2024
PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals
Wang S, Di Y, Yang Y, Salovska B, Li W, Hu L, Yin J, Shao W, Zhou D, Cheng J, Liu D, Yang H, Liu Y. PTMoreR-enabled cross-species PTM mapping and comparative phosphoproteomics across mammals. Cell Reports Methods 2024, 4: 100859. PMID: 39255793, PMCID: PMC11440062, DOI: 10.1016/j.crmeth.2024.100859.Peer-Reviewed Original ResearchConceptsP-siteSurrounding amino acid sequenceKinase-substrate networkQuantitative phosphoproteomic analysisFunctional enrichment analysisPhosphoproteomic resultsKinase motifsComparative phosphoproteomicsPTM sitesPhosphorylation eventsPhosphoproteomic analysisProteomic analysisEnrichment analysisMammalian speciesSpeciesEvolutionary anglePhosphoproteomeMotifEnvironmental factorsNon-human speciesPTMProteomicsKinaseMammalsProtein
2023
An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells
Zhou W, Li W, Wang S, Salovska B, Hu Z, Tao B, Di Y, Punyamurtula U, Turk B, Sessa W, Liu Y. An optogenetic-phosphoproteomic study reveals dynamic Akt1 signaling profiles in endothelial cells. Nature Communications 2023, 14: 3803. PMID: 37365174, PMCID: PMC10293293, DOI: 10.1038/s41467-023-39514-1.Peer-Reviewed Original ResearchConceptsPhosphorylation sitesSerine/threonine kinase AktMass spectrometry-based phosphoproteomicsThreonine kinase AktAkt-dependent phosphorylationAberrant Akt activationEndothelial cellsKinase substrateKinase AktCell signalingPhosphorylation profilePhenotypic outcomesDownstream signalingAkt activationAkt1 phosphorylationHuman diseasesSystem-level analysisAKT1Vascular endothelial cellsRich resourcePhosphorylationSignalingGrowth factorAktCells
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 ResearchMeSH KeywordsIsotope LabelingMass SpectrometryPhosphorylationProtein Processing, Post-TranslationalProteolysisProteomeConceptsPost-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
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
2018
Radio-sensitizing effects of VE-821 and beyond: Distinct phosphoproteomic and metabolomic changes after ATR inhibition in irradiated MOLT-4 cells
Šalovská B, Janečková H, Fabrik I, Karlíková R, Čecháková L, Ondrej M, Link M, Friedecký D, Tichý A. Radio-sensitizing effects of VE-821 and beyond: Distinct phosphoproteomic and metabolomic changes after ATR inhibition in irradiated MOLT-4 cells. PLOS ONE 2018, 13: e0199349. PMID: 30001349, PMCID: PMC6042708, DOI: 10.1371/journal.pone.0199349.Peer-Reviewed Original ResearchMeSH KeywordsAmino Acid MotifsAtaxia Telangiectasia Mutated ProteinsBinding SitesBiomarkersCell Cycle CheckpointsCell Line, TumorComputational BiologyGamma RaysGene OntologyHumansMetabolomeMetabolomicsPhosphoproteinsPhosphorylationProtein BindingProtein Kinase InhibitorsProteomeProteomicsPyrazinesRadiation ToleranceRadiation-Sensitizing AgentsSignal TransductionSulfonesTOR Serine-Threonine KinasesConceptsVE-821MOLT-4 cellsCellular metabolismOncogene-induced replication stressATR inhibitionATM-deficient cellsDNA damage responseATR/Chk1 pathwayCell biology techniquesDownregulation of mTORAnti-cancer strategyCurrent anti-cancer strategiesReplication stressPhosphorylation sitesDamage responseIrradiation-induced oxidative stressQuantitative proteomicsDNA repairChk1 pathwayCellular eventsBiology techniquesSpecific inhibitorMain regulatorTumor-specific abnormalitiesMTOR inhibition
2014
Radiosensitization of Human Leukemic HL-60 Cells by ATR Kinase Inhibitor (VE-821): Phosphoproteomic Analysis
Šalovská B, Fabrik I, Ďurišová K, Link M, Vávrová J, Řezáčová M, Tichý A. Radiosensitization of Human Leukemic HL-60 Cells by ATR Kinase Inhibitor (VE-821): Phosphoproteomic Analysis. International Journal Of Molecular Sciences 2014, 15: 12007-12026. PMID: 25003641, PMCID: PMC4139827, DOI: 10.3390/ijms150712007.Peer-Reviewed Original ResearchConceptsDNA-dependent protein kinaseVE-821HL-60 cellsNano-liquid chromatography-tandem mass spectrometry analysisCell cycleSequence motif analysisDNA damage responseRadiation-induced double-strand breaksATR kinase inhibitorsDNA damage repairDNA damaging agentsHuman leukemic HL-60 cellsDouble-strand breaksSpecific ATR inhibitorActivity of kinasesInhibitor VE-821Leukemic HL-60 cellsCell cycle arrestQuantitative phosphoproteomicsATR kinaseMotif analysisPhosphorylation sitesCellular processesDamage responsePhosphoproteomic analysis
2013
Radio-sensitization of human leukaemic MOLT-4 cells by DNA-dependent protein kinase inhibitor, NU7441
Tichy A, Durisova K, Salovska B, Pejchal J, Zarybnicka L, Vavrova J, Dye N, Sinkorova Z. Radio-sensitization of human leukaemic MOLT-4 cells by DNA-dependent protein kinase inhibitor, NU7441. Radiation And Environmental Biophysics 2013, 53: 83-92. PMID: 24100951, DOI: 10.1007/s00411-013-0494-5.Peer-Reviewed Original ResearchConceptsDNA-dependent protein kinasePhosphorylation of H2A.XMOLT-4 cellsDNA-dependent protein kinase inhibitorDNA repair signalingProtein kinase inhibitorsAnti-apoptotic Mcl-1Cleavage of PARPHistone H2A.X.Cdc25A phosphataseProtein kinaseRepair signalingMolecular mechanismsNU7441Mcl-1Detection of IRDNA damageSpecific inhibitorPhosphorylationDetection of proteinsH2A.XSubsequent inductionKinase inhibitorsWestern blottingApoptosis
2011
Phosphoproteomics: Searching for a needle in a haystack
Tichy A, Salovska B, Rehulka P, Klimentova J, Vavrova J, Stulik J, Hernychova L. Phosphoproteomics: Searching for a needle in a haystack. Journal Of Proteomics 2011, 74: 2786-2797. PMID: 21839867, DOI: 10.1016/j.jprot.2011.07.018.Peer-Reviewed Original ResearchConceptsCharacterization of phosphoproteinsReversible phosphorylationCellular processesSignal transductionCell divisionNon-phosphorylated peptidesGene expressionInsufficient ionizationLow abundanceTryptic protein digestsMass spectrometryCritical roleProtein digestsEnrichment techniquePhosphoproteomePhosphoproteomicsPhosphoproteinPowerful toolTransductionPhosphorylationPhosphopeptidesProteinAbundanceApoptosisDifferentiation