Analytical and Bioanalytical Chemistry

, Volume 408, Issue 24, pp 6729–6740 | Cite as

An approach to optimize sample preparation for MALDI imaging MS of FFPE sections using fractional factorial design of experiments

  • Janina Oetjen
  • Delf Lachmund
  • Andrew Palmer
  • Theodore Alexandrov
  • Michael Becker
  • Tobias Boskamp
  • Peter Maass
Research Paper

Abstract

A standardized workflow for matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI imaging MS) is a prerequisite for the routine use of this promising technology in clinical applications. We present an approach to develop standard operating procedures for MALDI imaging MS sample preparation of formalin-fixed and paraffin-embedded (FFPE) tissue sections based on a novel quantitative measure of dataset quality. To cover many parts of the complex workflow and simultaneously test several parameters, experiments were planned according to a fractional factorial design of experiments (DoE). The effect of ten different experiment parameters was investigated in two distinct DoE sets, each consisting of eight experiments. FFPE rat brain sections were used as standard material because of low biological variance. The mean peak intensity and a recently proposed spatial complexity measure were calculated for a list of 26 predefined peptides obtained by in silico digestion of five different proteins and served as quality criteria. A five-way analysis of variance (ANOVA) was applied on the final scores to retrieve a ranking of experiment parameters with increasing impact on data variance.

Graphical abstract

MALDI imaging experiments were planned according to fractional factorial design of experiments for the parameters under study. Selected peptide images were evaluated by the chosen quality metric (structure and intensity for a given peak list), and the calculated values were used as an input for the ANOVA. The parameters with the highest impact on the quality were deduced and SOPs recommended.

Keywords

MALDI imaging MS Fractional design of experiments SOP 

Supplementary material

216_2016_9793_MOESM1_ESM.pdf (386 kb)
ESM 1(PDF 386 kb)
216_2016_9793_MOESM2_ESM.xlsx (35 kb)
ESM 2(XLSX 35 kb)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2016

Authors and Affiliations

  1. 1.MALDI Imaging LabUniversity of BremenBremenGermany
  2. 2.Center for Industrial MathematicsUniversity of BremenBremenGermany
  3. 3.Structural and Computational Biology UnitEuropean Molecular Biology LaboratoryHeidelbergGermany
  4. 4.SCiLS GmbHBremenGermany
  5. 5.Skaggs School of Pharmacy and Pharmaceutical SciencesUniversity of California San DiegoLa JollaUSA
  6. 6.Bruker Daltonics GmbHBremenGermany

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