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

By V. Demichev, Lukasz Szyrwiel, Fengchao Yu, G. Teo, George A. Rosenberger, Agathe Niewienda, D. Ludwig, Jens Decker, Stephanie Kaspar-Schoenefeld, K. Lilley and 3 more. Nature Communications, 2022

327 citations recorded by the source corpus.

The 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. The dia-PASEF technology uses ion mobility separation to reduce signal interferences and increase sensitivity of mass spectrometry-based proteomics. The authors present algorithms and a software solution, which boost proteomic depth in dia-PASEF experiments by up to 83% compared to previous work, and are specifically beneficial for fast proteomic experiments and those with low sample amounts.

Subfields: Molecular Biology, Spectroscopy

View Paper: https://www.semanticscholar.org/paper/915d5d4efe5f563a76d5e909e8ece1915315d505