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Updated: May 29, 2026

Proteomic Sample Preparation from Formalin Fixed and Paraffin Embedded Tissue
Published on: September 2, 2013
Preserved and Accessible: Quantifying PFAS in Formalin-Fixed and Paraffin-Embedded Tissues for Retrospective Exposure
Kushal Biswas1, Jennifer J Schlezinger2, Anila Bello3
1Department of Biomedical and Nutritional Sciences, Zuckerberg College of Health Sciences, University of Massachusetts Lowell, Lowell, Massachusetts 01854, United States.
Archived tissues can be used to measure per- and polyfluoroalkyl substances (PFAS) using a new LC-ESI-MS/MS method. Formalin fixation and paraffin embedding affect PFAS recovery, with longer-chain compounds and higher-burden tissues showing better retention.
Area of Science:
- Environmental Chemistry
- Toxicology
- Analytical Chemistry
Background:
- Formalin-fixed tissues are an underutilized resource for historical chemical exposure reconstruction.
- Per- and polyfluoroalkyl substances (PFAS) are persistent contaminants requiring robust biomonitoring methods.
- Fixation and embedding processes may impact analyte stability and quantification accuracy.
Purpose of the Study:
- To develop and validate a liquid chromatography-electrospray tandem mass spectrometry (LC-ESI-MS/MS) method for quantifying six PFAS in various mouse tissues.
- To assess the impact of formalin fixation and paraffin embedding on PFAS recovery and stability.
- To provide insights into compound- and matrix-specific recovery patterns for retrospective PFAS analysis.
Main Methods:
- Developed an LC-ESI-MS/MS method to quantify six target PFAS (PFHxS, PFOA, PFOS, PFNA, PFDA, PFUnA).
- Analyzed matched sets of flash-frozen, formalin-fixed, and formalin-fixed paraffin-embedded mouse tissues (liver, kidney, ileum, brain).
- Tracked PFAS recovery and loss through fixation, storage, and deparaffinization steps.
Main Results:
- Mean sum of PFAS in fresh tissues ranged from 279.2 ng/g (brain) to 22,628.4 ng/g (liver).
- Formalin fixation yielded 76.7-83.8% PFAS recovery, with 12.6-19.9% in formalin solution.
- Paraffin embedding resulted in 57.4-75.1% recovery, with additional losses during processing. Longer-chain PFAS and higher-burden tissues showed better retention.
Conclusions:
- Quantification of PFAS in archived formalin-fixed and paraffin-embedded tissues is feasible.
- Systematic data on compound- and matrix-specific PFAS recovery patterns are provided.
- Further validation is needed for short/ultrashort PFAS, and correction factors may be required for human tissues with low PFAS loads.
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