Rationale There is a need for fast, post‐ionization separation during the analysis of complex mixtures. In this study, we evaluate the use of a high‐resolution mobility analyzer with high‐resolution and ultrahigh‐resolution mass spectrometry for unsupervised molecular feature detection. Goals include the study of the reproducibility of trapped ion mobility spectrometry (TIMS) across platforms, applicability range, and potential challenges during routine analysis. Methods A TIMS analyzer was coupled to time‐of‐flight mass spectrometry (TOF MS) and Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR MS) instruments for the analysis of singly charged species in the m / z 150–800 range of a complex mixture (Suwannee River Fulvic Acid Standard). Molecular features were detected using an unsupervised algorithm based on chemical formula and IMS profiles. Results TIMS‐TOF MS and TIMS‐FT‐ICR MS analysis provided 4950 and 7760 m / z signals, 1430 and 3050 formulas using the general C x H y N 0–3 O 0–19 S 0–1 composition, and 7600 and 22 350 [ m / z ; chemical formula; K; CCS] features, respectively. Conclusions TIMS coupled to TOF MS and FT‐ICR MS showed similar performance and high reproducibility. For the analysis of complex mixtures, both platforms were able to capture the major trends and characteristics; however, as the chemical complexity at the level of nominal mass increases with m / z ( m / z >300–350), only TIMS‐FT‐ICR MS was able to report the lower abundance compositional trends.