Overview of VaLID
Visualization and phosphoLipid IDentification (VaLID) is a web-based application linking a convenient search engine, a phospholipid database, and multiple visualization features for identification and dissemination of large-scale lipidomic datasets. Unlike other engines, VaLID returns all theoretically possible species based on m/z and user-defined MS conditions. While useful for lipid discovery, the user is cautioned that the database includes lipids (and bond configurations) that may not be biologically relevant or have not (or have yet to be) detected in biological samples. To assist in decision-making, a “best prediction” feature is available whereby lipids listed in blue are predicted to be the most likely based on prevalence in mammalian cells (Miyazaki and Ntambi, 2008). Many curated species detected in brain tissue by the Neurodegeneration Laboratory can also be downloaded in multiple high-resolution representations for further visualization and model production. VaLID follows the Lipid Maps classification and nomenclature system in lipid naming (Fahy et al., 2011).
References
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Fahy E, Cotter D, Sud M, Subramaniam S (2011) Lipid classification, structures and tools. Biochimica et Biophysica Acta 1811(11): 637-647.
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Miyazaki M, Ntambi JM (2008) Fatty acid desaturation and chain elongation in mammals. In: Biochemistry of Lipids, Lipoproteins and Membranes (Vance DE, Vance JE, eds), pp 191-211. Oxford: Elsevier.
Predicting the potential identity of a lipid in your lipidomic dataset based on m/z
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Ionic Mass: Enter an m/z value in the mass input box. You can choose to use the exact mass or the average mass of the most abundant isotopic species.
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Chain Lengths: Limit your search to lipids with even numbers of carbons, odd numbers of carbons in their sn-1 and sn-2 chains or search all possible combinations.
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Mass Tolerance: Select the mass tolerance range appropriate to your mass spectrometer.
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Lipid Subclass: You can search within the following subclasses:
PA [GP10]: glycerophosphates
PPA [GP11]: glyceropyrophosphates
PC [GP01]: glycerophosphocholines
PE [GP02]: glycerophosphoethanolamines
PG [GP04]: glycerophosphoglycerols
PGP [GP05]: glycerophosphoglycerophosphates
PI and PIPX [GP06-09]: glycerophosphoinositols and glycerophosphoinositol mono-, bis- and tris-phosphates
PS [GP03]: glycerophosphoserines
CDP-DG [GP13]: cytidine 5'-diphosphate glycerols
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Fatty Chain Linkage: Choose all possible sn-1 and sn-2 linkages or limit your search to alkenyl-acyl, alkyl-acyl, diacyl, dialkyl, or lyso-lipids (with mono-acyl, alkyl, or alkenyl linkages).
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Ion: Select the appropriate ion type for your dataset.
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Click the Search Button: This will prompt VaLID to search through its databases for the search terms specified in the above steps.
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Results: You will be provided with three lists:
Possible Lipids Include: Lists all computed possible chain length and linkage compositions.
Possible Isomeric Lipids Include: Lists the structural isomers at sn-1 and sn-2 positions for each species.
Possible Lipids Include: A second list labelled Possible Lipids Include, this time containing a list of the the Total Carbon numbers - i.e., the headgroup followed by the total number of carbons in both sn-1 and sn-2 chains, and the total number of unsaturations - for each species in the above two lists.
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Display All: The structures and all possible double bond placements of each species can be computed and displayed by highlighting the lipid of interest and choosing “Display all.” Each structure can be rotated in 2D by selecting and moving mouse/trackpad. Molecule name (default) and SMILES can be displayed on bottom left of each window by selecting these options in the Table menu. On a Mac computer, the structure can be rotated in 3D, multiple viewing options changed, and file exported by holding down the control button and clicking on the molecule.
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Best Prediction: Lipids highlighted in blue in either list are predicted to be the most likely species based on prevalence in mammalian cells. Clicking on this button will display only these species.
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Structural Representations: VaLID high-resolution models are provided for the lipids highlighted in red. Clicking on this button will display these models and allow you to save them to your own computer. The models are also available in list form by clicking on the Lipid Models tab. In addition to the options available at low resolution through the Display All tab, high-resolution images in Skeletal, Ball and stick, Space filling, and Valid view are available through the structural representations button for download. VaLID view is a flexible, polygonal mesh model that serves as a hybrid between a traditional molecular model and an organic or ‘biological approximation’. Generated using the 3D modeling software Autodesk Maya, these models can be assembled into more comprehensive and detailed three-dimensional representations of the lipid bilayer.
Downloading high-resolution structures (Skeletal, Ball and stick, Space filling, and VaLID view)
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If structure is found using the m/z prediction database, follow #11 above.
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Click on the Lipid Models tab and follow download instructions.
Using VaLID to search literature
With VaLID 3.2, we introduced the ability to search two external literature sources: PubMed and the Human Metabolome Database. To use this feature, follow these steps:
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Search for the lipid of interest using VaLID (follow steps #1-8, above).
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Select the lipid of interest in either the Possible Lipids Include or the Possible Isomeric Lipids Include upper results fields.
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Press either the PubMed Search button, or the HMDB Search button.
Some points to keep in mind when using this feature:
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If clicking either buttons, but the search does not appear, check your pop-up blocker. Since these searches open a new tab or window, the search window might be blocked by the popup blocker. Enabling popups for VaLID will fix this issue.
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The search terms will change, depending upon which of the VaLID search boxes is selected. So make sure you select the proper sn-1/sn-2 orientation to search.
Download instructions
To download one of the images, click on the name of the lipid of interest. This will bring you to that individual lipid's page – the same page as if you found the lipid through VaLID's search feature, and selected the Structural Representation button – with the four options: Skeletal, Ball and stick, Space filling and VaLID view. To download high-resolution (300 dpi) images, click on the representation you wish to save. This will open up a new window with the image. From here, right click (or control-click on a mac) the image and select Save Image As.
List of Available Lipid Models
Possible Lipids Include:
Possible Isomeric Lipid Species Include:
Possible Lipids Include:
Display All
The structures and all possible double bond placements of each species can be computed and displayed by highlighting the lipid of interest and choosing “Display all.” Each structure can be rotated in 2D by selecting and moving mouse/trackpad. Molecule name (default) and SMILES can be displayed on bottom left of each window by selecting these options in the Table menu. On a Mac, the structure can be rotated in 3D, multiple viewing options changed, and file exported by holding down the control button and clicking on the molecule.
Best Prediction
Lipids highlighted in blue in either list are predicted to be the most likely species based on prevalence in mammalian cells. Clicking on this button will display only these species.
Structural Representations
VaLID high-resolution models are provided for the lipids highlighted in red. Clicking on this button will display these models and allow you to save them to your own computer. The models are also available in list form by clicking on the Lipid Models tab. In addition to the options available at low resolution through the Display All tab, high-resolution images in Skeletal, Ball and stick, Space filling, and Valid view are available through the structural representations button for download. VaLID view is a flexible, polygonal mesh model that serves as a hybrid between a traditional molecular model and an organic or ‘biological approximation’. Generated using the 3D modeling software Autodesk Maya, these models can be assembled into more comprehensive and detailed three-dimensional representations of the lipid bilayer.
Frequently Asked Questions
When troubleshooting, please review this list of common reasons for VaLID failing to run. If you are still experiencing difficulties running our tool, please contact ldomic@uottawa.ca for further assistance. Please include your input dataset and a description of the problem that you experienced. We will reproduce the problem and provide you with a solution.
1. Why does the first search take so long? And why do subsequent searches take no time at all?
Note: Initial searches may take longer than a minute, depending upon the connection speed, and search options selected.
When a new search is started the program loads all the lipids with the mass you are searching for, as well as lipids with mass ratios 25 m/z above and below the target mass, into memory. This 50 m/z cached buffer range allows for searches close to the original search to occur much faster than if the program reloaded the database each time.
2. Where can I find information on the lipid nomenclature used?
VaLID follows the Lipid Maps classification and nomenclature system in lipid naming, as described by Fahy et al., 2011.
Reference
Fahy E, Cotter D, Sud M, Subramaniam S (2011) Lipid classification, structures and tools. Biochimica et Biophysica Acta 1811(11): 637-647.
3. When searching through “All” lipid subclasses, why did the progress bar reach 100%, then start over from zero?
The progress bar reports the progress of searching through the database for one lipid subclass. When the “All” lipid subclass search is selected, the program will report progress through each database in turn. The progress bar is reset each time a new database begins to load. As of version 2.0.0, should more than one database need to be loaded, text beside the progress bar will show how many sheets have been loaded, and how many have yet to be loaded.
4. How can I contribute to the VaLID database?
We welcome all suggestions and input.
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If you have published MS data and would like your curated lipids modeled by the Canadian Institutes of Health Research Training Program in Neurodegenerative Lipidomics (CTPNL), please email ldomic@uottawa.ca with your dataset and reference and we will work to adding your species to our structural representation database referencing your dataset.
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If you have evidence that a given species should be listed as part of our best prediction database based on prevalence in mammalian cells, please email ldomic@uottawa.ca and we will update the database and cite your reference.
Contact us
Cite the use of VaLID in a publication
Cite predictions performed using VaLID
Glycerophospholipid identities were predicted based on m/z and appropriate ion type taking into consideration the mass tolerance of the QTRAP 5500 using VaLID version 3.2.0 (McDowell et al., 2014).
Cite the use of images/structural database
Structural images were obtained from the VaLID structural database version 3.2.0) (Blanchard et al., 2013).
References
Blanchard AP, McDowell GSV, Valenzuela N, Xu H, Gelbard S, Bertrand M, Slater GW, Figeys D, Fai S, Bennett SAL (2013) Visualization and Phospholipid Identification (VaLID): An online integrated search engine capable of identifying and visualizing glycerophospholipids with given mass. Bioinformatics, 29: 284-285, doi: 10.1093/bioinformatics/bts662
McDowell GSV, Blanchard AP, Taylor GP, Figeys D, Fai S, Bennett SAL (2014) Predicting glycerophosphoinositol identities in lipidomic datasets using VaLID (Visualization and Phospholipid Identification) - an online bioinformatics search engine. BioMed Research International, 2014:818670. doi: 10.1155/2014/818670
Acknowledgements
This resource was developed with the support of the Canadian Institute of Health Research CIHR MOP 89999 (operating) to SALB and DF, STIHR/CIHR Training Program in Neurodegenerative Lipidomics (CPTNL) TGF-96121 (trainee support) to SALB, DF, and SF, and the Natural Sciences and Engineering Research Council CREATE to DF and GWS. SF acknowledges the support of CFI and ORF. APB, GSVM recieved CTPNL studentships; SG and NV recieved CTPNL post-professional fellowships; HX and MB received CTPNL post-doctoral fellowships. APB was also supported by Fonds de la recherche en santé du Quebec (FRSQ). HX received a MITACs post-doctoral fellowship. This program uses ChemAxon's Marvin to display the generated chemical structures, Marvin 5.5.1.0, 2011, ChemAxon .
Public Server
VaLID: https://complimet.ca/shiny/valid/
Software License
VaLID is free software. You can redistribute it and/or modify it under the terms of the GNU General Public License v3 (or later versions) as published by the Free Software Foundation. As per the GNU General Public License, VaLID is distributed as a bioinformatic tool to assist users WITHOUT ANY WARRANTY and without any implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. All limitations of warranty are indicated in the GNU General Public License.