2024
BERNN: 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 Research
2020
Cerebrospinal fluid proteome evaluation in major depressive disorder by mass spectrometry
Franzen AD, Lam TT, Williams KR, Nairn AC, Duman RS, Sathyanesan M, Kumar V, Carpenter LL, Newton SS. Cerebrospinal fluid proteome evaluation in major depressive disorder by mass spectrometry. BMC Psychiatry 2020, 20: 481. PMID: 32998701, PMCID: PMC7528485, DOI: 10.1186/s12888-020-02874-9.Peer-Reviewed Original ResearchMeSH KeywordsDepressive Disorder, MajorGene Expression ProfilingHumansMass SpectrometryProteomeProteomicsConceptsPR domain zinc finger protein 1Bioinformatics analysisZinc finger protein 1Quantitative mass spectrometryFinger protein 1Potential biological functionsMajor canonical pathwaysPeroxisome proliferator-activated receptor gamma coactivatorProliferator-activated receptor gamma coactivatorCellular functionsCellular movementCellular compromiseCell signalingCellular developmentOrganismal injuryBiological functionsReceptor gamma coactivatorCanonical pathwaysSignal transducerUpstream regulatorTranscription 3Protein profilesDifferential expressionProtein synthesisProteomics software
2019
Identification of new biomarkers of bronchopulmonary dysplasia using metabolomics
Piersigilli F, Lam TT, Vernocchi P, Quagliariello A, Putignani L, Aghai ZH, Bhandari V. Identification of new biomarkers of bronchopulmonary dysplasia using metabolomics. Metabolomics 2019, 15: 20. PMID: 30830433, DOI: 10.1007/s11306-019-1482-9.Peer-Reviewed Original ResearchConceptsBronchopulmonary dysplasiaPreterm neonatesNew biomarkersNeonatal intensive care unitMost preterm infantsIntensive care unitNovel specific biomarkersTracheal aspirate samplesSub-group analysisGestational age differencesPreterm infantsCare unitAspirate samplesNeonatesSpecific biomarkersFirst weekC16-OHIsoleucine levelsSelect metabolitesBiomarkersDysplasiaPartial least squares discriminant analysisLeast squares discriminant analysisSquares discriminant analysisAge differences
2018
ProteomicsBrowser: MS/proteomics data visualization and investigation
Peng G, Wilson R, Tang Y, Lam TT, Nairn AC, Williams K, Zhao H. ProteomicsBrowser: MS/proteomics data visualization and investigation. Bioinformatics 2018, 35: 2313-2314. PMID: 30462190, PMCID: PMC6596887, DOI: 10.1093/bioinformatics/bty958.Peer-Reviewed Original Research
2017
MELK Promotes Melanoma Growth by Stimulating the NF-κB Pathway
Janostiak R, Rauniyar N, Lam TT, Ou J, Zhu LJ, Green MR, Wajapeyee N. MELK Promotes Melanoma Growth by Stimulating the NF-κB Pathway. Cell Reports 2017, 21: 2829-2841. PMID: 29212029, PMCID: PMC5726781, DOI: 10.1016/j.celrep.2017.11.033.Peer-Reviewed Original ResearchConceptsMaternal embryonic leucine zipper kinaseMelanoma growthSkin cancer-related deathsMelanoma cellsNF-κB pathway activityMAPK pathwayCancer-related deathNF-κB pathwayEmbryonic leucine zipper kinaseLeucine zipper kinaseMELK knockdownCurrent therapiesMELK inhibitionImportant downstream mediatorShort-term benefitsPharmacological inhibitionTranscription factor E2F1Downstream mediatorBRAFV600E inhibitorsSequestosome 1Pathway activityMELK functionMediatorsCell culturesInhibitionThe repeat region of cortactin is intrinsically disordered in solution
Li X, Tao Y, Murphy JW, Scherer AN, Lam TT, Marshall AG, Koleske AJ, Boggon TJ. The repeat region of cortactin is intrinsically disordered in solution. Scientific Reports 2017, 7: 16696. PMID: 29196701, PMCID: PMC5711941, DOI: 10.1038/s41598-017-16959-1.Peer-Reviewed Original ResearchConceptsCortactin repeatsRepeat regionActin filamentsHydrogen-deuterium exchange mass spectrometryAdjacent helical regionsMulti-domain proteinsExchange mass spectrometryExtensive biophysical analysisCircular dichroismHydrophobic core regionSmall-angle X-ray scatteringBiophysical analysisHelical regionCortactinRepeatsSimilar copiesUnfolded peptidesProteinMotifSize exclusion chromatographyMass spectrometryFilamentsExclusion chromatographyX-ray scatteringRegionBrain Region and Isoform-Specific Phosphorylation Alters Kalirin SH2 Domain Interaction Sites and Calpain Sensitivity
Miller MB, Yan Y, Machida K, Kiraly DD, Levy AD, Wu YI, Lam TT, Abbott T, Koleske AJ, Eipper BA, Mains RE. Brain Region and Isoform-Specific Phosphorylation Alters Kalirin SH2 Domain Interaction Sites and Calpain Sensitivity. ACS Chemical Neuroscience 2017, 8: 1554-1569. PMID: 28418645, PMCID: PMC5517348, DOI: 10.1021/acschemneuro.7b00076.Peer-Reviewed Original ResearchConceptsLong-term potentiationCalpain sensitivityEffects of cocaineRat nucleus accumbensAdult rat nucleus accumbensRho GDP/GTP exchange factorRegion-specific effectsChronic cocaineNucleus accumbensSynaptic functionBrain regionsKALRN geneSpine morphologyPrefrontal cortexKal7CocainePotentiationFunctional significanceCalpainPhosphorylation
2013
Palmitoylation of Superoxide Dismutase 1 (SOD1) Is Increased for Familial Amyotrophic Lateral Sclerosis-linked SOD1 Mutants*
Antinone SE, Ghadge GD, Lam TT, Wang L, Roos RP, Green WN. Palmitoylation of Superoxide Dismutase 1 (SOD1) Is Increased for Familial Amyotrophic Lateral Sclerosis-linked SOD1 Mutants*. Journal Of Biological Chemistry 2013, 288: 21606-21617. PMID: 23760509, PMCID: PMC3724620, DOI: 10.1074/jbc.m113.487231.Peer-Reviewed Original ResearchMeSH KeywordsAmyotrophic Lateral SclerosisAnimalsBlotting, WesternCell Line, TumorCell MembraneCysteineDisulfidesHEK293 CellsHumansLipoylationLuminescent ProteinsMass SpectrometryMiceMice, TransgenicMutationNeuronsOxidation-ReductionProtein Processing, Post-TranslationalSpinal CordSuperoxide DismutaseSuperoxide Dismutase-1ConceptsWild-type SOD1Familial amyotrophic lateral sclerosisSuperoxide dismutase 1Copper chaperoneCysteine mutagenesisReversible post-translational modificationAcyl-biotin exchangeDisulfide bondingPost-translational modificationsMass spectrometryWild-type superoxide dismutase 1PalmitoylationSOD1 maturationMotor neuron cell lineProtein structureSOD1 mutantsNeuron cell lineAmyotrophic lateral sclerosisZn-superoxide dismutaseHEK cellsResidues 6ChaperonesCell linesMutagenesisDismutase 1
2010
N-Glycosylation at the SynCAM (Synaptic Cell Adhesion Molecule) Immunoglobulin Interface Modulates Synaptic Adhesion*
Fogel AI, Li Y, Giza J, Wang Q, Lam TT, Modis Y, Biederer T. N-Glycosylation at the SynCAM (Synaptic Cell Adhesion Molecule) Immunoglobulin Interface Modulates Synaptic Adhesion*. Journal Of Biological Chemistry 2010, 285: 34864-34874. PMID: 20739279, PMCID: PMC2966101, DOI: 10.1074/jbc.m110.120865.Peer-Reviewed Original ResearchConceptsN-glycosylationTrans-synaptic interactionsN-glycansSite-specific N-glycansSynaptic cell adhesion molecule 1Site-specific N-glycosylationTrans-synaptic adhesionPost-translational modificationsSelect adhesion moleculesMutational studiesSynaptic adhesionGlycosylation sitesHeterophilic interactionsIg1 domainSynapse inductionPostsynaptic membraneAdhesion moleculesNeurobiological questionsSynaptic cleftStructural modelingPresynaptic terminalsDifferential mannerSialic acidCell adhesion molecule-1Adhesion
2009
Palmitoylation of Nicotinic Acetylcholine Receptors
Alexander JK, Govind AP, Drisdel RC, Blanton MP, Vallejo Y, Lam TT, Green WN. Palmitoylation of Nicotinic Acetylcholine Receptors. Journal Of Molecular Neuroscience 2009, 40: 12-20. PMID: 19693711, PMCID: PMC3523180, DOI: 10.1007/s12031-009-9246-z.Peer-Reviewed Original ResearchMeSH KeywordsAcetylcholineAcylationAlpha7 Nicotinic Acetylcholine ReceptorAnimalsBinding SitesBiological AssayBrainCell LineElectric OrganHumansLigandsLipoylationMass SpectrometryNeuromuscular JunctionProtein Processing, Post-TranslationalProtein SubunitsProtein TransportReceptors, NicotinicSynaptic TransmissionTorpedoConceptsNicotinic acetylcholine receptorsSites of palmitoylationLigand-gated ion channelsDifferent posttranslational modificationsDisulfide bond formationMass spectrometry strategyLigand binding siteLow abundant proteinsAcetylcholine receptorsProtein palmitoylationPosttranslational modificationsSubunit assemblyPalmitoylationAbundant proteinsMuscle-type nAChRsIon channelsLoss of ligandBinding sitesSubunitsSitesReceptorsPhosphorylationTraffickingGlycosylationSensitive assay
2007
Posttranslational modifications on protein kinase c isozymes. Effects of epinephrine and phorbol esters
Robles-Flores M, Meléndez L, García W, Mendoza-Hernández G, Lam TT, Castañeda-Patlán C, González-Aguilar H. Posttranslational modifications on protein kinase c isozymes. Effects of epinephrine and phorbol esters. Biochimica Et Biophysica Acta 2007, 1783: 695-712. PMID: 18295358, DOI: 10.1016/j.bbamcr.2007.07.011.Peer-Reviewed Original Research
2005
Multicomponent Internal Recalibration of an LC−FTICR-MS Analysis Employing a Partially Characterized Complex Peptide Mixture: Systematic and Random Errors
Yanofsky CM, Bell AW, Lesimple S, Morales F, Lam TT, Blakney GT, Marshall AG, Carrillo B, Lekpor K, Boismenu D, Kearney RE. Multicomponent Internal Recalibration of an LC−FTICR-MS Analysis Employing a Partially Characterized Complex Peptide Mixture: Systematic and Random Errors. Analytical Chemistry 2005, 77: 7246-7254. PMID: 16285672, DOI: 10.1021/ac050640q.Peer-Reviewed Original ResearchFourier Transform Ion Cyclotron Resonance Mass Spectrometry for the Analysis of Small Ubiquitin-like Modifier (SUMO) Modification: Identification of Lysines in RanBP2 and SUMO Targeted for Modification during the E3 AutoSUMOylation Reaction
Cooper HJ, Tatham MH, Jaffray E, Heath JK, Lam TT, Marshall AG, Hay RT. Fourier Transform Ion Cyclotron Resonance Mass Spectrometry for the Analysis of Small Ubiquitin-like Modifier (SUMO) Modification: Identification of Lysines in RanBP2 and SUMO Targeted for Modification during the E3 AutoSUMOylation Reaction. Analytical Chemistry 2005, 77: 6310-6319. PMID: 16194093, DOI: 10.1021/ac058019d.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceCyclotronsFourier AnalysisIonsLysineMass SpectrometryMethylationMolecular ChaperonesMolecular Sequence DataMolecular WeightNuclear Pore Complex ProteinsProtein BindingRecombinant ProteinsSequence AlignmentSmall Ubiquitin-Related Modifier ProteinsUbiquitinUbiquitin-Protein LigasesConceptsFourier transform ion cyclotron resonance mass spectrometryTransform ion cyclotron resonance mass spectrometryIon cyclotron resonance mass spectrometryFourier transform ion cyclotron resonanceCyclotron resonance mass spectrometryMass spectrometryTransform ion cyclotron resonanceElectron capture dissociationResonance mass spectrometryMass spectrometry techniquesSUMO modificationIon cyclotron resonanceIdentification of LysinesCapture dissociationFunctional analysisUbiquitin-like protein SUMOLysine residuesSmall ubiquitin-like modifier (SUMO) modificationFT-ICRAcceptor lysine residuesImportant cellular processesSpectrometry techniquesSite-directed mutagenesisSites of sumoylationSUMO polymersIdentifying bryostatins and potential precursors from the bryozoan Bugula neritina
Manning TJ, Land M, Rhodes E, Chamberlin L, Rudloe J, Phillips D, Lam TT, Purcell J, Cooper HJ, Emmett MR, Marshall AG. Identifying bryostatins and potential precursors from the bryozoan Bugula neritina. Natural Product Research 2005, 19: 467-491. PMID: 15938194, DOI: 10.1080/14786410412331280041.Peer-Reviewed Original ResearchConceptsGulf of MexicoGulf of CaliforniaPlasma mass spectrometryPacific OceanWestern rimPoint of harvestingGulfMarine speciesMexicoMass spectrometerPotential precursorsMass spectral featuresEmpirical formulaOriginal sourceOceanSedimentsFlight mass spectrometerMarine invertebratesSpectrometerRimBryozoansLate 1960sCaliforniaSquirtNational Cancer Institute study
2004
Identification of Sites of Ubiquitination in Proteins: A Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Approach
Cooper HJ, Heath JK, Jaffray E, Hay RT, Lam TT, Marshall AG. Identification of Sites of Ubiquitination in Proteins: A Fourier Transform Ion Cyclotron Resonance Mass Spectrometry Approach. Analytical Chemistry 2004, 76: 6982-6988. PMID: 15571350, DOI: 10.1021/ac0401063.Peer-Reviewed Original ResearchConceptsSites of ubiquitinationPolyubiquitin chainsFourier transform ion cyclotron resonance mass spectrometryTransform ion cyclotron resonance mass spectrometryIon electron capture dissociationIon cyclotron resonance mass spectrometryCyclotron resonance mass spectrometryLysine residuesTandem mass spectrometric techniquesElectron capture dissociationResonance mass spectrometryExtensive sequence coverageMass spectrometric techniquesConsequences of ubiquitinationCapture dissociationMass spectrometry approachPolyubiquitinated speciesSingle ubiquitinFT-ICRStructural elucidationCellular functionsUbiquitinated proteinsModified peptideUbiquitination modificationSpectrometric techniques
2003
Identification of Novel Interactions in HIV-1 Capsid Protein Assembly by High-resolution Mass Spectrometry
Lanman J, Lam TT, Barnes S, Sakalian M, Emmett MR, Marshall AG, Prevelige PE. Identification of Novel Interactions in HIV-1 Capsid Protein Assembly by High-resolution Mass Spectrometry. Journal Of Molecular Biology 2003, 325: 759-772. PMID: 12507478, DOI: 10.1016/s0022-2836(02)01245-7.Peer-Reviewed Original ResearchConceptsHigh-resolution mass spectrometryMass spectrometryHIV-1 capsid protein assembliesCapsid protein assemblySupramolecular structuresMature HIV-1 virionsHydrogen exchange protection factorsProtein assembliesChemical crosslinking experimentsCA tubesSpectrometryIntersubunit interactionsProtection factorSubunit interfaceC domain interactionsInteractionStructureSoluble capsid proteinAssemblyCryo-electron microscopy image reconstruction