articleNature CommunicationsJul 8, 2022GOLD OA

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

VDVadim DemichevŁSŁukasz SzyrwielFYFengchao YuGCGuo Ci TeoGRGeorge Rosenberger

The Francis Crick Institute · Cambridge Consultants (United Kingdom) · +7 more institutions

PubMed
Indexed incrossrefdatacitedoajpubmed

Abstract

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…

Citation impact

416
total citations
FWCI
40.83
Percentile
100%
References
36
Citations per year

Authors

13

Topics & keywords

Topics
Keywords
  • Workflow
  • Mass spectrometry
  • Computer science
  • Proteomics
  • Sample (material)
  • Software
  • Artificial neural network
  • Throughput
No related works found for this paper.

Funding