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
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
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 throughput
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