Infrared laser ablation sampling coupled with data independent high resolution UPLC-IM-MS/MS for tissue analysis.

Infrared laser ablation microsampling was used with data-dependent acquisition (DDA) and ion mobility-enhanced data-independent acquisition (HDMS) for mass spectrometry based bottom-up proteomics analysis of rat brain tissue. Results from HDMS and DDA analyses of the 12 laser ablation sampled tissue sections showed that HDMS consistently identified approximately seven times more peptides and four times more proteins than DDA. To evaluate the impact of ultra-performance liquid chromatography (UPLC) peak congestion on HDMS and DDA analysis, whole tissue digests from rat brain were analyzed at six different UPLC separation times. Analogous to results from laser ablated samples, HDMS analyses of whole tissue digests yielded about four times more proteins identified than DDA for all six UPLC separation times.