A new era in proteomics: spectral library free data independent acquisition (directDIA)

A new workflow with the simplicity of shotgun proteomics and the quantitative precision and reproducibility of data independent acquisition

Introduction

Discovery proteomics aims to understand global proteome dynamics for instance in cells, tissue or an organism. The key to gain a comprehensive picture of the biology lies in the quantitative precision, reproducibility and the unbiased nature of analysis at the highest possible protein coverage.

Modern discovery proteomics workflows mainly rely on high-resolution LC-MS/MS instruments. Until today data dependent acquisition based proteomics (DDA) is the most widely used discovery proteomics technique. A major limitation of DDA based proteomics however, is the semi-stochastic peptide selection for its identification. Therefore, the same peptides will not be identified reproducibly even when analyzing technical replicates. Despite the possibility of performing MS1 alignment, this results in high number of missing values in the data matrix that lead to problems in statistical analysis and an incomplete biological picture.