Analytical and Bioanalytical Chemistry

, Volume 407, Issue 2, pp 405–414 | Cite as

Applying ‘Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra’ (SWATH) for systematic toxicological analysis with liquid chromatography-high-resolution tandem mass spectrometry

  • Kathrin Arnhard
  • Anna Gottschall
  • Florian Pitterl
  • Herbert Oberacher
Research Paper


Liquid chromatography-tandem mass spectrometry (LC-MS/MS) has become an indispensable analytical technique in clinical and forensic toxicology for detection and identification of potentially toxic or harmful compounds. Particularly, non-target LC-MS/MS assays enable extensive and universal screening requested in systematic toxicological analysis. An integral part of the identification process is the generation of information-rich product ion spectra which can be searched against libraries of reference mass spectra. Usually, ‘data-dependent acquisition’ (DDA) strategies are applied for automated data acquisition. In this study, the ‘data-independent acquisition’ (DIA) method ‘Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra’ (SWATH) was combined with LC-MS/MS on a quadrupole-quadrupole-time-of-flight (QqTOF) instrument for acquiring informative high-resolution tandem mass spectra. SWATH performs data-independent fragmentation of all precursor ions entering the mass spectrometer in 21m/z isolation windows. The whole m/z range of interest is covered by continuous stepping of the isolation window. This allows numerous repeat analyses of each window during the elution of a single chromatographic peak and results in a complete fragment ion map of the sample. Compounds and samples typically encountered in forensic casework were used to assess performance characteristics of LC-MS/MS with SWATH. Our experiments clearly revealed that SWATH is a sensitive and specific identification technique. SWATH is capable of identifying more compounds at lower concentration levels than DDA does. The dynamic range of SWATH was estimated to be three orders of magnitude. Furthermore, the >600,000 SWATH spectra matched led to only 408 incorrect calls (false positive rate = 0.06 %). Deconvolution of generated ion maps was found to be essential for unravelling the full identification power of LC-MS/MS with SWATH. With the available software, however, only semi-automated deconvolution was enabled, which rendered data interpretation a laborious and time-consuming process.

Graphical Abstract

High-resolution LC-MS/MS with SWATH represents a sensitive and specific compound identification tool that has vast potential to become a leading technique in systematic toxicological analysis. SWATH solves the problem of unused precursor ions often encountered with data-dependent acquisition methods by acquiring complete fragment ion maps of a sample


Systematic toxicological analysis Information-dependent acquisition control Information-independent acquisition control Sequential Windowed Acquisition of All Theoretical Fragment Ion Mass Spectra (SWATH) Liquid chromatography-tandem mass spectrometry Tandem mass spectral library 



We thank the members of our casework unit for providing samples. Furthermore, we want to thank Lyle Burton, Jeffery Rivera, David Cox and Ron Bonner (AB Sciex) as well as Bernd Berger (Wiley) for helping us to integrate the ‘Wiley Registry of Tandem Mass Spectral Data, MSforID’ into MasterView.

Supplementary material

216_2014_8262_MOESM1_ESM.pdf (227 kb)
ESM 1 (PDF 226 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2014

Authors and Affiliations

  • Kathrin Arnhard
    • 1
  • Anna Gottschall
    • 1
  • Florian Pitterl
    • 1
  • Herbert Oberacher
    • 1
  1. 1.Institute of Legal Medicine and Core Facility MetabolomicsMedical University of InnsbruckInnsbruckAustria

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