The full analytical characterization of therapeutic monoclonal antibodies (mAbs) requires a large variety of complementary information that can be obtained by chromatographic methods. A series of protocols papers has been proposed to cover the chromatographic techniques and the enzymatic and chemical sample preparation procedures generally applied for the analytical characterization of therapeutic mAbs. The present protocol paper focuses on denaturing chromatographic techniques hyphenated to mass spectrometry, namely reversed-phase liquid chromatography (RPLC) and hydrophilic interaction chromatography (HILIC), to assess the subtle mAbs structural heterogeneity resulting from glycosylation patterns and post-transcriptional modifications (PTMs). In this paper, some generic protocols are provided, using a wide range of therapeutic mAbs approved by Food and Drug Administration (FDA) and European Medicines Agency (EMA), to illustrate the possibilities offered by the last generation of RPLC and HILIC columns when performing LC-MS analysis at the middle-up level.