2024
A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs
Brown C, Ghosh S, McAllister R, Kumar M, Walker G, Sun E, Aman T, Panda A, Kumar S, Li W, Coleman J, Liu Y, Rothman J, Bhattacharyya M, Gupta K. A proteome-wide quantitative platform for nanoscale spatially resolved extraction of membrane proteins into native nanodiscs. Nature Methods 2024, 1-10. PMID: 39609567, DOI: 10.1038/s41592-024-02517-x.Peer-Reviewed Original ResearchTarget membrane proteinsMembrane proteinsMembrane contextSynaptic vesicle membrane proteinVesicle membrane proteinsMammalian membrane proteinsMembrane-active polymersExtraction of membrane proteinsNative nanodiscsOrganellar membranesNative membrane environmentMultiprotein complexesMolecular contextCellular membranesMembrane environmentQuantitative platformBioanalytical approachesExtraction efficiencyOpen-access databasesProteinMembraneExtraction conditionsNanodiscsTarget MPPTMoreR-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 speciesPTMProteomicsKinaseMammalsProteinFibroblast expression of transmembrane protein smoothened governs microenvironment characteristics after acute kidney injury
Gui Y, Fu H, Palanza Z, Tao J, Lin Y, Min W, Qiao Y, Bonin C, Hargis G, Wang Y, Yang P, Kreutzer D, Wang Y, Liu Y, Yu Y, Liu Y, Zhou D. Fibroblast expression of transmembrane protein smoothened governs microenvironment characteristics after acute kidney injury. Journal Of Clinical Investigation 2024, 134: e165836. PMID: 38713523, PMCID: PMC11213467, DOI: 10.1172/jci165836.Peer-Reviewed Original ResearchNidogen-1Expression of transmembrane proteinsCell-matrix interactionsAcute kidney injuryExtracellular matrix proteinsWnt signaling pathwayGlobal proteomeHedgehog signalingTransmembrane proteinsTubular cell apoptosisSignaling pathwayCell apoptosisMatrix proteinsIntegrin B1Kidney fibroblastsMesenchymal cell activationKidney injuryHedgehogProteinMitigate acute kidney injurySMOPreserved kidney functionAcute kidney injury pathogenesisFibroblastsPhosphoproteome
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
MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells
Jeong J, Shin JH, Li W, Hong JY, Lim J, Hwang JY, Chung JJ, Yan Q, Liu Y, Choi J, Wysolmerski J. MAL2 mediates the formation of stable HER2 signaling complexes within lipid raft-rich membrane protrusions in breast cancer cells. Cell Reports 2021, 37: 110160. PMID: 34965434, PMCID: PMC8762588, DOI: 10.1016/j.celrep.2021.110160.Peer-Reviewed Original ResearchMeSH KeywordsAntineoplastic Agents, ImmunologicalBreast NeoplasmsCell ProliferationCytoskeletal ProteinsDrug Resistance, NeoplasmEndocytosisFemaleHumansMembrane MicrodomainsMyelin and Lymphocyte-Associated Proteolipid ProteinsPhosphoproteinsPlasma Membrane Calcium-Transporting ATPasesReceptor, ErbB-2Sodium-Hydrogen ExchangersTrastuzumabTumor Cells, CulturedConceptsLipid raft formationBreast cancer cellsLipid raftsLipid raft resident proteinsCancer cellsRaft formationRaft-resident proteinsProximity ligation assayProtein complexesMembrane protrusionsProtein interactionsPlasma membraneLigation assayMAL2Membrane stabilityStructural organizationPotential therapeutic targetPhysical interactionMembrane retentionProteinRaftsTherapeutic targetCellsIntracellular calcium concentrationLow intracellular calcium concentration
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 ResearchConceptsRelative protein quantificationData-independent acquisitionData-dependent acquisitionMass spectrometry-based proteomicsSpectrometry-based proteomicsProtein quantificationOverall protein profileAbundant proteinsProtein profilesManual curationProteinMass spectrometry experimentsReproducibility of conclusionsBiological investigationsAbundanceSpectrometry experimentsA Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS
Heusel M, Frank M, Köhler M, Amon S, Frommelt F, Rosenberger G, Bludau I, Aulakh S, Linder MI, Liu Y, Collins BC, Gstaiger M, Kutay U, Aebersold R. A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS. Cell Systems 2020, 10: 133-155.e6. PMID: 32027860, PMCID: PMC7042714, DOI: 10.1016/j.cels.2020.01.001.Peer-Reviewed Original ResearchConceptsSEC-SWATHHundreds of complexesThousands of proteinsAssembly state changesMitotic proteomeProtein complexesProteomic studiesGlobal screenHuman cellsComplex remodelingHigher-level organizationBiological researchKey hallmarksBiochemical reactionsInteractive exploration toolProteinFunctional stateSpecific changesComplexesProteomeCellsMitosisHallmarkRemodelingInterphase
2019
Capillary 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
2018
Similarities and Differences of Blood N-Glycoproteins in Five Solid Carcinomas at Localized Clinical Stage Analyzed by SWATH-MS
Sajic T, Liu Y, Arvaniti E, Surinova S, Williams EG, Schiess R, Hüttenhain R, Sethi A, Pan S, Brentnall TA, Chen R, Blattmann P, Friedrich B, Niméus E, Malander S, Omlin A, Gillessen S, Claassen M, Aebersold R. Similarities and Differences of Blood N-Glycoproteins in Five Solid Carcinomas at Localized Clinical Stage Analyzed by SWATH-MS. Cell Reports 2018, 23: 2819-2831.e5. PMID: 29847809, DOI: 10.1016/j.celrep.2018.04.114.Peer-Reviewed Original ResearchConceptsN-glycoproteinsAvailable proteomic dataSWATH mass spectrometryImmense clinical interestCancer-type specificProteomic changesProteomic dataN-glycositesProteomic workflowParticular carcinomaProtein compositionClinical stageMetastatic stageBlood samplesPatient plasmaSolid carcinomasEarly cancer detectionSWATH-MSTumor tissueSystemic responseCarcinomaProteinEarly detectionClinical interestCancer
2017
Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells
Liu Y, Borel C, Li L, Müller T, Williams EG, Germain PL, Buljan M, Sajic T, Boersema PJ, Shao W, Faini M, Testa G, Beyer A, Antonarakis SE, Aebersold R. Systematic proteome and proteostasis profiling in human Trisomy 21 fibroblast cells. Nature Communications 2017, 8: 1212. PMID: 29089484, PMCID: PMC5663699, DOI: 10.1038/s41467-017-01422-6.Peer-Reviewed Original ResearchConceptsSWATH mass spectrometryPost-transcriptional effectsMitochondrial proteomeProteome remodelingProteomic resourceTranscriptomic dataProteomic dataProtein abundanceProtein turnoverEntire chromosome 21ProteomeProtein expressionPhenotypic manifestationsChromosome 21Fibroblast cellsStoichiometric complexSignificant downregulationMonozygotic twin pair discordantTwin pair discordantMass spectrometryMajor determinantChromosomesProteinPair discordantAbundance
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 ResearchConceptsProtein 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
2015
Quantitative variability of 342 plasma proteins in a human twin population
Liu Y, Buil A, Collins BC, Gillet L, Blum LC, Cheng LY, Vitek O, Mouritsen J, Lachance G, Spector TD, Dermitzakis ET, Aebersold R. Quantitative variability of 342 plasma proteins in a human twin population. Molecular Systems Biology 2015, 11: msb145728. PMID: 25652787, PMCID: PMC4358658, DOI: 10.15252/msb.20145728.Peer-Reviewed Original ResearchConceptsQuantitative variabilityUnique plasma proteinsBlood-based biomarker studiesGenetic controlBiological processesDifferent proteinsDifferent traitsPlasma proteinsProteinAbundance variabilityProtein levelsHuman populationMass spectrometry techniquesSpecific plasma proteinsHuman plasma proteinsGenesRelative contributionTraitsHeritabilitySpectrometry techniquesTwin study designDifferent patternsPopulationClinical biomarkersVariability
2014
A repository of assays to quantify 10,000 human proteins by SWATH-MS
Rosenberger G, Koh CC, Guo T, Röst HL, Kouvonen P, Collins BC, Heusel M, Liu Y, Caron E, Vichalkovski A, Faini M, Schubert OT, Faridi P, Ebhardt HA, Matondo M, Lam H, Bader SL, Campbell DS, Deutsch EW, Moritz RL, Tate S, Aebersold R. A repository of assays to quantify 10,000 human proteins by SWATH-MS. Scientific Data 2014, 1: 140031. PMID: 25977788, PMCID: PMC4322573, DOI: 10.1038/sdata.2014.31.Peer-Reviewed Original Research
2011
A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer
Luo X, Liu Y, Wang R, Hu H, Zeng R, Chen H. A high-quality secretome of A549 cells aided the discovery of C4b-binding protein as a novel serum biomarker for non-small cell lung cancer. Journal Of Proteomics 2011, 74: 528-538. PMID: 21262398, DOI: 10.1016/j.jprot.2011.01.011.Peer-Reviewed Original ResearchConceptsNon-small cell lung cancerCellular proteomeCell lung cancerCancer secretomeLung cancerOne-dimensional gel electrophoresisA549 cellsBiomarker discoveryProteomic dataGene expressionSecretory proteinsIntracellular contaminationNovel promising biomarkerNovel serum biomarkersEnzyme-linked immunosorbent assaySecretomeProteinSerum proteomic dataClinical stagingProteomeSerum biomarkersGel electrophoresisC4BP levelsPromising biomarkerImmunosorbent assay