2024
A fluorescence-based assay for measuring polyamine biosynthesis aminopropyl transferase–mediated catalysis
Singh P, Choi J, Wang W, Lam T, Lechner P, Vanderwal C, Pou S, Nilsen A, Mamoun C. A fluorescence-based assay for measuring polyamine biosynthesis aminopropyl transferase–mediated catalysis. Journal Of Biological Chemistry 2024, 300: 107832. PMID: 39342998, PMCID: PMC11541840, DOI: 10.1016/j.jbc.2024.107832.Peer-Reviewed Original ResearchAminopropyl transferaseFluorescence-based assayLack of high-throughput assaysHigh-throughput screeningCarbon chain lengthChemical librariesMass spectrometryChain lengthHigh-throughput assayDrug discoveryMass spectrometry analysisSaccharomyces cerevisiaeThin-layer chromatographyFluorescence intensityCellular functionsSpectrometry analysisPolycationic moleculesFluorescent conjugatesIsoindoleAPT activityCatalysisAssayBenzeneAdductsEnzymeBERNN: 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 ResearchConceptsLC-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
2021
Cocaine self-administration induces sex-dependent protein expression in the nucleus accumbens
López AJ, Johnson AR, Euston TJ, Wilson R, Nolan SO, Brady LJ, Thibeault KC, Kelly SJ, Kondev V, Melugin P, Kutlu MG, Chuang E, Lam TT, Kiraly DD, Calipari ES. Cocaine self-administration induces sex-dependent protein expression in the nucleus accumbens. Communications Biology 2021, 4: 883. PMID: 34272455, PMCID: PMC8285523, DOI: 10.1038/s42003-021-02358-w.Peer-Reviewed Original ResearchConceptsProtein expression patternsExpression patternsQuantitative mass spectrometrySubstance use disordersCritical biological variableProteomic functionProtein regulationRegulated proteinsUnique molecular profileNucleus accumbensSexual dimorphismProteomeProtein expressionMolecular substratesDrug-induced plasticityMolecular profileChronic neuropsychiatric conditionsPreclinical evidenceBaseline differencesCocaine administrationReward-associated behaviorsUse disordersMass spectrometryMale subjectsBiological variables
2019
Development of Targeted Mass Spectrometry-Based Approaches for Quantitation of Proteins Enriched in the Postsynaptic Density (PSD)
Wilson RS, Rauniyar N, Sakaue F, Lam TT, Williams KR, Nairn AC. Development of Targeted Mass Spectrometry-Based Approaches for Quantitation of Proteins Enriched in the Postsynaptic Density (PSD). Proteomes 2019, 7: 12. PMID: 30986977, PMCID: PMC6630806, DOI: 10.3390/proteomes7020012.Peer-Reviewed Original ResearchParallel reaction monitoringPostsynaptic densityData-independent acquisition (DIA) approachElectron-dense regionsQuantitation of proteinsBiochemical fractionationMass spectrometry analysisMass spectrometry-based assayProtein abundanceExcitatory glutamatergic synapsesPSD compositionProtein compositionPSD proteinsInternal peptide standardsPSD fractionProteinTargeted Mass SpectrometrySpectrometry analysisGlutamatergic synapsesMass spectrometryPeptide standardsAbundanceNeuropsychiatric disordersCortical brain tissueWide variety
2017
The 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 scatteringRegionA multiregional proteomic survey of the postnatal human brain
Carlyle BC, Kitchen RR, Kanyo JE, Voss EZ, Pletikos M, Sousa AMM, Lam TT, Gerstein MB, Sestan N, Nairn AC. A multiregional proteomic survey of the postnatal human brain. Nature Neuroscience 2017, 20: 1787-1795. PMID: 29184206, PMCID: PMC5894337, DOI: 10.1038/s41593-017-0011-2.Peer-Reviewed Original ResearchConceptsProteomic surveyResident plasma membrane proteinsPostnatal human brainProtein dataPlasma membrane proteinsProtein abundance differencesQuantitative tandem mass spectrometryPost-translational eventsWhole transcriptome sequencingRNA expression dataMembrane proteinsFunctional variationExpression dataAbundance differencesBrain regionsTandem mass spectrometryHuman brainSimilar cortical regionsMass spectrometryEarly infancyRNACortical regionsSequencingProteinAbundance
2016
SILAC based protein profiling data of MKK3 knockout mouse embryonic fibroblasts
Srivastava A, Shinn AS, Lam TT, Lee PJ, Mannam P. SILAC based protein profiling data of MKK3 knockout mouse embryonic fibroblasts. Data In Brief 2016, 7: 418-422. PMID: 26977448, PMCID: PMC4782019, DOI: 10.1016/j.dib.2016.02.034.Peer-Reviewed Original ResearchMouse embryonic fibroblastsYale Protein Expression DatabaseIngenuity Pathway AnalysisEmbryonic fibroblastsKnockout mouse embryonic fibroblastsProtein Expression DatabaseWT mouse embryonic fibroblastsQuantitative mass spectrometryWhole cell lysatesTotal proteomeIntegrated DiscoveryMAP kinasePathway analysisAltered pathwaysCell lysatesMass spectrometry dataSILACPhosphopeptide enrichmentProtein levelsExpression databaseProteinSpectrometry dataPathwayFibroblastsMass spectrometry
2015
YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-Based Proteomics Research
Colangelo CM, Shifman M, Cheung KH, Stone KL, Carriero NJ, Gulcicek EE, Lam TT, Wu T, Bjornson RD, Bruce C, Nairn AC, Rinehart J, Miller PL, Williams KR. YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-Based Proteomics Research. Genomics Proteomics & Bioinformatics 2015, 13: 25-35. PMID: 25712262, PMCID: PMC4411476, DOI: 10.1016/j.gpb.2014.11.002.Peer-Reviewed Original ResearchConceptsMultiple reaction monitoringPeptides/proteinsYale Protein Expression DatabaseReaction monitoringProteomics researchMass spectrometry-based proteomics researchMS/MSMass spectrometryDatabase search resultsPeptide identificationSpectral librarySite localizationProteomics communityGroup of laboratoriesSpectrometryProtein Expression DatabaseMS
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
2006
Impact of environmental conditions on the marine natural product bryostatin 1
Manning TJ, Rhodes E, Land M, Parkman R, Sumner B, Lam TT, Marshall¶ A, Phillips D. Impact of environmental conditions on the marine natural product bryostatin 1. Natural Product Research 2006, 20: 611-628. PMID: 16835096, DOI: 10.1080/14786410500462645.Peer-Reviewed Original ResearchConceptsFourier transform ion cyclotron resonanceMarine natural productsUV/Vis absorbance spectroscopyAssisted Laser Desorption Ionization Mass SpectrometryMatrix-Assisted Laser Desorption Ionization Mass SpectrometryTransform ion cyclotron resonanceLaser desorption ionization mass spectrometryDesorption ionization mass spectrometryMetal oxide surfacesIonization mass spectrometryOxide surfaceAbsorbance spectroscopyNatural productsChemical environmentMolar massCation bindingMass spectrometryMolecular modelingUV lightChemical conditionsDifferent structuresAdsorptionSpectroscopyStructureSpectrometryInteraction of packaging motor with the polymerase complex of dsRNA bacteriophage
Lísal J, Kainov DE, Lam TT, Emmett MR, Wei H, Gottlieb P, Marshall AG, Tuma R. Interaction of packaging motor with the polymerase complex of dsRNA bacteriophage. Virology 2006, 351: 73-79. PMID: 16643976, DOI: 10.1016/j.virol.2006.03.025.Peer-Reviewed Original ResearchConceptsC-terminal faceP4 hexamersDsRNA bacteriophagesPackaging motorPolymerase complexHydrogen-deuterium exchangeSubunit interfaceProcapsidRNA loadingBiochemical studiesMolecular motorsEmpty capsidsHexamerViral capsidCapsidMass spectrometryGenomeDsRNAProcessivityBacteriophagesInteractionRegulationAssociates
2005
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
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 polymers
2003
Corrigendum to “Identification of Novel Interactions in HIV-1 Capsid Protein Assembly by High-resolution Mass Spectrometry” [J. Mol. Biol. (2003) 325, 759–772]
Lanman J, Lam T, Barnes S, Sakalian M, Emmett M, Marshall A, Prevelige P. Corrigendum to “Identification of Novel Interactions in HIV-1 Capsid Protein Assembly by High-resolution Mass Spectrometry” [J. Mol. Biol. (2003) 325, 759–772]. Journal Of Molecular Biology 2003, 334: 1133. DOI: 10.1016/j.jmb.2003.10.046.Peer-Reviewed Original ResearchIdentification 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