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
Proteomics 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
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
2005
Proteomics and the Analysis of Proteomic Data: An Overview of Current Protein‐Profiling Technologies
Gulcicek EE, Colangelo CM, McMurray W, Stone K, Williams K, Wu T, Zhao H, Spratt H, Kurosky A, Wu B. Proteomics and the Analysis of Proteomic Data: An Overview of Current Protein‐Profiling Technologies. Current Protocols In Bioinformatics 2005, 10: 13.1.1-13.1.31. PMID: 18428746, PMCID: PMC3863626, DOI: 10.1002/0471250953.bi1301s10.Peer-Reviewed Original ResearchConceptsProtein/peptide chemistryHundreds of proteinsProtein profiling technologiesPeptide chemistryBioanalytical chemistryProteomic methodologiesChromatographic separationProteomic dataMass spectrometryCellular biologyBiological fluidsCell typesChemistryRelative levelsDiverse scientific disciplinesProteomicsSpectrometryBiologyBioinformaticsProteinSeparationExpression
2003
Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data
Wu B, Abbott T, Fishman D, McMurray W, Mor G, Stone K, Ward D, Williams K, Zhao H. Comparison of statistical methods for classification of ovarian cancer using mass spectrometry data. Bioinformatics 2003, 19: 1636-1643. PMID: 12967959, DOI: 10.1093/bioinformatics/btg210.Peer-Reviewed Original Research
2002
Reverse-Phase HPLC Separation of Enzymatic Digests of Proteins
Stone K, Williams K. Reverse-Phase HPLC Separation of Enzymatic Digests of Proteins. 2002, 0: 533-540. DOI: 10.1385/1-59259-169-8:533.Peer-Reviewed Original ResearchReversed-phase HPLCEnzymatic digestsLaser desorption mass spectrometrySites of chemicalMatrix-assisted laser desorption mass spectrometryRelative elution positionsDesorption mass spectrometryMobile phase resultsReversed-phase HPLC separationTotal hydrophobicityAqueous mixturesMass spectrometryVolatile solventsReversephase HPLCHPLC separationLarge peptidesParticular separationComplex mixturesExcellent reproducibilitySlow kineticsEdman sequencingRetention coefficientTight bindingHydrophobic amino acidsHPLC
1998
Use of liquid chromatography‐electrospray ionization‐tandem mass spectrometry (LC‐ESI‐MS/MS) for routine identification of enzymatically digested proteins separated by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis
Stone K, Deangelis R, LoPresti M, Jones J, Papov V, Williams K. Use of liquid chromatography‐electrospray ionization‐tandem mass spectrometry (LC‐ESI‐MS/MS) for routine identification of enzymatically digested proteins separated by sodium dodecyl sulfate‐polyacrylamide gel electrophoresis. Electrophoresis 1998, 19: 1046-1052. PMID: 9638951, DOI: 10.1002/elps.1150190620.Peer-Reviewed Original ResearchConceptsSodium dodecyl sulfate-polyacrylamide gel electrophoresisQuadrupole ion trap mass spectrometerIon trap mass spectrometerDodecyl sulfate-polyacrylamide gel electrophoresisLow pmol levelSulfate-polyacrylamide gel electrophoresisIonization tandem mass spectrometryTrap mass spectrometerLiquid chromatography-electrospray ionization-tandem mass spectrometryLiquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) analysisMS/MS approachProtein identificationIonization tandem mass spectrometry analysisFmol levelFacile approachMass spectrometry analysisMass spectrometerEng et alMass spectrometryPmol levelLC-MS/MS approachTryptic digestMS approachSpectrometry analysisGel electrophoresis
1996
Purification and characterization of a recombinant hepatitis E protein vaccine candidate by liquid chromatography-mass spectrometry
McAtee C, Zhang Y, Yarbough P, Fuerst T, Stone K, Samander S, Williams K. Purification and characterization of a recombinant hepatitis E protein vaccine candidate by liquid chromatography-mass spectrometry. Journal Of Chromatography B 1996, 685: 91-104. PMID: 8930757, DOI: 10.1016/0378-4347(96)00143-0.Peer-Reviewed Original ResearchConceptsMass spectrometryCarboxyl terminusReversed phase liquid chromatographyAmino terminusLaser desorption mass spectrometryDesorption mass spectrometryMolecular massLiquid chromatography-mass spectrometryCarboxyl-terminal sequencingChromatography-mass spectrometryBaculovirus expression vectorSodium dodecyl sulfate-polyacrylamide gel electrophoresisDodecyl sulfate-polyacrylamide gel electrophoresisSulfate-polyacrylamide gel electrophoresisLC-MSLiquid chromatographyExpression vectorTerminal sequencingSequence analysisPolyacrylamide gel electrophoresisSpectrometryIntact proteinInternal sequencesDoublet proteinsTerminusMatrix-Assisted Laser Desorption Ionization Mass Spectrometry as a Complement to Internal Protein Sequencing
Williams K, Samandar S, Stone K, Saylor M, Rush J. Matrix-Assisted Laser Desorption Ionization Mass Spectrometry as a Complement to Internal Protein Sequencing. Springer Protocols Handbooks 1996, 541-555. DOI: 10.1007/978-1-60327-259-9_91.Peer-Reviewed Original ResearchLaser desorption ionization mass spectrometryDesorption ionization mass spectrometryIonization mass spectrometryMass spectrometryMatrix-Assisted Laser Desorption Ionization Mass SpectrometryInternal protein sequencingBiological moleculesMALDI-MSSimple instrumentationSpectrometryBiochemical laboratoryMass analysis methodProtein sequencingMoleculesHigh throughputReverse-Phase HPLC Separation of Enzymatic Digests of Proteins
Stone K, Williams K. Reverse-Phase HPLC Separation of Enzymatic Digests of Proteins. Springer Protocols Handbooks 1996, 427-434. DOI: 10.1007/978-1-60327-259-9_72.Peer-Reviewed Original ResearchReversed-phase HPLCEnzymatic digestsLaser desorption mass spectrometrySites of chemicalMatrix-assisted laser desorption mass spectrometryRelative elution positionsDesorption mass spectrometryMobile phase resultsReversed-phase HPLC separationTotal hydrophobicityAqueous mixturesMass spectrometryVolatile solventsHPLC separationLarge peptidesComplex mixturesParticular separationExcellent reproducibilitySlow kineticsEdman sequencingRetention coefficientTight bindingHydrophobic amino acidsHPLCRelative insolubility
1995
Identifying Sites of Posttranslational Modifications in Proteins Via HPLC Peptide Mapping
Williams K, Stone K. Identifying Sites of Posttranslational Modifications in Proteins Via HPLC Peptide Mapping. Methods In Molecular Biology 1995, 40: 157-175. PMID: 7633521, DOI: 10.1385/0-89603-301-5:157.Peer-Reviewed Original ResearchConceptsHPLC peptide mappingMass spectrometryPosttranslational modificationsIntact proteinPeptide mappingAtomic mass unitsAccurate massNet chargeDifferent posttranslational modificationsSulfoxide formationMass unitsCovalent changesOxidationSpectrometryProtein stabilityDeamidationProteinIsoelectric focusingPhosphorylationModification
1991
State‐of‐the‐art biomolecular core facilities: a comprehensive survey1
Niece R, Beach C, Cook R, Hathaway G, Williams K. State‐of‐the‐art biomolecular core facilities: a comprehensive survey1. The FASEB Journal 1991, 5: 2756-2760. PMID: 1916100, DOI: 10.1096/fasebj.5.13.1916100.Peer-Reviewed Original Research
1990
[21] Reversed-phase high-performance liquid chromatography for fractionation of enzymatic digests and chemical cleavage products of proteins
Stone K, Elliott J, Peterson G, McMurray W, Williams K. [21] Reversed-phase high-performance liquid chromatography for fractionation of enzymatic digests and chemical cleavage products of proteins. Methods In Enzymology 1990, 193: 389-412. PMID: 2074828, DOI: 10.1016/0076-6879(90)93429-o.Peer-Reviewed Original ResearchConceptsHigh-performance liquid chromatographyReversed-phase high-performance liquid chromatographyReversed phase high performance liquid chromatographyLiquid chromatographyEnzymatic digestsHigh peak capacityMass spectrometric approachProtein chemistsSpectrometric approachMass spectrometryPeak capacityComplex mixturesMolecular weightChemical cleavageGradient timeCleavage productsChromatographyTryptic peptidesPeptidesDigestsChemistsSpectrometryFractionationProductsPrimary structure