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
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 studiesSILACProteoformsPeptidoforms
2021
A peptidoform based proteomic strategy for studying functions of post‐translational modifications
Liu Y. A peptidoform based proteomic strategy for studying functions of post‐translational modifications. Proteomics 2021, 22: e2100316. PMID: 34878717, PMCID: PMC8959388, DOI: 10.1002/pmic.202100316.Peer-Reviewed Original Research
2019
motifeR: An Integrated Web Software for Identification and Visualization of Protein Posttranslational Modification Motifs
Wang S, Cai Y, Cheng J, Li W, Liu Y, Yang H. motifeR: An Integrated Web Software for Identification and Visualization of Protein Posttranslational Modification Motifs. Proteomics 2019, 19: e1900245. PMID: 31622013, DOI: 10.1002/pmic.201900245.Peer-Reviewed Original ResearchConceptsUser-friendly web toolWeb softwarePublic datasetsBioinformatics backgroundLarge datasetsWeb toolMotif discoveryOptional featuresDatasetPresentation of motivesExponential growthLocation probabilitySoftwareKinase-substrate relationsModification sitesProtein post-translational modificationsPost-translational modificationsUsabilityUsersToolToolkitNetworkModification motifsPhosphoproteomic datasetsSite enrichmentCapillary zone electrophoresis-tandem mass spectrometry with ultraviolet photodissociation (213 nm) for large-scale top–down proteomics
McCool EN, Chen D, Li W, Liu Y, Sun L. Capillary zone electrophoresis-tandem mass spectrometry with ultraviolet photodissociation (213 nm) for large-scale top–down proteomics. Analytical Methods 2019, 11: 2855-2861. PMID: 31608127, PMCID: PMC6788745, DOI: 10.1039/c9ay00585d.Peer-Reviewed Original ResearchN-terminal acetylationPost-translational modificationsCapillary zone electrophoresis-tandem mass spectrometryN-terminal glycineSize-exclusion chromatography (SEC) fractionationProteomic datasetsZebrafish brainDifferent proteoformsBrain samplesProteoformsCZE-MS/MSProteomicsMass spectrometryTrimethylationAcetylationCalmodulinProteinUltraviolet photodissociationMyristoylationBackbone cleavageSEC fractionsMolecular weightGlobal scaleHigh throughputExperimental evidence
2017
Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS
Rosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmström L, Aebersold R. Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Nature Biotechnology 2017, 35: 781-788. PMID: 28604659, PMCID: PMC5593115, DOI: 10.1038/nbt.3908.Peer-Reviewed Original ResearchConceptsPost-translational modifications