Maximally-multiplexed proteome quantification platform for isotopic metabolic and chemical labeling

Quantitative proteomic platforms based on precursor intensity in mass spectrometry (MS1-level) uniquely support in vivo metabolic labeling with superior quantification accuracy but suffers from limited multiplexity (≤3-plex) and frequent missing quantities. Herein, we present a maximally-multiplexed MS1-level quantification platform that comprises new six-plex in vivo SILAC or in vitro di-ethylation with a dedicated algorithm. We demonstrate accurate and missing quantity-free quantification of highly complex samples with broad dynamic ranges. With our platform, we globally profile the proteome dynamics under the heat shock response of HeLa cells.