2024
Proteomic Profile of Circulating Extracellular Vesicles in the Brain after Δ9-Tetrahydrocannabinol Inhalation
Lallai V, Lam T, Garcia-Milian R, Chen Y, Fowler J, Manca L, Piomelli D, Williams K, Nairn A, Fowler C. Proteomic Profile of Circulating Extracellular Vesicles in the Brain after Δ9-Tetrahydrocannabinol Inhalation. Biomolecules 2024, 14: 1143. PMID: 39334909, PMCID: PMC11430348, DOI: 10.3390/biom14091143.Peer-Reviewed Original ResearchConceptsImmediate early gene c-fosChronic THC exposureEarly gene c-fosCannabinoid 1 receptorGene c-fosSex-specific mannerTHC exposurePsychoactive componentExtracellular vesiclesCentral signaling mechanismDrug effectsTHCChoroid plexus epithelial cellsFemale ratsC-fosPlexus epithelial cellsBrainCannabisRelease of EVsRegulate intercellular communicationCerebrospinal fluidEpithelial cellsIntercellular signaling mediatorsEV signalingIntercellular communicationOptimal conditions for carrying out trypsin digestions on complex proteomes: From bulk samples to single cells
Mansuri M, Bathla S, Lam T, Nairn A, Williams K. Optimal conditions for carrying out trypsin digestions on complex proteomes: From bulk samples to single cells. Journal Of Proteomics 2024, 297: 105109. PMID: 38325732, PMCID: PMC10939724, DOI: 10.1016/j.jprot.2024.105109.Peer-Reviewed Original ResearchComplex proteomesProtein cleavage activityOptimal conditionsTrypsin digestion protocolReversed phase HPLC separationMass spectrometry workflowMS-based proteomicsMass spectrometric analysisC-terminal amino acid residuesTrypsin digestionChromatographic separationDigestion protocolAmino acid residuesHPLC separationMS/MS analysisGlobal proteomic analysisSingle cellsSample matrixSpectrometric analysisCleavage specificityGeneration of peptidesAcid residuesDown proteinsProteomic analysisCleavage activity
2023
Differential Effects of Cocaine and Morphine on the Diurnal Regulation of the Mouse Nucleus Accumbens Proteome
Ketchesin K, Becker-Krail D, Xue X, Wilson R, Lam T, Williams K, Nairn A, Tseng G, Logan R. Differential Effects of Cocaine and Morphine on the Diurnal Regulation of the Mouse Nucleus Accumbens Proteome. Journal Of Proteome Research 2023, 22: 2377-2390. PMID: 37311105, PMCID: PMC10392613, DOI: 10.1021/acs.jproteome.3c00126.Peer-Reviewed Original ResearchConceptsNucleus accumbensDiurnal regulationMouse nucleus accumbensPhase-dependent regulationBrain regionsDiurnal rhythmAdministration of psychostimulantsEffects of cocaineSubstance use disordersDifferential effectsMolecular rhythmsProtein rhythmsQuantitative proteomicsProteomic dataProteomeMorphine administrationUse of substancesRhythm alterationsGlucocorticoid signalingUse disordersMorphineSubstance useProtein expressionCocaineSignificant alterationsUncovering biology by single-cell proteomics
Mansuri M, Williams K, Nairn A. Uncovering biology by single-cell proteomics. Communications Biology 2023, 6: 381. PMID: 37031277, PMCID: PMC10082756, DOI: 10.1038/s42003-023-04635-2.Peer-Reviewed Original Research
2017
Use of a Targeted Urine Proteome Assay (TUPA) to identify protein biomarkers of delayed recovery after kidney transplant
Williams KR, Colangelo CM, Hou L, Chung L, Belcher JM, Abbott T, Hall IE, Zhao H, Cantley LG, Parikh CR. Use of a Targeted Urine Proteome Assay (TUPA) to identify protein biomarkers of delayed recovery after kidney transplant. Proteomics Clinical Applications 2017, 11 PMID: 28261998, PMCID: PMC5549272, DOI: 10.1002/prca.201600132.Peer-Reviewed Original ResearchConceptsImmediate graft functionKidney transplantGraft functionLong-term graft outcomeMore effective treatmentsProtein biomarkersIGF patientsGraft outcomeIGF levelsPoor outcomeEffective treatmentKidney implantationClinical relevanceBiomarker panelPotential biomarkersUrine proteomeDGFTransplantBiomarkersPatientsOutcomesTreatmentEarly stagesAssaysPrognosisData-Independent Acquisition and Parallel Reaction Monitoring Mass Spectrometry Identification of Serum Biomarkers for Ovarian Cancer
Rauniyar N, Peng G, Lam TT, Zhao H, Mor G, Williams KR. Data-Independent Acquisition and Parallel Reaction Monitoring Mass Spectrometry Identification of Serum Biomarkers for Ovarian Cancer. Biomarker Insights 2017, 12: 1177271917710948. PMID: 28615921, PMCID: PMC5462478, DOI: 10.1177/1177271917710948.Peer-Reviewed Original Research
2015
Development of a Targeted Urine Proteome Assay for kidney diseases
Cantley LG, Colangelo CM, Stone KL, Chung L, Belcher J, Abbott T, Cantley JL, Williams KR, Parikh CR. Development of a Targeted Urine Proteome Assay for kidney diseases. Proteomics Clinical Applications 2015, 10: 58-74. PMID: 26220717, PMCID: PMC5003777, DOI: 10.1002/prca.201500020.Peer-Reviewed Original ResearchConceptsKidney diseaseUrinary proteinGraft functionImmediate graft functionDelayed graft functionKidney transplant patientsMultiple kidney diseasesTransplant patientsKidney transplantClinical relevancePotential biomarkersUrine proteomeDiseaseAvailable biofluidBiomarkersPatientsProtein biomarkersAssaysSingle assayProteome changesHuman urineQuantifiable proteinsTransplantProteinPeptidesDevelopment of a highly automated and multiplexed targeted proteome pipeline and assay for 112 rat brain synaptic proteins
Colangelo CM, Ivosev G, Chung L, Abbott T, Shifman M, Sakaue F, Cox D, Kitchen RR, Burton L, Tate SA, Gulcicek E, Bonner R, Rinehart J, Nairn AC, Williams KR. Development of a highly automated and multiplexed targeted proteome pipeline and assay for 112 rat brain synaptic proteins. Proteomics 2015, 15: 1202-1214. PMID: 25476245, PMCID: PMC4698340, DOI: 10.1002/pmic.201400353.Peer-Reviewed Original ResearchYPED: 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
2014
Quantitative proteomics identification of potential protein biomarkers of early recovery after kidney transplant (591.5)
Williams K, Colangelo C, Stone K, Chung L, Abbott T, Belcher J, Marlier A, Cantley L, Parikh C. Quantitative proteomics identification of potential protein biomarkers of early recovery after kidney transplant (591.5). The FASEB Journal 2014, 28 DOI: 10.1096/fasebj.28.1_supplement.591.5.Peer-Reviewed Original ResearchKidney transplantUrine proteomeKidney transplant recipientsPotential urine biomarkersKidney transplant patientsDeceased donor kidneysDGF patientsGraft functionTransplant patientsTransplant recipientsSerum creatinineDonor kidneysUrine biomarkersUrine proteinEarly biomarkersEarly recoveryMass spectrometric-based approachesPotential protein biomarkersFirst weekIGFUrine samplesBiomarkersPatientsTransplantDGF
2013
Quantitative proteomics
Gulcicek E, Williams K. Quantitative proteomics. Methods 2013, 61: 183-185. DOI: 10.1016/j.ymeth.2013.06.016.Peer-Reviewed Original ResearchProteomics and the Analysis of Proteomic Data: 2013 Overview of Current Protein‐Profiling Technologies
Bruce C, Stone K, Gulcicek E, Williams K. Proteomics and the Analysis of Proteomic Data: 2013 Overview of Current Protein‐Profiling Technologies. Current Protocols In Bioinformatics 2013, 41: 13.21.1-13.21.17. PMID: 23504934, PMCID: PMC3688054, DOI: 10.1002/0471250953.bi1321s41.Peer-Reviewed Original ResearchConceptsMore post-translational modificationsStudy of proteomesPost-translational modificationsFragment ionsChemical structureProtein profiling technologiesMass spectrometryProteolytic peptidesCharge ratioProteomic dataProtein sequencesSpectral dataPrecursor proteinProteomeProteomicsProteinQuantitationSpectrometryIons
2012
Yale Center for Clinical Investigation: Leveraging Industry Partnerships and Research Cores
Sherwin R, Slayman C, Rockwell S, Herold K, Williams K, Carson R, Mane S, Seow H, Max J, Johnson T. Yale Center for Clinical Investigation: Leveraging Industry Partnerships and Research Cores. Clinical And Translational Science 2012, 5: 435-436. PMID: 23253663, PMCID: PMC5350809, DOI: 10.1111/cts.12016.Peer-Reviewed Original ResearchA molecular characterization of the choroid plexus and stress-induced gene regulation
Sathyanesan M, Girgenti MJ, Banasr M, Stone K, Bruce C, Guilchicek E, Wilczak-Havill K, Nairn A, Williams K, Sass S, Duman JG, Newton SS. A molecular characterization of the choroid plexus and stress-induced gene regulation. Translational Psychiatry 2012, 2: e139-e139. PMID: 22781172, PMCID: PMC3410626, DOI: 10.1038/tp.2012.64.Peer-Reviewed Original ResearchConceptsStress-induced gene regulationGene expression changesGene expression analysisCP gene expressionGlial fibrillary acidic proteinChoroid plexusMolecular functionsGene regulationSitu hybridization analysisTranscriptomic characterizationHigh-resolution tandem mass spectrometryTarget genesExpression analysisGene expressionExpression changesTarget proteinsCP proteinsMolecular characterizationAdult choroid plexusHybridization analysisCP functionGene profilesProteinBlood-cerebrospinal fluid barrierResolution tandem mass spectrometry
2009
Reverse-Phase HPLC Separation of Enzymatic Digests of Proteins
Stone K, Williams K. Reverse-Phase HPLC Separation of Enzymatic Digests of Proteins. Springer Protocols Handbooks 2009, 941-950. DOI: 10.1007/978-1-59745-198-7_102.Peer-Reviewed Original ResearchLaser desorption mass spectrometrySites of chemicalHigh pressureUltra-high pressureRelative elution positionsBroad peakDesorption mass spectrometryPowerful techniquePhase resultsMobile phase resultsReversed-phase HPLCEnzymatic digestsLC systemRelevant parametersMatrix-assisted laser desorption mass spectrometryMass spectrometric approachReversed-phase HPLC separationReversephase HPLCTotal hydrophobicitySpectrometric approachAqueous mixturesMass spectrometryVolatile solventsResolutionHPLC separationEnzymatic Digestion of Proteins in Solution and in SDS Polyacrylamide Gels
Stone K, Gulcicek E, Williams K. Enzymatic Digestion of Proteins in Solution and in SDS Polyacrylamide Gels. Springer Protocols Handbooks 2009, 905-917. DOI: 10.1007/978-1-59745-198-7_99.Peer-Reviewed Original ResearchProtein of interestSDS-polyacrylamide gelsMass spectrometryGel digestion procedureChemical sequencingLaser desorption ionization mass spectrometryDesorption ionization mass spectrometryElectrospray ionization sourceIonization mass spectrometryComplex biological mixturesMass spectral acquisitionProtein identification analysisTandem mass spectrometrySDS-PAGEMass spectrometric analysisPolyacrylamide gelsIonization sourceNumerous genomesBiological mixturesPeptide mass dataProtein databaseCleavage procedureMass spectrometerGel matrixLC system
2008
The putative oncoprotein DEK, part of a chimera protein associated with acute myeloid leukaemia, is an autoantigen in juvenile rheumatoid arthritis
SIERAKOWSKA H, WILLIAMS K, SZER I, SZER W. The putative oncoprotein DEK, part of a chimera protein associated with acute myeloid leukaemia, is an autoantigen in juvenile rheumatoid arthritis. Clinical & Experimental Immunology 2008, 94: 435-439. PMID: 8252804, PMCID: PMC1534440, DOI: 10.1111/j.1365-2249.1993.tb08214.x.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid SequenceAnimalsArthritis, JuvenileAutoantigensCells, CulturedChild, PreschoolChromatography, High Pressure LiquidChromatography, Ion ExchangeChromosomal Proteins, Non-HistoneElectrophoresis, Polyacrylamide GelHeLa CellsHumansLeukemia, MyeloidMolecular Sequence DataMolecular WeightOncogene ProteinsPeptide MappingPoly-ADP-Ribose Binding ProteinsRatsConceptsJuvenile rheumatoid arthritisAcute myeloid leukemiaRheumatoid arthritisMyeloid leukemiaRare subtypeLeukaemic cellsBone marrowImmunoblot assayRat tissuesDEK proteinArthritisFive-step chromatographic procedureAutoantigensLeukemiaOncogene DEKAntigenSerumPartial amino acid sequencingDEKAmino acid sequencingOncoprotein DEKPatientsSpleenProteinMarrow
2007
X!!Tandem, an Improved Method for Running X!Tandem in Parallel on Collections of Commodity Computers
Bjornson RD, Carriero NJ, Colangelo C, Shifman M, Cheung KH, Miller PL, Williams K. X!!Tandem, an Improved Method for Running X!Tandem in Parallel on Collections of Commodity Computers. Journal Of Proteome Research 2007, 7: 293-299. PMID: 17902638, PMCID: PMC3863625, DOI: 10.1021/pr0701198.Peer-Reviewed Original ResearchIdentification of Proteins Based on MS/MS Spectra and Location of Posttranslational Modifications
Stone K, Crawford M, McMurray W, Williams N, Williams K. Identification of Proteins Based on MS/MS Spectra and Location of Posttranslational Modifications. Methods In Molecular Biology 2007, 386: 57-77. DOI: 10.1007/1-59745-430-3_2.Peer-Reviewed Original Research
2006
Statistical Methods in Proteomics
Yu W, Wu B, Huang T, Li X, Williams K, Zhao H. Statistical Methods in Proteomics. Springer Handbooks 2006, 623-638. DOI: 10.1007/978-1-84628-288-1_34.Peer-Reviewed Original Research