2025
Online Alkaline-pH Reversed-Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Traditional Phosphoproteomic Analysis via Influencing Charge State Distribution of Phosphopeptides
Wang Y, Gao J, Xie W, Tang M, Chen X, Chen L, Chen H, Yang Z, Gao Q, Liu Y, Zhou H. Online Alkaline-pH Reversed-Phase Nanoelectrospray-Tandem Mass Spectrometry Complements Traditional Phosphoproteomic Analysis via Influencing Charge State Distribution of Phosphopeptides. Journal Of Proteome Research 2025, 24: 2443-2453. PMID: 40205994, DOI: 10.1021/acs.jproteome.4c01091.Peer-Reviewed Original ResearchConceptsNanoelectrospray tandem mass spectrometryPhosphopeptide enrichment techniquesNanoelectrospray ionizationTandem MSMass spectrometerC18 columnNormal adjacent tissuesMass spectrometryPairs of hepatocellular carcinomaPhosphorylated peptidesLiquid chromatography fractionationPhosphopeptidesHigh pHActual polarizationBiological functionsPhosphoproteomic analysisChromatography fractionsIonizationSpectrometryLow pHEnrichment techniquesHepatocellular carcinomaSpectrometerAdjacent tissuesGlobal phosphorylation
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
A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology
Di Y, Li W, Salovska B, Ba Q, Hu Z, Wang S, Liu Y. A basic phosphoproteomic-DIA workflow integrating precise quantification of phosphosites in systems biology. Biophysics Reports 2023, 9: 82-98. PMID: 37753060, PMCID: PMC10518521, DOI: 10.52601/bpr.2023.230007.Peer-Reviewed Original ResearchPost-translational modificationsData-independent acquisitionSystems biologySite-specific phosphorylation eventsImportant post-translational modificationMost human proteinsCritical protein functionsPhosphorylation eventsProtein functionPhosphoproteomic studiesPhosphoproteomic analysisBioinformatics AdvancesHuman proteinsMass spectrometry technologyBioinformatics analysisLarge-scale quantificationExperimental workflowHigh-resolution mass spectrometry technologySpectrometry technologyPhosphoproteomicsPhosphorylationBiologyProteinSystems medicineSingle experiment
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