Featured Publications
Multi-omic measurements of heterogeneity in HeLa cells across laboratories
Liu Y, Mi Y, Mueller T, Kreibich S, Williams EG, Van Drogen A, Borel C, Frank M, Germain PL, Bludau I, Mehnert M, Seifert M, Emmenlauer M, Sorg I, Bezrukov F, Bena FS, Zhou H, Dehio C, Testa G, Saez-Rodriguez J, Antonarakis SE, Hardt WD, Aebersold R. Multi-omic measurements of heterogeneity in HeLa cells across laboratories. Nature Biotechnology 2019, 37: 314-322. PMID: 30778230, DOI: 10.1038/s41587-019-0037-y.Peer-Reviewed Original ResearchMeSH KeywordsDNA Copy Number VariationsGenome, HumanGenomicsHeLa CellsHumansProteomeReproducibility of ResultsTranscriptomeConceptsCell linesGenome-wide copy numberMulti-omic measurementsHuman cultured cellsProtein turnover ratesPhenotypic responsesGenomic variabilityDifferent cell linesHeLa variantsSpecific cell linesCopy numberHeLa cellsCultured cellsHeLa cell linePhenotypic variabilityProgressive divergenceTurnover rateCellsBiological variationTechnical variationUniform conditionsTranscriptomeProteomeSuccessive passagesLines
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
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 ResearchMulti-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry
Collins BC, Hunter CL, Liu Y, Schilling B, Rosenberger G, Bader SL, Chan DW, Gibson BW, Gingras AC, Held JM, Hirayama-Kurogi M, Hou G, Krisp C, Larsen B, Lin L, Liu S, Molloy MP, Moritz RL, Ohtsuki S, Schlapbach R, Selevsek N, Thomas SN, Tzeng SC, Zhang H, Aebersold R. Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry. Nature Communications 2017, 8: 291. PMID: 28827567, PMCID: PMC5566333, DOI: 10.1038/s41467-017-00249-5.Peer-Reviewed Original ResearchMeSH KeywordsHEK293 CellsHumansLaboratoriesLaboratory Proficiency TestingMass SpectrometryProteomeProteomicsReproducibility of ResultsConceptsSpectrometry studies
2016
TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics
Röst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R. TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics. Nature Methods 2016, 13: 777-783. PMID: 27479329, PMCID: PMC5008461, DOI: 10.1038/nmeth.3954.Peer-Reviewed Original Research
2013
Quantitative measurements of N‐linked glycoproteins in human plasma by SWATH‐MS
Liu Y, Hüttenhain R, Surinova S, Gillet L, Mouritsen J, Brunner R, Navarro P, Aebersold R. Quantitative measurements of N‐linked glycoproteins in human plasma by SWATH‐MS. Proteomics 2013, 13: 1247-1256. PMID: 23322582, DOI: 10.1002/pmic.201200417.Peer-Reviewed Original Research