Effective mobility as a robust criterion for compound annotation and identification in metabolomics: Toward a mobility-based library. Drouin Nicolas,Pezzatti Julian,Gagnebin Yoric,González-Ruiz Víctor,Schappler Julie,Rudaz Serge Analytica chimica acta Capillary electrophoresis (CE) presents many advantageous features as an analytical technique in metabolomics, such as very low consumption of a sample or the possibility to easily detect very polar and ionizable compounds. However, CE remains an approach only used by a few research groups due to a relatively lower sensitivity and, higher analysis time compared to liquid chromatography. To circumvent these drawbacks, herein we propose a generic CE-mass spectrometry (MS) approach using positive electrospray ionization mode and performing normal- and reverse-polarity CE separations to analyze anionic and acidic compounds. Preliminary experiments showed better sensitivity using the ESI positive mode compared to the ESI negative mode on a set of representative anionic compounds from different biochemical families. This approach was applied to the investigation of an available library of metabolites. More than 450 compounds out of the 596 in the library were detected, with the possibility to monitor negatively ionizable compounds through their ammonium adducts. Migration time of each data point was converted to an effective mobility (μ) scale and used for peak alignment in data pre-processing; μ features were used as a robust migration index for peak annotation and identification criterion. For the first time, a large database based on experimental μ was built, allowing for the straightforward annotation of detected features in biological samples and demonstrating how CE-MS can complement other analytical techniques commonly used in metabolomics. 10.1016/j.aca.2018.05.063