Abstract
Demands in research investigating small molecules by applying untargeted approaches have been a key motivator for the development of repositories for mass spectrometry spectra and automated tools to aid compound identification. Comparatively little attention has been afforded to using retention times (RTs) to distinguish compounds and for liquid chromatography there are currently no coordinated efforts to share and exploit RT information. We therefore present PredRet; the first tool that makes community sharing of RT information possible across laboratories and chromatographic systems (CSs). At http://predret.org , a database of RTs from different CSs is available and users can upload their own experimental RTs and download predicted RTs for compounds which they have not experimentally determined in their own experiments. For each possible pair of CSs in the database, the RTs are used to construct a projection model between the RTs in the two CSs. The number of compounds for which RTs can be predicted and the accuracy of the predictions are dependent upon the compound coverage overlap between the CSs used for construction of projection models. At the moment, it is possible to predict up to 400 RTs with a median error between 0.01 and 0.28 min depending on the CS and the median width of the prediction interval ranging from 0.08 to 1.86 min. By comparing experimental and predicted RTs, the user can thus prioritize which isomers to target for further characterization and potentially exclude some structures completely. As the database grows, the number and accuracy of predictions will increase.
Highlights
I n the untargeted analysis of complex mixtures, one of the major bottlenecks is the identification of compounds
We present PredRet, a Web-based service that allows easy sharing of retention time (RT) data and unsupervised mapping of retention times (RTs) between different chromatographic systems (CSs)
In the PredRet system the RTs of compounds measured in two different CSs are used to build a generalized additive model (GAM) that describe the relationship between RTs in the two systems
Summary
We present PredRet, a Web-based service that allows easy sharing of retention time (RT) data and unsupervised mapping of RTs between different chromatographic systems (CSs). Overlap in the compound coverage is required to construct models between CSs. In the upper part of Figure 3A, the corresponding number of predictions for each system are reported in blue. We implemented a process that tries to detect erroneous entries In this step we go back to each model and detect compounds for which the data point lies more than twice the PI width from the predicted value. If the compound is only used in a single model (i.e., exists in only two CSs), both entries are assumed to be wrong and the compound will be excluded from predictions This process insures that no grossly erroneous data is used for predictions if avoidable. The PI of a prediction for 3-hydroxy-2-methylbutyric acid might not match the experimental RT if the database entry and the experimental data was obtained from different diastereoisomers
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