2020
SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles
Rosenberger G, Heusel M, Bludau I, Collins BC, Martelli C, Williams EG, Xue P, Liu Y, Aebersold R, Califano A. SECAT: Quantifying Protein Complex Dynamics across Cell States by Network-Centric Analysis of SEC-SWATH-MS Profiles. Cell Systems 2020, 11: 589-607.e8. PMID: 33333029, PMCID: PMC8034988, DOI: 10.1016/j.cels.2020.11.006.Peer-Reviewed Original ResearchConceptsProtein-protein interactionsProtein complexesCell statesProtein complex dynamicsNative protein complexesMacromolecular complex formationPaper's transparent peer review processProtein interaction networksSEC-SWATHMultiple cell statesNetwork-centric analysisCellular processesInteraction networksMass spectrometric data analysisProteome OrganizationMolecular mechanismsRegulatory roleMass spectrometric analysisNetwork-based studyMultiplexed characterizationComplex formationSpectrometric data analysisSpectrometric analysisAlgorithmic toolkitState-specific changes
2016
Deep Phosphoproteomic Measurements Pinpointing Drug Induced Protective Mechanisms in Neuronal Cells
Yu C, Gao J, Zhou Y, Chen X, Xiao R, Zheng J, Liu Y, Zhou H. Deep Phosphoproteomic Measurements Pinpointing Drug Induced Protective Mechanisms in Neuronal Cells. Frontiers In Physiology 2016, 7: 635. PMID: 28066266, PMCID: PMC5179568, DOI: 10.3389/fphys.2016.00635.Peer-Reviewed Original ResearchAlzheimer's diseaseNeuro-2a cellsTau protein phosphorylationIrreversible neurological disordersDrug effectsNeurological disordersNeuronal cellsOlder populationClass IProtective mechanismPhosphorylation levelsNeuron systemDrug candidatesOxidative damageDiseaseMolecular mechanismsCellsInflammationQuantitative phosphoproteomeSILAC labelingPhosphoproteomic approachPhosphorylation changesNOS1PhosphorylationMice