In modern mass spectrometry (MS)-based proteomics, high acquisition speed, depth, quantitative accuracy, and data completeness across many runs are the key to reconstructing signaling pathways and protein expression profiles in health and disease. Combining data-independent acquisition (DIA) with parallel accumulation – serial fragmentation (PASEF), diaPASEF uses the correlation between mass-to-charge (m/z) and ion mobility (IM) in trapped ion mobility mass spectrometry (TIMS) and has shown great promise for high throughput applications. However, so far, the implicit trade-off between variable window width, cycle time, and diaPASEF windows placement in the two-dimensional m/z to IM space on the depth and quantitative accuracy has not been addressed. Here, we explore library-based diaPASEF methods (LiDIA-PASEF) applied to high throughput (phospho-)proteomics.
MP 257 – LiDIA-PASEF: A framework using experimental libraries for optimal acquisition of (phospho)proteomes by diaPASEF
by Eva Bryderup