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 ResearchMeSH KeywordsAmino Acid MotifsAmino Acid SequenceAnimalsHumansMammalsMicePhosphoproteinsPhosphorylationProtein Processing, Post-TranslationalProteomeProteomicsSoftwareSpecies SpecificityConceptsP-siteSurrounding amino acid sequenceKinase-substrate networkQuantitative phosphoproteomic analysisFunctional enrichment analysisPhosphoproteomic resultsKinase motifsComparative phosphoproteomicsPTM sitesPhosphorylation eventsPhosphoproteomic analysisProteomic analysisEnrichment analysisMammalian speciesSpeciesEvolutionary anglePhosphoproteomeMotifEnvironmental factorsNon-human speciesPTMProteomicsKinaseMammalsProtein
2023
The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics
Huang X, Gan Z, Cui H, Lan T, Liu Y, Caron E, Shao W. The SysteMHC Atlas v2.0, an updated resource for mass spectrometry-based immunopeptidomics. Nucleic Acids Research 2023, 52: d1062-d1071. PMID: 38000392, PMCID: PMC10767952, DOI: 10.1093/nar/gkad1068.Peer-Reviewed Original ResearchAnimalsDatabases, ProteinHumansInternetMass SpectrometryPeptidesProtein Processing, Post-TranslationalProteomicsPost‐translational modification and phenotype
Salovska B, Liu Y. Post‐translational modification and phenotype. Proteomics 2023, 23: e2200535. PMID: 36799530, DOI: 10.1002/pmic.202200535.Peer-Reviewed Original ResearchPhenotypeProtein Processing, Post-Translational
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 ResearchMeSH KeywordsIsotope LabelingMass SpectrometryPhosphorylationProtein Processing, Post-TranslationalProteolysisProteomeConceptsPost-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
2020
Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments*
Tsai TH, Choi M, Banfai B, Liu Y, MacLean B, Dunkley T, Vitek O. Selection of Features with Consistent Profiles Improves Relative Protein Quantification in Mass Spectrometry Experiments*. Molecular & Cellular Proteomics 2020, 19: 944-959. PMID: 32234965, PMCID: PMC7261813, DOI: 10.1074/mcp.ra119.001792.Peer-Reviewed Original ResearchMeSH KeywordsDatabases, ProteinMass SpectrometryProtein Processing, Post-TranslationalProteinsProteomicsReproducibility of ResultsSensitivity and SpecificitySoftwareConceptsRelative protein quantificationData-independent acquisitionData-dependent acquisitionMass spectrometry-based proteomicsSpectrometry-based proteomicsProtein quantificationOverall protein profileAbundant proteinsProtein profilesManual curationProteinMass spectrometry experimentsReproducibility of conclusionsBiological investigationsAbundanceSpectrometry experiments
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 ResearchMeSH KeywordsAnimalsComputational BiologyDatabases, ProteinHumansMass SpectrometryProtein Processing, Post-TranslationalProteomeProteomicsSoftwareConceptsUser-friendly web toolWeb softwarePublic datasetsBioinformatics backgroundLarge datasetsWeb toolMotif discoveryOptional featuresDatasetPresentation of motivesExponential growthLocation probabilitySoftwareKinase-substrate relationsModification sitesProtein post-translational modificationsPost-translational modificationsUsabilityUsersToolToolkitNetworkModification motifsPhosphoproteomic datasetsSite enrichment
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 ResearchMeSH KeywordsAlgorithmsApolipoprotein A-IHumansMass SpectrometryPeptidesPhosphopeptidesProtein Processing, Post-TranslationalProteomicsTwinsConceptsPost-translational modifications
2016
On the Dependency of Cellular Protein Levels on mRNA Abundance
Liu Y, Beyer A, Aebersold R. On the Dependency of Cellular Protein Levels on mRNA Abundance. Cell 2016, 165: 535-550. PMID: 27104977, DOI: 10.1016/j.cell.2016.03.014.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsGene Expression RegulationHumansProtein BiosynthesisProtein Processing, Post-TranslationalProteinsProteomicsRNA, MessengerTranscription, GeneticConceptsProtein levelsGene expression regulationCellular protein levelsLong‐term state changeGenotype-phenotype relationshipsExpression regulationMRNA fluctuationsProtein biosynthesisGenomic informationProteomic profilingTranscript levelsGene expressionBiological processesMRNA abundanceLife science researchMRNA levelsShort-term adaptationComplete understandingProtein concentrationBiosynthesisCentral importanceLocal availabilityTranscriptsTemporal variationProtein