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
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 experimentsIsoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation
Salovska B, Zhu H, Gandhi T, Frank M, Li W, Rosenberger G, Wu C, Germain P, Zhou H, Hodny Z, Reiter L, Liu Y. Isoform‐resolved correlation analysis between mRNA abundance regulation and protein level degradation. Molecular Systems Biology 2020, 16: msb199170. PMID: 32175694, PMCID: PMC7073818, DOI: 10.15252/msb.20199170.Peer-Reviewed Original ResearchConceptsProtein degradationGenome-wide correlation analysisGene dosage variationProtein abundance levelsStable isotope-labeled amino acidsIndividual protein isoformsSpecific biological processesAlternative splicing isoformsData-independent acquisition mass spectrometryIsotope-labeled amino acidsAcquisition mass spectrometryProtein degradation ratesIntron retentionCellular functionsProtein isoformsSplicing isoformsCellular organellesTranscriptome variabilitySame geneTurnover controlRegulatory mechanismsBiological processesSpecific mRNAsTight associationAbundance levels
2019
Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins
Shao W, Guo T, Toussaint N, Xue P, Wagner U, Li L, Charmpi K, Zhu Y, Wu J, Buljan M, Sun R, Rutishauser D, Hermanns T, Fankhauser C, Poyet C, Ljubicic J, Rupp N, Rüschoff J, Zhong Q, Beyer A, Ji J, Collins B, Liu Y, Rätsch G, Wild P, Aebersold R. Comparative analysis of mRNA and protein degradation in prostate tissues indicates high stability of proteins. Nature Communications 2019, 10: 2524. PMID: 31175306, PMCID: PMC6555818, DOI: 10.1038/s41467-019-10513-5.Peer-Reviewed Original ResearchConceptsProtein degradationMass spectrometric methodDegradation of mRNAAnalysis of mRNASpectrometric methodStability of proteinsMass spectrometryRNA-seqIndicator of sample qualitySWATH mass spectrometryDegree of protein degradationMRNA degradationClinical sample cohortsProteomic analysisClinical tissuesProteinMRNAMolecular measurementsConfounding conclusionsAssessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition
Li W, Chi H, Salovska B, Wu C, Sun L, Rosenberger G, Liu Y. Assessing the Relationship Between Mass Window Width and Retention Time Scheduling on Protein Coverage for Data-Independent Acquisition. Journal Of The American Society For Mass Spectrometry 2019, 30: 1396-1405. PMID: 31147889, DOI: 10.1007/s13361-019-02243-1.Peer-Reviewed Original Research
2017
Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses
Rosenberger G, Bludau I, Schmitt U, Heusel M, Hunter CL, Liu Y, MacCoss MJ, MacLean BX, Nesvizhskii AI, Pedrioli PGA, Reiter L, Röst HL, Tate S, Ting YS, Collins BC, Aebersold R. Statistical control of peptide and protein error rates in large-scale targeted data-independent acquisition analyses. Nature Methods 2017, 14: 921-927. PMID: 28825704, PMCID: PMC5581544, DOI: 10.1038/nmeth.4398.Peer-Reviewed Original ResearchComparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues
Faktor J, Sucha R, Paralova V, Liu Y, Bouchal P. Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues. Proteomics 2017, 17 PMID: 27966270, DOI: 10.1002/pmic.201600323.Peer-Reviewed Original ResearchMeSH KeywordsHumansLimit of DetectionMass SpectrometryNeoplasmsProteinsProteomicsSignal-To-Noise RatioConceptsDifferent clinical-pathological characteristicsClinical pathological characteristicsHuman cancer tissuesClinical studiesCancer tissuesBreast tumorsTumor tissueCoefficient of varianceNumerous conditionsCancer researchMass spectrometry-based proteomic approachMultiple protein analytesProteomic approachTissueSequential window acquisition
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
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
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