dia-PASEF data analysis using FragPipe and DIA-NN for deep proteomics of low sample amounts

• DOI: 10.1038/s41467-022-31492-0
• Publication Date: 2022-07-08T09:03:09Z
• Authors: Vadim Demichev; Lukasz Szyrwiel; Fengchao Yu; Guo Ci Teo; George Rosenberger; Agathe Niewienda; Daniela Ludwig; Jens Decker; Stephanie Kaspar-...; Kathryn S. Lilley; Michael Mülleder; Alexey I. Nesvizh...; Markus Ralser
• Keywords: Chemical Biology & High Throughput; 0301 basic medicine; Data Analysis; Proteomics; 0303 health sciences; /82/16; Proteome; /631/45/612; Science; /82/58; Q; article; /631/553/794; Article; Mass Spectrometry; 03 medical and health sciences; Metabolism; Ecology,Evolution & Ethology; Humans; Synthetic Biology; Peptides; /631/1647/2067; Computational & Systems Biology

AbstractThe dia-PASEF technology uses ion mobility separation to reduce signal interferences and increase sensitivity in proteomic experiments. Here we present a two-dimensional peak-picking algorithm and generation of optimized spectral libraries, as well as take advantage of neural network-based processing of dia-PASEF data. Our computational platform boosts proteomic depth by up to 83% compared to previous work, and is specifically beneficial for fast proteomic experiments and those with low sample amounts. It quantifies over 5300 proteins in single injections recorded at 200 samples per day throughput using Evosep One chromatography system on a timsTOF Pro mass spectrometer and almost 9000 proteins in single injections recorded with a 93-min nanoflow gradient on timsTOF Pro 2, from 200 ng of HeLa peptides. A user-friendly implementation is provided through the incorporation of the algorithms in the DIA-NN software and by the FragPipe workflow for spectral library generation.