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 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