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Publications - Stress and Develop Biology

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Publications

Stanstrup; J. Neumann, S.; Vrhovšek,U. PredRet: prediction of retention time by direct mapping between multiple chromatographic systems Anal. Chem 87, 9421–9428, (2015) DOI: 10.1021/acs.analchem.5b02287

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.
Publications

Schymanski, E.L.; Gallampois, C.M.J.; Krauss, M.; Meringer, M.; Neumann, S.; Schulze, T.; Wolf, S.; Brack, W. Consensus Structure Elucidation Combining GC/EI-MS, Structure Generation, and Calculated Properties Anal. Chem 84 (7), 3287–3295, (2012) DOI: 10.1021/ac203471y

KowThis article explores consensus structure elucidation on the basis of GC/EI-MS, structure generation, and calculated properties for unknown compounds. Candidate structures were generated using the molecular formula and substructure information obtained from GC/EI-MS spectra. Calculated properties were then used to score candidates according to a consensus approach, rather than filtering or exclusion. Two mass spectral match calculations (MOLGEN-MS and MetFrag), retention behavior (Lee retention index/boiling point correlation, NIST Kovat’s retention index), octanol–water partitioning behavior (log), and finally steric energy calculations were used to select candidates. A simple consensus scoring function was developed and tested on two unknown spectra detected in a mutagenic subfraction of a water sample from the Elbe River using GC/EI-MS. The top candidates proposed using the consensus scoring technique were purchased and confirmed analytically using GC/EI-MS and LC/MS/MS. Although the compounds identified were not responsible for the sample mutagenicity, the structure-generation-based identification for GC/EI-MS using calculated properties and consensus scoring was demonstrated to be applicable to real-world unknowns and suggests that the development of a similar strategy for multidimensional high-resolution MS could improve the outcomes of environmental and metabolomics studies.
Publications

Böttcher, C.; von Roepenack-Lahaye, E.; Willscher, E.; Scheel, D.; Clemens, S. Evaluation of matrix effects in metabolite profiling based on capillary liquid chromatography electrospray ionization quadrupole time-of-flight mass spectrometry Anal. Chem 79, 1507 1513, (2007)

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