CCSbase
Welcome to our CCS database. Click on a tab below to see instructions for each of the functionality
Querying the Database
Once you are on the Experimental Database tab, click on Query Database to get started. You will see something like this:
Fill in the input fields as needed. You do not have to fill in all the input fields. Once you are done, click on "Search" to get your results.
The User can use either "and" or "or" in the 'Name' field but not both.
Ex. "Something and Something and Something" or "Something or Something or Something" would work. "Something and Something or Something" would not.
| Class | Abbreviation | Examples |
|---|---|---|
| Glycerophosphocholines | PC (LPC for lyso species) | PC(P-16:0/18:2(9Z,12Z)) |
| Glycerophosphoethanolamines | PE (LPE for lyso species) | PE(O-16:0/20:4(5Z,8Z,11Z,14Z)) |
| Glycerophosphoserines | PS (LPS for lyso species) | PS(16:0/18:1(9Z)) |
| Glycerophosphoglycerols | PG (LPG for lyso species) | - |
| Glycerophosphates | PA (LPA for lyso species) | PA(16:0/0:0) or LPA(16:0) |
| Glycerophosphoinositols | PI (LPI for lyso species) | PI(18:0/18:0) |
| Glycerophosphoinositol monophosphates | PIP | - |
| Glycerophosphoinositol bis-phosphates | PIP2 | - |
| Glycerophosphoinositol tris-phosphates | PIP3 | - |
| Glycerophosphoglycerophosphoglycerols (Cardiolipins) | CL | CL(1'-[16:0/18:1(11Z)],3'-[16:0/18:1(11Z)]) |
| Glycerophosphoglycerophosphates | PGP | - |
| Glyceropyrophosphates | PPA | - |
| CDP-glycerols | CDP-DG | - |
| Glycosylglycerophospholipids | [glycan]-GP | - |
| Glycerophosphoinositolglycans | [glycan]-PI | - |
| Glycerophosphonocholines | PnC | - |
| Glycerophosphonoethanolamines | PnE | - |
Lipid names are abbreviated following the format used by LipidMAPS (more info [here]). For example, a phosphatidylcholine substituted with oleic and palmitic fatty acids would have the abbreviation 'PC(18:1/16:0)'. Lipid species for which the specific fatty acid composition is not known are represented by their sum composition, e.g. 'PC(34:1)'.
The following abbreviations are also used:
• LysPG → lysyl-phosphatidylglycerol
• AlaPG → alanyl-phosphatidylglycerol
• GlcADG → glucuronosyl-diacylglycerol
• AcylPG → acyl-phosphatidylglycerol
• N-AcylPE → N-acyl-phosphatidylethanolamine
Viewing the Plot
You can view the plot for the database by clicking on "View Plot". The plot has multiple functions that you can use. The functions are as follows:
*Blue line next to the icon means that function is being used*
Making Batch-Queries
Batch-Queries can be made by uploading a csv file. A sample csv file can be downloaded as well.
Make sure the column names are as follows:
Further instructions are in "Batch-Query" tab
Making Predictions
The user can make predictions of ccs value by specifying an adduct and a smile structure. The user can also make batch-predictions by uploading a csv file. A sample csv file can be downloaded in the "Predictions" tab.
Make sure the column names are as follows:
