Public database repository

Proteomics repository IDs for DDA and DIA LCMS2 datasets

Project Title Investigator Collaborator Datasets Species Tissue Acquisition Approach Enzymes Panorama Public Mass IVE Proteome Xchange PRIDE DOI Submit Date Publish Date Pub Med
Annotation of DDA MS2 spectra for sea urchin embryo DIA assay library constructionAndrew Griffith, Ning Li, Leah MacNivenDonal ManahanLMR0017Strongylocentrotus purpuratusEmbryoDDABottom-upTrypsin MSV000086194PXD021638 10.25345/C5VB6022-Sep-2020  
Construction of a DIA assay library for sea urchin embryosAndrew Griffith, Ning Li, Leah MacNivenDonal ManahanLMR0017Strongylocentrotus purpuratusEmbryoDIABottom-upTrypsinKueltz Lab - UCDavis/DIA assays/LMR0017_Stropu-Embryo    22-Sep-2020  
Integration of time- and dose-dependent effects of salinity stress on the renal proteome of euryhaline tilapiaLarken Root LR0013_Oremo-KidneyOreochromis mossambicusKidneyDDABottom-upTrypsin MSV000086128PXD021439 10.25345/C5JX8T12-Sep-2020  
Optimization of bottom-up and middle-down proteomics for analyzing environmental effects on the epigenetic histone code of tilapiaElizabeth Mojica EAM0011, 12, 13, 14Oreochromis mossambicusGill epithelium, Kidney, TestesDDAMiddle-down, Bottom-upV8 (Glu-C), Trypsin MSV000085954PXD020920 10.25345/C57N0715-Aug-2020  
Identification of the global histone posttranslational modification landscape in testes of euryhaline tilapiaElizabeth Mojica EAM0008-10_Oremo-TestesOreochromis mossambicusTestesDDAMiddle-down, Bottom-upV8 (Glu-C), Trypsin MSV000085723PXD020314 doi:10.25345/C56J1811-Jul-2020  
Identification of the global histone posttranslational modification landscape in gill epithelium of euryhaline tilapiaElizabeth Mojica EAM0008-10_Oremo-GillOreochromis mossambicusGill epitheliumDDAMiddle-down, Bottom-upV8 (Glu-C), Trypsin MSV000085719PXD020311 doi:10.25345/C5QJ2910-Jul-2020  
Identification of the global histone posttranslational modification landscape in kidney of euryhaline tilapiaElizabeth Mojica EAM0008-10_Oremo-KidneyOreochromis mossambicusKidneyDDAMiddle-down, Bottom-upV8 (Glu-C), Trypsin MSV000085702PXD020264 doi:10.25345/C5JX7F08-Jul-2020  
Integration of time- and dose-dependent effects of salinity stress on the branchial proteome of euryhaline tilapiaLarken Root LR0011_Oremo-Gill, LR0012_Oremo-Gill, DK0022_Oremo-GillOreochromis mossambicusGillDDABottom-upTrypsin MSV000085745PXD020364 doi:10.25345/C5HT8G01-Jul-2020  
   XW0003_Oremo-OmBcellsOreochromis mossambicusOmB cellsDDA       30-Jun-2020  
   AY0003_Gasac-EmbryoGasterosteus aculeatusEmbryoDDA       29-Jun-2020  
Regulation of the branchial proteome and transcriptome during salinity acclimation of Nile tilapiaLarken Root, Leah MacNivenAvner Cnaani, Aurora Campo (ARO) Volcani Center, Israel)LMR0015_Oreni-GillOreochromis niloticusGillDIABottom-upTrypsin     28-Jun-2020  
Regulation of the branchial proteome and transcriptome during salinity acclimation of Nile tilapiaLarken Root, Leah MacNivenAvner Cnaani, Aurora Campo (ARO) Volcani Center, Israel)LMR0015_Oreni-GillOreochromis niloticusGillDDABottom-upTrypsin MSV000085639PXD020064 doi:10.25345/C51H9D28-Jun-2020  
Salinity-dependent regulation of the kidney proteome of Oreochromis niloticusLarken Root, Leah MacNivenAvner Cnaani, Aurora Campo (ARO) Volcani Center, Israel)LMR0015_Oreni-KidneyOreochromis niloticusKidneyDDABottom-upTrypsin MSV000085637PXD020056 doi:10.25345/C5DQ7427-Jun-202025-Aug-2020 
A data-independent acquisition (DIA) assay library for quantitation of environmental effects on the kidney proteome of Oreochromis niloticusLarken Root, Leah MacNivenAvner Cnaani, Aurora Campo (ARO) Volcani Center, Israel)LMR0015_Oreni-KidneyOreochromis niloticusKidneyDIABottom-upTrypsinKueltz-Lab_2020-1.url    27-Jun-202028-Aug-2020 
   TW0003-04_Oremo-OmBcellsOreochromis mossambicusOmB cellsDDA   MSV000085638PXD020057 doi:10.25345/C5573M26-Jun-2020  
   TW0003-04_Oremo-OmBcellsOreochromis mossambicusOmB cellsDIA       26-Jun-2020  
  Jason Podrabsky (Portland State University, OR)JL0014_Ausli-ALWS40NEcellsAustrofundulus limnaeusPSU-ALWS40NE cellsDDA   MSV000085631PXD020017 doi:10.25345/C5CT6G25-Jun-2020  
  Jason Podrabsky (Portland State University, OR)JL0014_Ausli-ALWS40NEcellsAustrofundulus limnaeusPSU-ALWS40NE cellsDIA       25-Jun-2020  
Proteomics of Osmoregulatory Responses in Threespine Stickleback GillsJohn Li DK0028-40_Gasac-GillGasterosteus aculeatusGillDIABottom-upTrypsinb9QCDP.url PXD017662 10.1093/icb/icaa04230-Dec-201919-Feb-202032458981
An osmolality/salinity-responsive enhancer 1 (OSRE1) in intron 1 promotes salinity induction of tilapia glutamine synthetaseChanhee Kim XW0003_Oremo-OmBcellsOreochromis mossambicusOmB cellsDIABottom-upTrypsinlUknq6.url   10.1038/s41598-020-69090-z30-Sep-201931-Oct-201932694739
Early-life exposure to the endocrine disruptor 17-α-ethinylestradiol induces delayed effects in adult brain, liver and ovotestis proteomes of a self-fertilizing fishAnne-Sophie VoisinFrederic Silvestre (University of Namur, Belgium)AS0001_Kryma-GonadKryptolebias marmoratusGonadDDABottom-upTrypsin MSV000082816PXD010766 10.1016/j.jprot.2018.12.00813-Aug-201825-Jun-202030550985
Early-life exposure to the endocrine disruptor 17-α-ethinylestradiol induces delayed effects in adult brain, liver and ovotestis proteomes of a self-fertilizing fishAnne-Sophie VoisinFrederic Silvestre (University of Namur, Belgium)AS0001_Kryma-BrainKryptolebias marmoratusBrainDDABottom-upTrypsin MSV000082814PXD010764 10.1016/j.jprot.2018.12.00813-Aug-201825-Jun-202030550985
Early-life exposure to the endocrine disruptor 17-α-ethinylestradiol induces delayed effects in adult brain, liver and ovotestis proteomes of a self-fertilizing fishAnne-Sophie VoisinFrederic Silvestre (University of Namur, Belgium)AS0001_Kryma-LiverKryptolebias marmoratusLiverDDABottom-upTrypsin MSV000082815PXD010765 10.1016/j.jprot.2018.12.00813-Aug-201825-Jun-202030550985
Proteomics of discrete brain nuclei from Mangrove killifishCheng-Yu Li, Dietmar KültzRyan Earley (University of Alabama, AL)RE0001_Kryma-BrainKryptolebias marmoratusBrainDDABottom-upTrypsin MSV000082806PXD010729  08-Aug-2018  
Contrasting seasonal and aseasonal environments across stages of the annual cycle in the rufous‐collared sparrow, Zonotrichia capensis : Differences in endocrine function, proteome and body conditionJohn Li, Dietmar KültzPaulina Gonzalez-Gomes (Universidad Autonoma de Chile), John Wingfield (UC Davis)XW0004_Zonca-kidneyZonotrichia capensisKidneyDDABottom-upTrypsin MSV000082314PXD009617 10.1111/1365-2656.1284626-Apr-201825-Jun-202029741769
Contrasting seasonal and aseasonal environments across stages of the annual cycle in the rufous-collared sparrow, Zonotrichia capensis: Differences in endocrine function, proteome and body conditionJohn Li, Dietmar KültzPaulina Gonzalez-Gomes (Universidad Autonoma de Chile), John Wingfield (UC Davis)XW0004_Zonca-plasmaZonotrichia capensisPlasmaDDABottom-upTrypsin MSV000082313PXD009616 10.1111/1365-2656.1284626-Apr-201826-Apr-201829741769
Development of a gill assay library for ecological proteomics of threespine sticklebacks (Gasterosteus aculeatus)John Li, Bryn LevitanSilvia Gómez-Jiménez (CIAD, Hermosillo, Mexico)MXLSAKBH_Gasac-GillGasterosteus aculeatusGillDIABottom-upTrypsinJoLi-01.urlMSV000081795PXD008395 10.1074/mcp.RA118.00097309-Dec-201709-Aug-201830093419
Skeletal stiffening in an amphibious fish out of water is a response to increased body weightDietmar KültzPatricia Wright (University of Guelph, Canada)DK0024_Kryma-GillKryptolebias marmoratusGillDDABottom-upTrypsin MSV000080634PXD006100 10.1242/jeb.16163815-Mar-201702-Oct-201729046415
Osmolality/salinity-responsive enhancers (OSREs) control induction of osmoprotective genes in euryhaline fishXiaodan Wang XW0003_Oremo-OmBcellsOreochromis mossambicusOmB cellsDIABottom-upTrypsinXW2016-1.url   10.1073/pnas.161471211401-Jan-201626-Oct-201628289196
Population-specific renal proteomes of marine and freshwater three-spined sticklebacksJohn Li, Dietmar Kültz JL0005_Gasac-KidneyGasterosteus aculeatusKidneyDIABottom-upTrypsinAccess_Kultz-et-al-2015.url   10.1016/j.jprot.2015.10.00215-Dec-201415-Oct-201526463136
Population‐specific plasma proteomes of marine and freshwater three‐spined sticklebacks (Gasterosteus aculeatus)John Li, Dietmar Kültz JL0005_Gasac-PlasmaGasterosteus aculeatusPlasmaDIABottom-upTrypsinStickle1-2015Proteomics.url   10.1002/pmic.20150013230-Oct-201407-Aug-201526223892
Alterations in the proteome of the respiratory tract in response to single and multiple exposures to naphthaleneJohn Li, Romina SacchiAlan Buckpitt (UC Davis, CA)DK0025_Musmu-LungOE, DK0030_Musmu-Lung, DK0031_Musmu-OEMus musculusLung and olfactory epitheliumDDABottom-upTrypsin   PRD00084610.1002/pmic.20140044508-Dec-201317-Apr-201525825134
Quantitative molecular phenotyping of gill remodeling in a cichlid fish responding to salinity stressJohn Li, Dietmar Kültz DK0022_Oremo-GillOreochromis mossambicusGillDDABottom-upTrypsin   PRD00075310.1074/mcp.M113.02982714-Feb-201324-Sep-201324065692