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
2019
Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1
Mehnert M, Li W, Wu C, Salovska B, Liu Y. Combining Rapid Data Independent Acquisition and CRISPR Gene Deletion for Studying Potential Protein Functions: A Case of HMGN1. Proteomics 2019, 19: e1800438. PMID: 30901150, DOI: 10.1002/pmic.201800438.Peer-Reviewed Original ResearchConceptsChromosomal protein HMG-14DIA-MSDIA mass spectrometryPotential protein functionsCRISPR-Cas gene editingImmune regulation processesCancer cellsExtracellular proteomeChromatin structureHistone inactivationFunctional annotationProtein functionCellular functionsRegulation eventsImportant functional implicationsHMG 14Gene knockoutEnrichment analysisData-independent acquisitionHMGN1Protein deletionCRISPR experimentsGene editingStress pathwaysIndependent acquisitionQuantification 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