2003
A proteomics approach to understanding protein ubiquitination
Peng J, Schwartz D, Elias J, Thoreen C, Cheng D, Marsischky G, Roelofs J, Finley D, Gygi S. A proteomics approach to understanding protein ubiquitination. Nature Biotechnology 2003, 21: 921-926. PMID: 12872131, DOI: 10.1038/nbt849.Peer-Reviewed Original ResearchConceptsProtein ubiquitinationProteomic approachUbiquitin conjugatesPolyubiquitin chain topologyAmino acid sequence determinationUbiquitin-protein conjugatesSaccharomyces cerevisiae lysateUbiquitination sitesUnexpected diversityMultidimensional liquid chromatographyProtein modificationLarge-scale analysisLysine residuesSequence determinationUbiquitinationUbiquitinTandem mass spectrometryMass spectrometryProteinGlobal scaleDiversityLysatesResiduesChain topologyTrypsin
2002
Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC−MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome
Peng J, Elias J, Thoreen C, Licklider L, Gygi S. Evaluation of Multidimensional Chromatography Coupled with Tandem Mass Spectrometry (LC/LC−MS/MS) for Large-Scale Protein Analysis: The Yeast Proteome. Journal Of Proteome Research 2002, 2: 43-50. PMID: 12643542, DOI: 10.1021/pr025556v.Peer-Reviewed Original ResearchConceptsStrong cation exchangeTandem mass spectrometryMass spectrometryMS/MS spectraComplex protein mixturesReversed-phase chromatographyTwo-dimensional separationMS/MS analysisMultidimensional chromatographyMS/MSMS spectraFraction collectionCation exchangeProtein mixturesSCX chromatographyRP-LCLiquid chromatographyMS analysisChromatographyPeptide identificationSEQUEST algorithmSpectrometryYeast protein databaseSingle analysisLarge-scale protein analysisAutomation of Nanoscale Microcapillary Liquid Chromatography−Tandem Mass Spectrometry with a Vented Column
Licklider L, Thoreen C, Peng J, Gygi S. Automation of Nanoscale Microcapillary Liquid Chromatography−Tandem Mass Spectrometry with a Vented Column. Analytical Chemistry 2002, 74: 3076-3083. PMID: 12141667, DOI: 10.1021/ac025529o.Peer-Reviewed Original ResearchConceptsPeptide mixturesSample introduction stepComplex peptide mixturesTandem MS experimentsMS analysisReversed phase LC-MS/MS analysisLiquid chromatography-tandem mass spectrometry analysisColumn enrichmentPeptide samplesElectrospray sourceMass spectrometry analysisMS experimentsCapillary columnLarge sample volumesMass spectrometryLC-MS/MS analysisColumn washingIntroduction stepChromatography fractionsLine separationSpectrometry analysisNano-LCLoop injectorSample volumeColumn