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 ResearchConceptsP-siteSurrounding amino acid sequenceKinase-substrate networkQuantitative phosphoproteomic analysisFunctional enrichment analysisPhosphoproteomic resultsKinase motifsComparative phosphoproteomicsPTM sitesPhosphorylation eventsPhosphoproteomic analysisProteomic analysisEnrichment analysisMammalian speciesSpeciesEvolutionary anglePhosphoproteomeMotifEnvironmental factorsNon-human speciesPTMProteomicsKinaseMammalsProtein
2020
NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses
Wang S, Li W, Hu L, Cheng J, Yang H, Liu Y. NAguideR: performing and prioritizing missing value imputations for consistent bottom-up proteomic analyses. Nucleic Acids Research 2020, 48: e83-e83. PMID: 32526036, PMCID: PMC7641313, DOI: 10.1093/nar/gkaa498.Peer-Reviewed Original ResearchSelection 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 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 ResearchConceptsUser-friendly web toolWeb softwarePublic datasetsBioinformatics backgroundLarge datasetsWeb toolMotif discoveryOptional featuresDatasetPresentation of motivesExponential growthLocation probabilitySoftwareKinase-substrate relationsModification sitesProtein post-translational modificationsPost-translational modificationsUsabilityUsersToolToolkitNetworkModification motifsPhosphoproteomic datasetsSite enrichmentAssessing 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
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