MaxQuant.Live Enables Enhanced Selectivity and Identification of Peptides Modified by Endogenous SUMO and Ubiquitin

Small ubiquitin-like modifiers (SUMO) and ubiquitin are frequent post-translational modifications of proteins that play pivotal roles in all cellular processes. We previously reported mass spectrometry-based proteomics methods enable profiling lysines modified by endogenous SUMO or an unbiased manner, without the need for genetic engineering. Here we investigated applicability precursor filtering enabled MaxQuant.Live to our workflows, which efficiently avoided sequencing precursors too small be but otherwise indistinguishable mass-to-charge ratio. Using filtering, achieved a much higher selectivity peptides, ultimately resulting up 30% more sites identified from replicate samples. Real-time exclusion unmodified peptides MQL resulted 90% SUMO-modified 25% pure sample, demonstrating great digging deeper into modificomes. adapted strategy new Exploris 480 spectrometer, achieving comparable gains identification rates. Collectively, via significantly increased rates SUMO- ubiquitin-modified exact same samples, requirement prior knowledge spectral libraries.