Drift time-specific collision energies enable deep-coverage data-independent acquisition proteomics

Nat Methods. 2014 Feb;11(2):167-70. doi: 10.1038/nmeth.2767. Epub 2013 Dec 15.


We present a data-independent acquisition mass spectrometry method, ultradefinition (UD) MS(E). This approach utilizes ion mobility drift time-specific collision-energy profiles to enhance precursor fragmentation efficiency over current MS(E) and high-definition (HD) MS(E) data-independent acquisition techniques. UDMS(E) provided high reproducibility and substantially improved proteome coverage of the HeLa cell proteome compared to previous implementations of MS(E), and it also outperformed a state-of-the-art data-dependent acquisition workflow. Additionally, we report a software tool, ISOQuant, for processing label-free quantitative UDMS(E) data.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromatography, Liquid
  • HeLa Cells
  • Humans
  • Ions / chemistry*
  • Peptide Fragments / analysis*
  • Proteome / analysis*
  • Proteomics*
  • Software
  • Tandem Mass Spectrometry / methods*


  • Ions
  • Peptide Fragments
  • Proteome