A Data-Dependent Acquisition Ladder for Ultrasensitive (Neuro)Proteomics

We report here a data acquisition strategy that expands the detectable and quantifiable proteome from trace amounts of protein digests using microanalytical capillary electrophoresis (µCE) electrospray ionization (ESI) high-resolution mass spectrometry (HRMS). Data-dependent acquisition (DDA) was programmed to progressively exclude high-intensity peptide signals from repeated analysis of the sample, essentially forming a ladder of DDA measurements.