WITHDRAWN: Heralds of parallel MS: Data-independent acquisition surpassing sequential identification of data dependent acquisition in proteomics

Abstract

Comprehensive, reproducible and precise analysis of large sample cohorts is one of the key objectives of quantitative proteomics. Here, we present an implementation of data-independent acquisition using its parallel acquisition nature that surpasses the serial limitation of data-dependent acquisition on a quadrupole ultra-high field Orbitrap mass spectrometer. In deep single shot data-independent acquisition, we quantified over 7,500 proteins of human cell lines and 9,000 proteins of mouse tissues, with fewer than 2.5% missing proteins and median coefficients of variation of down to 5% among replicates. In very complex mixtures, we could quantify more than 15,000 proteins, outperforming data-dependent acquisition methods by more than two-fold. Using this method, we investigated large-protein networks before and after the critical period for whisker experience-induced synaptic strength in the murine somatosensory cortex 1 barrel field. This work shows that parallel mass spectrometry enables proteome profiling for discovery with high coverage, reproducibility, precision and scalability.