Nature Communications (Jul 2022)

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

  • Vadim Demichev,
  • Lukasz Szyrwiel,
  • Fengchao Yu,
  • Guo Ci Teo,
  • George Rosenberger,
  • Agathe Niewienda,
  • Daniela Ludwig,
  • Jens Decker,
  • Stephanie Kaspar-Schoenefeld,
  • Kathryn S. Lilley,
  • Michael Mülleder,
  • Alexey I. Nesvizhskii,
  • Markus Ralser

DOI
https://doi.org/10.1038/s41467-022-31492-0
Journal volume & issue
Vol. 13, no. 1
pp. 1 – 8

Abstract

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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.