2024
BERNN: Enhancing classification of Liquid Chromatography Mass Spectrometry data with batch effect removal neural networks
Pelletier S, Leclercq M, Roux-Dalvai F, de Geus M, Leslie S, Wang W, Lam T, Nairn A, Arnold S, Carlyle B, Precioso F, Droit A. BERNN: Enhancing classification of Liquid Chromatography Mass Spectrometry data with batch effect removal neural networks. Nature Communications 2024, 15: 3777. PMID: 38710683, PMCID: PMC11074280, DOI: 10.1038/s41467-024-48177-5.Peer-Reviewed Original ResearchConceptsLC-MS experimentsLC-MSLiquid chromatography mass spectrometry dataComplex biological samplesMass spectrometry dataLiquid chromatography mass spectrometryChromatography mass spectrometryMass spectrometrySpectrometry dataEffective removalBiological samplesExperimental conditionsBatch effect removalSample processing protocolBatch effectsSpectrometryBatch effect correction methodsCorrecting batch effectsRemoval of batch effects
2015
YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-Based Proteomics Research
Colangelo CM, Shifman M, Cheung KH, Stone KL, Carriero NJ, Gulcicek EE, Lam TT, Wu T, Bjornson RD, Bruce C, Nairn AC, Rinehart J, Miller PL, Williams KR. YPED: An Integrated Bioinformatics Suite and Database for Mass Spectrometry-Based Proteomics Research. Genomics Proteomics & Bioinformatics 2015, 13: 25-35. PMID: 25712262, PMCID: PMC4411476, DOI: 10.1016/j.gpb.2014.11.002.Peer-Reviewed Original ResearchConceptsMultiple reaction monitoringPeptides/proteinsYale Protein Expression DatabaseReaction monitoringProteomics researchMass spectrometry-based proteomics researchMS/MSMass spectrometryDatabase search resultsPeptide identificationSpectral librarySite localizationProteomics communityGroup of laboratoriesSpectrometryProtein Expression DatabaseMS
2006
Impact of environmental conditions on the marine natural product bryostatin 1
Manning TJ, Rhodes E, Land M, Parkman R, Sumner B, Lam TT, Marshall¶ A, Phillips D. Impact of environmental conditions on the marine natural product bryostatin 1. Natural Product Research 2006, 20: 611-628. PMID: 16835096, DOI: 10.1080/14786410500462645.Peer-Reviewed Original ResearchConceptsFourier transform ion cyclotron resonanceMarine natural productsUV/Vis absorbance spectroscopyAssisted Laser Desorption Ionization Mass SpectrometryMatrix-Assisted Laser Desorption Ionization Mass SpectrometryTransform ion cyclotron resonanceLaser desorption ionization mass spectrometryDesorption ionization mass spectrometryMetal oxide surfacesIonization mass spectrometryOxide surfaceAbsorbance spectroscopyNatural productsChemical environmentMolar massCation bindingMass spectrometryMolecular modelingUV lightChemical conditionsDifferent structuresAdsorptionSpectroscopyStructureSpectrometry
2003
Corrigendum to “Identification of Novel Interactions in HIV-1 Capsid Protein Assembly by High-resolution Mass Spectrometry” [J. Mol. Biol. (2003) 325, 759–772]
Lanman J, Lam T, Barnes S, Sakalian M, Emmett M, Marshall A, Prevelige P. Corrigendum to “Identification of Novel Interactions in HIV-1 Capsid Protein Assembly by High-resolution Mass Spectrometry” [J. Mol. Biol. (2003) 325, 759–772]. Journal Of Molecular Biology 2003, 334: 1133. DOI: 10.1016/j.jmb.2003.10.046.Peer-Reviewed Original ResearchIdentification of Novel Interactions in HIV-1 Capsid Protein Assembly by High-resolution Mass Spectrometry
Lanman J, Lam TT, Barnes S, Sakalian M, Emmett MR, Marshall AG, Prevelige PE. Identification of Novel Interactions in HIV-1 Capsid Protein Assembly by High-resolution Mass Spectrometry. Journal Of Molecular Biology 2003, 325: 759-772. PMID: 12507478, DOI: 10.1016/s0022-2836(02)01245-7.Peer-Reviewed Original ResearchConceptsHigh-resolution mass spectrometryMass spectrometryHIV-1 capsid protein assembliesCapsid protein assemblySupramolecular structuresMature HIV-1 virionsHydrogen exchange protection factorsProtein assembliesChemical crosslinking experimentsCA tubesSpectrometryIntersubunit interactionsProtection factorSubunit interfaceC domain interactionsInteractionStructureSoluble capsid proteinAssemblyCryo-electron microscopy image reconstruction