mass spectrometryPolyfluoroalkyl substance analysisPolyfluoroalkyl substancesMobility spectrometryDefect filteringNontargeted workflowsIon mobilityWastewater samplesMass matchingMass spectrometryPFAS analysisTrace levelsTarget annotationsComplex mixturesAnalytical chemistsIonsSpectrometryStandard mixEnvironmental samplesChemistsHMBOX1 reverses autophagy mediated 5-fluorouracil resistance through promoting HACE1-induced ubiquitination and degradation of ATG5 in colorectal cancer
Gao Y, Fu S, Peng Y, Zhou Y, Zhu J, Zhang X, Cai C, Han Y, Shen H, Zeng S. HMBOX1 reverses autophagy mediated 5-fluorouracil resistance through promoting HACE1-induced ubiquitination and degradation of ATG5 in colorectal cancer. Autophagy 2025, 21: 1556-1577. PMID: 40126194, PMCID: PMC12282998, DOI: 10.1080/15548627.2025.2477443.Peer-Reviewed Original ResearchColorectal cancer cellsColorectal cancerCancer cellsColorectal cancer tissuesColorectal cancer tissues of patientsLiquid chromatography-tandem mass spectrometryChromatography-tandem mass spectrometryFetal human colonProgression-free survivalClinical colorectal cancer tissuesFirst-line treatmentCell Counting Kit-8Cancer tissues of patientsPostoperative colorectal cancerCaspase 3Transmission electron microscopyCounting Kit-8Tissues of patientsMass spectrometryCleaved caspase 3Stable diseaseComplete responsePartial responseOverall survivalRegulation of chemoresistanceAutomated 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 spectrometryPatientsReviewEndocrinologyApproaching infinite selectivity in membrane-based aqueous lithium extraction via solid-state ion transport
Patel S, Iddya A, Pan W, Qian J, Elimelech M. Approaching infinite selectivity in membrane-based aqueous lithium extraction via solid-state ion transport. Science Advances 2025, 11: eadq9823. PMID: 40020050, PMCID: PMC11870030, DOI: 10.1126/sciadv.adq9823.Peer-Reviewed Original ResearchSolid-state electrolytesLithium extractionHopping of lithium ionsPart-per-billion detection limitsIon-ion selectivityLimitations of mass spectrometryIon transportNext-generation membranesLithium-ionIon migrationPart-per-billionExtract lithiumIon-ionLithium supplyMass spectrometryBattery technologySelectivity valuesMembrane transport propertiesLithiumMembrane materialsNanoporous membranesTransport propertiesIonsElectrolyteSpectrometry
2024
Expanding PFAS Identification with Transformation Product Libraries: Nontargeted Analysis Reveals Biotransformation Products in Mice
Liu S, Dukes D, Koelmel J, Stelben P, Finch J, Okeme J, Lowe C, Williams A, Godri D, Rennie E, Parry E, McDonough C, Pollitt K. Expanding PFAS Identification with Transformation Product Libraries: Nontargeted Analysis Reveals Biotransformation Products in Mice. Environmental Science And Technology 2024, 59: 119-131. PMID: 39704186, PMCID: PMC12097807, DOI: 10.1021/acs.est.4c07750.Peer-Reviewed Original ResearchConceptsMass spectral libraryTransformation productsLiquid chromatography-high resolution mass spectrometryProduct libraryPolyfluoroalkyl substancesBiological transformation productsSpectral libraryFragmentation rulesBehavior of PFASPotential transformation productsMass spectrometryToxicity predictionChemical subclassesReaction productsLiver S9 fractionBiotransformation productsEnzymatic reactionsMutagenic toxicityReactionMouse liver S9 fractionBiological systemsS9 fractionDealkylationChemicalSpectrometryUnraveling O‑Glycan Diversity of Mucins: Insights from SmE Mucinase and Ultraviolet Photodissociation Mass Spectrometry
Helms A, Chang V, Malaker S, Brodbelt J. Unraveling O‑Glycan Diversity of Mucins: Insights from SmE Mucinase and Ultraviolet Photodissociation Mass Spectrometry. Analytical Chemistry 2024, 96: 19230-19237. PMID: 39576755, PMCID: PMC11653425, DOI: 10.1021/acs.analchem.4c02011.Peer-Reviewed Original ResearchUltraviolet photodissociationUltraviolet photodissociation mass spectrometryPhotodissociation Mass SpectrometryDomain proteinsMicroheterogeneity of glycosylationStructural characterizationMass spectrometryGlycan mappingTandem repeatsMUC-16Target proteasesPhotodissociationDiverse classSpectrometryTIM-1ProteinGlycoproteinRapid high-throughput screening of multiple typical mycotoxins in cereals
Chen Y, Nian Q, Zhang Q, Xia Y, Li J, Xu Q, Wang C. Rapid high-throughput screening of multiple typical mycotoxins in cereals. Food Chemistry 2024, 465: 142097. PMID: 39571444, DOI: 10.1016/j.foodchem.2024.142097.Peer-Reviewed Original ResearchDART-MSHigh-throughput screeningReal time mass spectrometryFood safety hazardsTime mass spectrometryMagnetic solid-phase extraction methodSolid-phase extraction methodMatrix effectsMycotoxinsMass spectrometryMultiple mycotoxinsCo-extractionCerealsExtraction methodCoated magnetic particlesPurification abilityWheatCornRiceSafety hazardsCo-contaminantsSpectrometryFoodPolydopamineEvaluation of various mass spectrometry mode based on gas chromatography for quantifying the polycyclic aromatic hydrocarbon metabolites in human urine
Bao S, Qian J, Qiu T, Jiang W, Gu W, Qu Y, Bai X, Yu X, Jiang Y, Tang S, Lv Y, Shi X, Lu Y. Evaluation of various mass spectrometry mode based on gas chromatography for quantifying the polycyclic aromatic hydrocarbon metabolites in human urine. Journal Of Chromatography A 2024, 1739: 465521. PMID: 39566290, DOI: 10.1016/j.chroma.2024.465521.Peer-Reviewed Original ResearchElectron ionizationHuman urinePolycyclic aromatic hydrocarbonsGas chromatographyOH-PAHsHydroxylated polycyclic aromatic hydrocarbonsTandem mass spectrometryRange of compoundsMethod validation criteriaMass spectrometry technologyAromatic hydrocarbonsMass spectrometryHuman exposure to polycyclic aromatic hydrocarbonsExposure to polycyclic aromatic hydrocarbonsPolycyclic aromatic hydrocarbon metabolitesNational human biomonitoring programSample volumeHuman biomonitoring programsHuman biological monitoringIonizationBiomonitoring programsUrine samplesHydrocarbon metabolitesBiological monitoringMinute concentrationsLongitudinal biomonitoring of mycotoxin exposure during pregnancy in the Yale Pregnancy Outcome Prediction Study
Krausová M, Ayeni K, Gu Y, Borutzki Y, O'Bryan J, Perley L, Silasi M, Wisgrill L, Johnson C, Warth B. Longitudinal biomonitoring of mycotoxin exposure during pregnancy in the Yale Pregnancy Outcome Prediction Study. Environment International 2024, 194: 109081. PMID: 39615253, DOI: 10.1016/j.envint.2024.109081.Peer-Reviewed Original ResearchPregnancy Outcome Prediction studyPregnant womenOutcome prediction studiesTandem mass spectrometryLiquid chromatography tandem mass spectrometryPlasma matrixUrine methodMass spectrometryUrinary dataHuman biomonitoringCarcinogen ochratoxin ASerum methodNeoplastic effectsSerumLC-MS/MSMonomethyl etherUnborn childSerum samplesTime pointsUrineBiomarkers of exposurePregnancyAdverse health effectsWomenHuman biomonitoring guidance valuesO-Glycoproteomics: Methods, Challenges, and New Opportunities
Riley N, Malaker S. O-Glycoproteomics: Methods, Challenges, and New Opportunities. 2024, 118-162. DOI: 10.1039/9781839166433-00118.Peer-Reviewed Original ResearchElectron transfer dissociationMass spectrometryBeam-type collision-induced dissociationSupplemental collisional activationCollision-induced dissociationSolid-phase extractionCollisional activationTransfer dissociationGlycopeptide analysisTandem MSO-glycoproteomeDissociationO-glycoproteinsSite-specific localizationGlycopeptidesEThcDO-glycansSpectrometryGlycoproteomicsSpectraElectron
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