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
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
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 acquisition