Evaluation of TIMS-derived peptide mobility measurements: calibration strategy and MS1/MS2 discrepancies

The widespread adoption of trapped ion mobility coupled to mass spectrometry for proteome analysis necessitates high-quality data measurement of both ion mobility and mass spectra. In this study, the accuracy of ion mobility measurements in the context of mass spectral (MS) library building and searching is evaluated. Key factors influencing measurement accuracy, such as calibration strategy and the timing of acquisition relative to the chromatographic apex, are systematically investigated. A calibration system based on a synthetic peptide mixture is shown to improve calibration performance. Further, reproducibility of MS1- and MS2-associated mobility measurements in data-dependent acquisition (DDA) is analyzed. Overall, this work identifies methods to improve ion mobility measurement accuracy for proteomics analyses using a standardized synthetic peptide mixture.