ProteomicsProteomeIsotope LabelingMass SpectrometryTandem Mass SpectrometryChromatography, LiquidElectrophoresis, Gel, Two-DimensionalOxygen IsotopesSpectrometry, Mass, Matrix-Assisted Laser Desorption-IonizationProteinsPeptidesDatabases, ProteinChemical FractionationNitrogen IsotopesComputational BiologyReproducibility of ResultsProtein Array AnalysisSoftwareMetabolic Networks and PathwaysAmino Acid SequenceMolecular Sequence DataIsotopesComplex MixturesGene Expression ProfilingProtein Interaction MappingProtein Processing, Post-TranslationalSequence Analysis, ProteinProtein Interaction MapsSpectrometry, Mass, Electrospray IonizationCluster AnalysisBlood ProteinsPeptide MappingAlgorithmsBiological MarkersSystems BiologyProteolysisBlotting, WesternStaining and LabelingSmall Ubiquitin-Related Modifier ProteinsHeLa CellsSignal TransductionCell Line, TumorReference StandardsProtein BindingChromatography, High Pressure LiquidArabidopsisArabidopsis ProteinsPeptide FragmentsBacterial ProteinsMultiprotein ComplexesAmino AcidsTumor Markers, BiologicalModels, BiologicalNeoplasm ProteinsProteasome Endopeptidase ComplexPlant ProteinsStress, PhysiologicalSaccharomyces cerevisiae ProteinsProtein TransportCell LineSaccharomyces cerevisiaeMembrane ProteinsSubcellular FractionsUbiquitinationGene Expression RegulationGenomicsPhosphorylationLysineCells, CulturedRNA InterferenceElectrophoresis, Polyacrylamide GelTwo-Dimensional Difference Gel ElectrophoresisPlant LeavesMetabolomicsRNA, Small InterferingUp-RegulationGene Expression Regulation, PlantNuclear Proteins