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
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 studiesSILACProteoformsPeptidoformsSILAC-IodoTMT for Assessment of the Cellular Proteome and Its Redox Status
Vajrychova M, Salovska B, Pimkova K, Fabrik I, Hodny Z. SILAC-IodoTMT for Assessment of the Cellular Proteome and Its Redox Status. Methods In Molecular Biology 2022, 2603: 259-268. PMID: 36370286, DOI: 10.1007/978-1-0716-2863-8_21.Peer-Reviewed Original ResearchConceptsHigh-resolution mass spectrometryIodoacetyl tandem mass tagLiquid chromatography separationMass spectrometry-based approachQuantification of proteinsStable isotope labelingChromatography separationTandem mass tagsMass spectrometryCysteine modificationCellular proteomeGlobal proteomeIsotope labelingMass tagsModification levelsAmino acidsRedox statusProteomeCell culturesSpectrometrySILACSeparationProteinAcidTags
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 samplesLimited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome
Sztacho M, Šalovská B, Červenka J, Balaban C, Hoboth P, Hozák P. Limited Proteolysis-Coupled Mass Spectrometry Identifies Phosphatidylinositol 4,5-Bisphosphate Effectors in Human Nuclear Proteome. Cells 2021, 10: 68. PMID: 33406800, PMCID: PMC7824793, DOI: 10.3390/cells10010068.Peer-Reviewed Original ResearchConceptsGene expressionHuman nuclear proteomeLimited proteolysisLabel-free quantitative mass spectrometryNuclear pore complexGene ontology analysisCell cycle regulationQuantitative mass spectrometryNuclear proteomeProtein effectorsPore complexPol IIRNA splicingOntology analysisMRNA splicingCycle regulationPIP2 bindingProtein interactionsDNA repairBioinformatics analysisNuclear envelopeFunctional domainsMass spectrometry identifiesSpecific proteinsCell cycle
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
2019
Quantification of cellular protein and redox imbalance using SILAC-iodoTMT methodology
Vajrychova M, Salovska B, Pimkova K, Fabrik I, Tambor V, Kondelova A, Bartek J, Hodny Z. Quantification of cellular protein and redox imbalance using SILAC-iodoTMT methodology. Redox Biology 2019, 24: 101227. PMID: 31154163, PMCID: PMC6545335, DOI: 10.1016/j.redox.2019.101227.Peer-Reviewed Original ResearchConceptsCellular proteomeCysteine oxidationProtein thiol residuesRedox statusCellular protein expressionRedox changesCellular redox statusOrganismal physiologyVersatile experimental approachProtein functionCellular proteinsTranscription factorsRedox homeostasisReporter ion quantificationOxidation processMetabolic labelingFunctional analysisProtein turnoverNew analytical methodThiol residuesIon quantificationRedox alterationsRedox modulatingBiological relevanceRedox imbalance
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