2022
Toward a hypothesis‐free understanding of how phosphorylation dynamically impacts protein turnover
Li W, Salovska B, Fornasiero E, Liu Y. Toward a hypothesis‐free understanding of how phosphorylation dynamically impacts protein turnover. Proteomics 2022, 23: e2100387. PMID: 36422574, PMCID: PMC10964180, DOI: 10.1002/pmic.202100387.Peer-Reviewed Original ResearchConceptsPost-translational modificationsProtein turnoverDynamic stable isotope labelingCell starvationStable isotope labelingData-independent acquisition mass spectrometryAcquisition mass spectrometryProteome levelTurnover diversityPhosphoproteomic datasetsPhosphorylation stoichiometryMetabolic labelingIsotope labelingMass spectrometryPhosphorylationAmino acidsCell culturesBiological perspectiveStarvationTurnoverTurnover measurementsRecent studiesSILACProteoformsPeptidoforms
2021
BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples
Salovska B, Li W, Di Y, Liu Y. BoxCarmax: A High-Selectivity Data-Independent Acquisition Mass Spectrometry Method for the Analysis of Protein Turnover and Complex Samples. Analytical Chemistry 2021, 93: 3103-3111. PMID: 33533601, PMCID: PMC8959401, DOI: 10.1021/acs.analchem.0c04293.Peer-Reviewed Original ResearchConceptsData-independent acquisitionProtein turnoverDIA mass spectrometryStable isotope labelingValuable biological insightsRelative protein quantificationSerum starvation stressIsotopic labeling approachSILAC experimentsStarvation stressConventional DIA methodGas-phase separation strategyBiological insightsDegradation regulationIsotope labelingCultured cellsAmino acidsDIA-MSProtein quantificationLabeling approachPeptide pairsCell culturesBiological investigationsMultiplexed acquisitionComplex samples
2020
Global and Site-Specific Effect of Phosphorylation on Protein Turnover
Wu C, Ba Q, Lu D, Li W, Salovska B, Hou P, Mueller T, Rosenberger G, Gao E, Di Y, Zhou H, Fornasiero EF, Liu Y. Global and Site-Specific Effect of Phosphorylation on Protein Turnover. Developmental Cell 2020, 56: 111-124.e6. PMID: 33238149, PMCID: PMC7855865, DOI: 10.1016/j.devcel.2020.10.025.Peer-Reviewed Original ResearchConceptsProtein turnoverProtein lifetimeCyclin-dependent kinase substrateStable isotope-labeled amino acidsSite-specific phosphorylationPulse-labeling approachIsotope-labeled amino acidsMass spectrometry-based methodCell fitnessKinase substratePhosphorylation sitesPhosphorylated sitesProteomic methodsCell signalingSpectrometry-based methodsLive cellsAmino acidsPhosphositesRich resourceDisease biologyLabeling approachPhosphorylationModification typesGlutamic acidTurnover