Robust dimethyl-based multiplex-DIA doubles single-cell proteome depth via a reference channel.

ABSTRACT: Single-cell proteomics aims to characterize biological function and heterogeneity at the level of proteins in an unbiased manner. It is currently limited in proteomic depth, throughput, and robustness, which we address here by a streamlined multiplexed workflow using data-independent acquisition (mDIA). We demonstrate automated and complete dimethyl labeling of bulk or single-cell samples, without losing proteomic depth. Lys-N digestion enables five-plex quantification at MS1 and MS2 level. Because the multiplexed channels are quantitatively isolated from each other, mDIA accommodates a reference channel that does not interfere with the target channels. Our algorithm RefQuant takes advantage of this and confidently quantifies twice as many proteins per single cell compared to our previous

SUBMITTER: Thielert M 

PROVIDER: S-EPMC10495816 | biostudies-literature | 2023 Sep

REPOSITORIES: biostudies-literature