From Complexity to Clarity: Smarter PFAS Identification Workflows in Compound Discoverer Software

Per- and polyfluoroalkyl substances (PFAS) have become a major global concern due to their persistence, bioaccumulation, and potential health impacts. With thousands of known PFAS compounds, and new variants continuing to emerge, identifying and quantifying them across complex environmental and biological samples is an ongoing analytical challenge.

Thermo Fisher Scientific: From Complexity to Clarity: Smarter PFAS Identification Workflows in Compound Discoverer Software

Why PFAS analysis matters

PFAS are used in everything from firefighting foams to non-stick coatings, yet their chemical stability means they persist in the environment and accumulate in living organisms. Regulators and scientists around the world are racing to better understand their distribution, fate, and toxicity.

But with tens of thousands of PFAS, many without available reference standards, traditional targeted analysis alone isn’t enough. Analysts increasingly rely on non-targeted analysis (NTA) workflows powered by high-resolution accurate-mass (HRAM) mass spectrometry and advanced software to uncover the full picture.

Addressing the challenges of PFAS identification

Successful non-targeted PFAS analysis requires overcoming several analytical hurdles:

1. Acquiring high-quality MS¹ and MS² data with ultra-high mass resolution and accuracy.
2. Detecting low-abundance PFAS hidden within thousands of background compounds.
3. Leveraging comprehensive spectral libraries and databases for confident identification.
4. Applying data filtering and scoring tools to assign confidence levels to annotations.
5. Using visualization and statistical tools to interpret and compare complex datasets.

Thermo Scientific Compound Discoverer 3.5 software brings together all the components needed for robust PFAS identification—integrating HRAM Orbitrap MS data with an expanded suite of PFAS-specific libraries and databases.

In a single workflow, users can:

• Detect and annotate compounds automatically from LC-MS data.
• Determine possible elemental formulas using isotope pattern and accurate mass information.
• Compare MS² spectra against mzCloud, NIST 2023, and in silico PFAS libraries.
• Cross-reference annotations with the EPA PFAS Structure List and the NIST Suspect List of PFAS.
• Use PFAS-specific fragment and neutral loss databases to strengthen identification confidence.

With these resources combined, the software enables confident annotation of more than 40,000 PFAS compounds!

New tools for confident, streamlined PFAS identification

Compound Discoverer software introduces several new features designed to simplify and accelerate PFAS NTA workflows:

• Apply PFAS Scoring Node: Automatically calculates PFAS-specific parameters and a new PFAS Score—no R scripting required.
• PFAS Plot: A visual tool that uses mass-defect metrics to highlight probable PFAS in complex datasets, following methods from Kaufman et al. (2022).
• Expanded suite of libraries and databases: Combines mzCloud, NIST, in silico, PFAS fragment databases, and a new neutral loss database for greater confidence.
• Advanced data visualization: Tools like Kendrick Mass Defect and Molecular Network plots reveal homologous PFAS series and related compound families.
• Built-in statistical analysis tools: Compare PFAS composition between samples using Principal Component Analysis, Differential analysis and Hierarchical Cluster Analysis.

Thermo Fisher Scientific From Complexity to Clarity Smarter PFAS Identification Workflows in Compound Discoverer Software

From complexity to clarity

By uniting Orbitrap HRAM data with the most comprehensive PFAS libraries available, Compound Discoverer 3.5 software streamlines non-targeted PFAS analysis—helping laboratories move from data complexity to confident chemical clarity.

Watch the on-demand webinar to see the full workflow in action and learn how Compound Discoverer software can enhance your PFAS analysis.

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Zoe Julian

Zoe Julian is a Product Marketing Manager for Chromatography and Mass Spectrometry software at Thermo Fisher Scientific. With over 12 years' experience of working with chromatography and mass spectrometry techniques with a background in GC and GC-MS(/MS) organic environmental analysis, she has helped many laboratories and industries improve their workflows through a unique understanding of their challenges. Transitioning to a focus on Chromeleon CDS she has shown customers how software solutions can improve their productivity and support their day-to-day operations.