Predicting glycerophosphoinositol identities in lipidomic datasets using VaLID (Visualization and Phospholipid Identification)--an online bioinformatic search engine.
The capacity to predict and visualize all theoretically possible glycerophospholipid molecular identities present in lipidomic datasets is currently limited. To address this issue, we expanded the search-engine and compositional databases of the online Visualization and Phospholipid Identification (VaLID) bioinformatic tool to include the glycerophosphoinositol superfamily. VaLID v1.0.0 originally allowed exact and average mass libraries of 736,584 individual species from eight phospholipid classes: glycerophosphates, glyceropyrophosphates, glycerophosphocholines, glycerophosphoethanolamines, glycerophosphoglycerols, glycerophosphoglycerophosphates, glycerophosphoserines, and cytidine 5'-diphosphate 1,2-diacyl-sn-glycerols to be searched for any mass to charge value (with adjustable tolerance levels) under a variety of mass spectrometry conditions. Here, we describe an update that now includes all possible glycerophosphoinositols, glycerophosphoinositol monophosphates, glycerophosphoinositol bisphosphates, and glycerophosphoinositol trisphosphates. This update expands the total number of lipid species represented in the VaLID v2.0.0 database to 1,473,168 phospholipids. Each phospholipid can be generated in skeletal representation. A subset of species curated by the Canadian Institutes of Health Research Training Program in Neurodegenerative Lipidomics (CTPNL) team is provided as an array of high-resolution structures. VaLID is freely available and responds to all users through the CTPNL resources web site.
Neural Regeneration Laboratory, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5 ; Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5 ; CIHR Training Program in Neurodegenerative Lipidomics, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5.
Graeme S V
GS
McDowell
Neural Regeneration Laboratory, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5 ; Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5 ; CIHR Training Program in Neurodegenerative Lipidomics, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5.
Alexandre P
0000-0002-7224-0287
AP
Blanchard
Neural Regeneration Laboratory, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5 ; Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5.
Graeme P
GP
Taylor
Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5 ; CIHR Training Program in Neurodegenerative Lipidomics, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5.
Daniel
0000-0002-5373-7546
D
Figeys
CIHR Training Program in Neurodegenerative Lipidomics, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5 ; Carleton Immersive Media Studio, Azrieli School of Architecture and Urbanism, Carleton University, ON, Canada K1S 5B6.
Stephen
S
Fai
Neural Regeneration Laboratory, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5 ; Ottawa Institute of Systems Biology, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5 ; CIHR Training Program in Neurodegenerative Lipidomics, Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, ON, Canada K1H 8M5.
Steffany A L
SA
Bennett
D000818:Animals; D057225:Data Mining; D016208:Databases, Factual; D006801:Humans; D007295:Inositol Phosphates / Q000378:metabolism*; D020407:Internet; D050356:Lipid Metabolism; D012984:Software
D007295:Inositol Phosphates; C014575:glycerylphosphoinositol