Data-Driven Rescoring of Metabolite Annotations Significantly Improves Sensitivity

When analyzing mass spectrometry imaging data sets, assigning a molecule to each of the thousands of generated images is a very complex task. Recent efforts have taken lessons from (tandem) mass spectrometry proteomics and applied them to imaging mass spectrometry metabolomics, with good results. Our goal is to go a step further in this direction and apply a well established, data-driven method to improve the results obtained from an annotation engine. By using a data-driven rescoring strategy, we are able to consistently improve the sensitivity of the annotation engine while maintaining control of statistics like estimated rate of false discoveries. All the code necessary to run a search and extract the additional features can be found at https://github.com/anasilviacs/sm-engine and to rescore the results from a search in https://github.com/anasilviacs/rescore-metabolites.