Analytical and Bioanalytical Chemistry

, Volume 408, Issue 28, pp 7905–7915 | Cite as

Optimization of LC-Orbitrap-HRMS acquisition and MZmine 2 data processing for nontarget screening of environmental samples using design of experiments

  • Meng Hu
  • Martin Krauss
  • Werner Brack
  • Tobias Schulze
Paper in Forefront


Liquid chromatography–high resolution mass spectrometry (LC-HRMS) is a well-established technique for nontarget screening of contaminants in complex environmental samples. Automatic peak detection is essential, but its performance has only rarely been assessed and optimized so far. With the aim to fill this gap, we used pristine water extracts spiked with 78 contaminants as a test case to evaluate and optimize chromatogram and spectral data processing. To assess whether data acquisition strategies have a significant impact on peak detection, three values of MS cycle time (CT) of an LTQ Orbitrap instrument were tested. Furthermore, the key parameter settings of the data processing software MZmine 2 were optimized to detect the maximum number of target peaks from the samples by the design of experiments (DoE) approach and compared to a manual evaluation. The results indicate that short CT significantly improves the quality of automatic peak detection, which means that full scan acquisition without additional MS2 experiments is suggested for nontarget screening. MZmine 2 detected 75–100 % of the peaks compared to manual peak detection at an intensity level of 105 in a validation dataset on both spiked and real water samples under optimal parameter settings. Finally, we provide an optimization workflow of MZmine 2 for LC-HRMS data processing that is applicable for environmental samples for nontarget screening. The results also show that the DoE approach is useful and effort-saving for optimizing data processing parameters.

Graphical Abstract


LTQ Orbitrap Design of experiments Environmental chemistry MZmine 2 LC-HRMS Cycle time 



The authors gratefully acknowledge the support by the European Marie Curie Initial Training Network EDA-EMERGE (grant agreement no. 290100), the European FP7 Collaborative Project SOLUTIONS (grant agreement no. 603437). MH was support by EDA-EMERGE (ESR09) and the HIGRADE Graduate School of the Helmholtz Centre for Environmental Research–UFZ.

Compliance with ethical standards

Conflict of interest

The authors declare that there is no conflict of interest.

Supplementary material

216_2016_9919_MOESM1_ESM.pdf (635 kb)
ESM 1 (PDF 634 kb)


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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.Department Effect-Directed AnalysisHelmholtz Centre for Environmental Research - UFZLeipzigGermany
  2. 2.Department of Ecosystem Analyses, Institute for Environmental ResearchRWTH Aachen UniversityAachenGermany

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