Redefining PFAS Workflow Applications: A New Horizon
How To Guide
Last Updated: August 1, 2024
(+ more)
Published: July 23, 2024
Credit: Thermo Fisher Scientific
Per- and polyfluoroalkyl substances (PFAS) are a global concern due to their persistence and environmental impact. Thus, detecting and quantifying both known and unknown PFAS compounds in the environment is critical to safeguard public health.
This comprehensive guide explores tailored workflows for PFAS detection across various matrices, from water to soil, emphasizing the importance of appropriate sampling, preparation, and advanced analytical methods.
Download this guide to discover:
- The significance accurate of PFAS detection and analysis
- Targeted and untargeted analysis methods tailored to different matrices
- Advanced analytical tools to enhance lab efficiency and data accuracy
Setting a new horizon
for PFAS workflow applications
PFAS, a global concern
Per- and polyfluoroalkyl substances (PFAS) are among the primary emerging
contaminants of concern. The detection and quantification of known PFAS and
the discovery of unknown PFAS substances has never been more important.
Determining the best workflow for your PFAS analysis can be challenging. Optimal
methods will vary depending on the matrix you are working with and goals of your
analysis. There are strategies to help you with either targeted analysis of known
PFAS compounds or the discovery of unknowns, from a variety of matrices.
2
3
Perfluorinated Perfluoroalkyl Sulfonamide Amino Carboxylates
Perfluoroalkyl Sulfonamido Amines
Perfluoroalkyl Acids (PFAAs)
Poly fluorinated
Perfluoroalkyl Sulfonic
Acids (PFSAs)
Perfluoroalkyl Carboxylic
Acids (PFCAs)
Fluorotelomer Sulfonates
Fluorotelomer Sulfonamido Betaines
Fluorotelomer Alcohols
4
Targeted analysis
• Identification and quantitation based on a known
candidate list of compounds
• Established or regulated methods available
• Confirms presence of a compound based on limit
of detection
Unknown screening
• Discover new or unexpected compounds
• Detection is independent of a candidate list
• Find new compounds of interest in previously run
samples by retrospective data analysis
PFAS transport through the environment and
analysis strategies
Household
products
Cleaning products
Personal care products
Paints, waxes, polishes
Food contact
materials
Non-stick cookware
Microwave popcorn bags
Fast food wrappers
Manufacturing
processes
Commercial products
Electronics
Petrochemicals
Fabrics
Stain resistant
carpets and fabrics
Waterproof or
resistant clothing
Aqueous
firefighting foam
Airports
Military bases
PFAS
sources
PFAS
exposure
Workflow
strategies
PFAS
PFAS
PFAS PFAS PFAS PFAS PFAS
Soil Runoff Leachate
Animals
Produce Fish
Humans
Plants
PFAS
PFAS
PFAS
Sample
collection
Sample
preparation Analysis Data
processing
The vast uses of PFAS compounds has resulted in a great
number of sources for these substances to enter the environment.
Common modes of transport are runoff, especially with firefighting
foams into water, or leachate from landfills, discharge from
manufacturing processes or improper disposal. Once in the
ecosystem, plants, animals and humans are all exposed to PFAS.
The C-F bonds in the PFAS molecule are very strong, which make
metabolism of these compounds very difficult. Therefore, PFAS
bioaccumulates over time and causes various health concerns.
The workflow for analyzing PFAS will depend on the goals of your
analysis. Many labs are doing targeted analysis where a specific list
of PFAS molecules are analyzed and quantified. It is estimated there
are over 5000 different types of PFAS compounds; some labs
will want to discover and identify unknown PFAS through
untargeted screening.
Water Drinking water Surface water Groundwater Wastewater
PFAS
Water
Drinking
water
Surface water,
groundwater, wastewater
Analysis
goal
Targeted
analysis
Screening or
unknown profiling
Targeted
analysis
Screening or
unknown profiling
Targeted
analysis
Screening or
unknown profiling
Sample
prep
Solid phase extraction
(SPE)
Dilution,
filtration,
acidification
Dilution, filtration,
acidification
or solid phase
extraction
Accelerated solvent extraction
SPE clean-up
Analytical
method
LC-MS/MS:
Triple quad mass
spectrometry
LC-HRAM:
High resolution
accurate mass
LC-MS/MS:
Triple quad mass
spectrometry
LC-HRAM:
High resolution
accurate mass
LC-MS/MS:
Triple quad mass
spectrometry
LC-HRAM:
High resolution
accurate mass
Data
acquisition
and
processing
Chromeleon CDS
TraceFinder software
Compound Discoverer software
Soil
Careful sampling is important in PFAS analysis. A representative
sample must be obtained without introducing any background
PFAS into the sample. PFAS can be found in many sources while
sampling and in the laboratory. Items to avoid when sampling
are waterproof clothing, adhesives, sampling device and materials
coming into contact with vehicle upholstery, and common blue
ice packs used in shipping. In the lab, avoid items such as
aluminum foil, sticky notes and some materials used in the flow
path of analytical instruments. It is important to use instruments
with minimal fluoropolymers. Polypropylene sampling vessels
must be used for water and soil samples as well as the devices
used to collect the sample.
PFAS workflows will be different based on the matrix you are
working with and the goals of your analysis, either targeted
analysis or unknown screening. Each matrix uses a different
sample preparation method. For water, solid phase extraction
(SPE) will be used for drinking water while other water types will
use dilution, filtration and/or acidification. For soils, accelerated
solvent extraction (ASE) is the optimal method. All the PFAS
workflows use liquid chromatography (LC) for separation, but
the best mass spectrometer is determined by the analysis type,
targeted or unknown screening.
The data processing software will depend on the type of
workflow. Both Thermo Scientific™ Chromeleon™ Chromatography
Data System (CDS) software or Thermo Scientific™ TraceFinder™
software are designed for targeted analysis and quantification.
Thermo Scientific™ Compound Discoverer™ software streamlines
compound identification and structural elucidation.
PFAS sampling
PFAS workflow
5
Everyday PFAS analysis in drinking water
SPE sample preparation to mass spectrometry analysis
Thermo Scientific™ Dionex™ AutoTrace™ 280
PFAS solid-phase extraction instrument
• Improves recovery and reproducibility
• Significantly reduces risk of background PFAS
• Improves lab efficiency
The AutoTrace 280 PFAS system ensures inertness and prevents
PFAS contamination into samples during extraction, while at the
same time delivering consistent and reliable performance.
Thermo Scientific™ TSQ™ Fortis triple
quadrupole mass spectrometer with the
Thermo Scientific™ Vanquish™ UHPLC system
fitted with the PFC free kit
• Excellent quantitative performance at low dwell times
• Enhanced confidence in data and outstanding robustness that
prolongs instrument uptime
• Simplicity and ease-of-use for users of all expertise levels
Established methods:
U.S. EPA 537.1
U.S. EPA 533
Orbitrap Exploris 120
Dionex ASE 350
Accelerated Solvent
Extractor
AutoTrace 280
H 27 x W 23
27.7 H x 21 W
Orbitrap Exploris 240 Orbitrap Exploris 120
H 26.75 x W 30
TSQ Altis Triple-Stage
Quadrupole
TSQ Fortis Triple-Stage
Quadrupole
Dionex ICS-6000 HPIC system
32.25 H x 21.65 W with Tablet Interface
Vanquish Core
32.25 H x 21.65 W
Vanquish Core
32.25 H x 21.65 W
Vanquish Core
AutoTH 27 x Dionex Integrion HPIC System
24.61 H x 11.8 W
TSQ Quantis Triple-Stage
Quadrupole
Thermo Fisher Scientific can supply and support everything
you need to detect and quantify PFAS in drinking water. Many
established methods, including regulatory, require collection into
polypropylene bottles, followed by sample preparation by SPE
and analysis using triple quad mass spectrometry.
3.75 5.0 7.5 10.0 12.5 15.0
0
2.5e4
5.0e4
8.0e4
1
2,3
4,5
22
6
7,8
9,10
11,12,13
17,18 15,16
14 25
20,21
19 24 23
Min.
Counts
Excellent separation of all 18 PFAS compounds and isotropically labeled
standards in under 15 minutes.
General targeted PFAS analysis workflow in drinking water samples based on either US EPA Method 537.1 or US EPA Method 533.
Collect 250 mL sample
in a polypropylene bottle
and add preservative
Extract with
AutoTrace 280 PFAS
instrument
Add internal standards Data analysis with Chromeleon CDS
or TraceFinder software
Add surrogates
or isotope dilution analogues
Evaporate to
dryness and reconstitute
LC-MS/MS analysis using the
Vanquish UHPLC system and
TSQ Fortis mass spectrometer
01
03
05
04
06
07
02
6
All 18 target compounds spiked at 2 levels, show recoveries well within the method limits of 70–130% and reproducibility is under the required 20%.
Preparing PFAS water samples with the AutoTrace 280 PFAS shows negligible background.
PFAS blank LC-MS/MS chromatograms
-2.0e2
-1.3e2
0.0e0
1.3e2
2.5e2
3.8e2
5.0e2
6.3e2
7.5e2
8.8e2
1.0e3
1.1e3
1.3e3
1.4e3
PFBA
PFOA
PFMPA
PFPeA
PFBS
PFMBA
PFEESA
NFDHA
4:2 FTS PFHxA
PFPeS
HFPO-DA
PFHpA
PFHxS ADONA
6:2 FTS
PFHpS
PFNA PFOS
9Cl-PF3ONS
8:2 FTS PFDA
PFUnA
11Cl-PF3OUdS
PFDoA
Counts
4.0 5.0 6.0 7.0 8.0 9.0 10.0 11.0 12.0 13.0 14.0 15.0 16.0 17.0 Min.
Peak number Analyte Fortified conc.
(ng/L)
Mean recovery
(%) RSD Fortified conc.
(ng/L)
Mean recovery
(%) RSD
1 PFBS 16.0 107 3.3 80.0 98.3 3.6
2,3* PFHxA 16.0 108 2.3 80.0 106 2.6
4,5* HFPO-DA 16.0 84.1 7.5 80.0 88.6 6.3
6 PFHpA 16.0 113 2.7 80.0 117 1.3
7 PFHxS 16.0 120 3.4 80.0 123 2.1
8 ADONA 16.0 117 2.5 80.0 121 1.1
9,10* PFOA 16.0 113 2.5 80.0 119 1.6
11 PFNA 16.0 114 2.9 80.0 118 2.1
12,13* PFOS 16.0 113 4.5 80.0 117 2.9
14 9Cl-PF3ONS 16.0 96.1 4.1 80.0 103 2.6
15*,16 PFDA 16.0 105 3.2 80.0 111 2.1
17*,18 NMeFOSAA 16.0 103 5.2 80.0 110 5.2
19 PFUnA 16.0 96.8 5.0 80.0 103 3.1
20*21 NEtFOSAA 16.0 100 9.9 80.0 104 2.3
22 11Cl-PF3OUdS 16.0 88.5 5.5 80.0 97.1 4.8
23 PFDoA 16.0 89.8 4.4 80.0 97.3 3.4
24 PFTrA 16.0 89.6 3.8 80.0 95.8 3.7
25 PFTA 16.0 89.0 4.8 80.0 98.1 3.3
* Designates the isotope labeled internal standard or surrogate.
PFAS
7
8
Thermo Scientific™ TSQ™ Altis
triple quadrupole mass
spectrometer with the Vanquish
UHPLC system fitted with the
PFC free kit
• Ultimate sensitivity in matrices ranging from
simple to complex
• Outstanding instrument robustness enables
increased confidence with no loss of instrument
uptime
• Ultrafast selected reaction monitoring
(SRM) increases the number of molecular
quantifications in less time
27.7 H x 21 W
Orbitrap Exploris 240 Orbitrap Exploris 120
H 26.75 x W 30
TSQ Altis Triple-Stage
Quadrupole
TSQ Fortis Triple-Stage
Quadrupole
Dionex ICS-6000 HPIC system
32.25 H x 21.65 W with Tablet Interface
Vanquish Core
32.25 H x 21.65 W
Vanquish Core
Dionex AccelerExtractAutoTrace 280
H 27 x W 23
Dionex Integrion HPIC System
24.61 H x 11.8 W
e-Stage
11
Table 5. PFAS recoveries in different water matrices, low and high levels at 60 and 200 ng/L, respectively
Compound
Recoveries %
Reagent water Ground water Surface water Waste water
Low
level
High
level
Low
level
High
level
Low
level
High
level
Low
level
High
level
PFBA 77% 78% 71% 75% 74% 74% 58% 75%
PFPeA 84% 80% 104% 80% 115% 81% 88% 78%
PFBS 87% 81% 95% 81% 95% 79% 72% 77%
PFHxA 82% 81% 83% 79% 86% 80% 77% 74%
4:2 FTS 81% 82% 90% 78% 87% 79% 76% 91%
PFPeS 80% 80% 82% 79% 85% 78% 80% 83%
PFHpA 84% 81% 88% 80% 89% 80% 74% 81%
PFHxS 81% 81% 87% 78% 94% 81% 85% 85%
6:2 FTS 84% 82% 85% 80% 87% 94% 78% 79%
PFOA 83% 80% 88% 82% 123% 83% 83% 86%
PFHpS 81% 81% 84% 76% 83% 78% 79% 86%
PFNA 79% 81% 84% 80% 86% 80% 79% 82%
PFOS 91% 82% 91% 78% 93% 81% 79% 90%
8:2 FTS 85% 80% 81% 75% 76% 79% 78% 83%
PFNS 85% 75% 89% 79% 81% 76% 72% 78%
PFDA 80% 81% 86% 78% 85% 79% 74% 83%
NMeFOSAA 77% 81% 80% 77% 86% 81% 82% 84%
PFOSA 76% 76% 87% 75% 91% 75% 79% 81%
PFDS 82% 78% 89% 77% 85% 79% 72% 81%
PFUnA 76% 76% 80% 81% 75% 78% 75% 83%
NEtFOSAA 82% 79% 89% 77% 89% 81% 80% 85%
PFDoA 79% 82% 83% 78% 85% 82% 79% 85%
PFTriA 87% 86% 89% 79% 92% 91% 87% 89%
PFTreA 109% 103% 112% 91% 113% 119% 100% 110%
Most recoveries in different water matrices at 60 and 200 ng/L are within the
70% to 130% range.
Overlaid chromatograms of all PFAS compounds included in this method.
PFOS chromatogram of an injection of
1 ng/L, which is five times lower than the
reporting limit of quantitation.
Figure 1. Overlaid chromatograms of all PFAS compounds included in this method
Excellent quantitative results for PFAS direct analysis in the low ng/L range in
non-drinking water matrices using dilution and filtration for sample preparation.
Direct inject targeted PFAS methods
Established methods:
U.S. EPA 8327
ASTM D7979
These alternative methods are sometimes preferred for
groundwater, surface water and especially for wastewater. Direct
injection methods, like U.S. EPA 8327 or ASTM D7979 are based
on sample dilution, filtration and acidification followed by
LC-MS/MS analysis. This direct analysis method is for
24 diverse types of PFAS compounds in a wide variety
of non-drinking water matrices.
PFAS
9
AOF-CIC provides an easy-to-use and economical way to determine if other PFAS molecules might be present in your sample.
This technique can help to optimize the utilization of analytical instrumentation by selecting and only analyzing “suspicious” samples.
CIC chromatogram of industrial wastewater, diluted 1:10.
Total fluorine consists of both inorganic and organic components.
The organic part contains compounds that are adsorbable (AOF)
and extractable (EOF), both of which have a subset of analytes that
are typically targeted by LC-MS/MS analysis. There are also organic
compounds that are not captured be either of these approaches.
Thermo Scientific™ combustion ion
chromatography system
• Eliminates complex sample preparation steps using an
automated method
• Produces fewer environmental contaminants
• Highly sensitive
• Easy-to-use and saves time
0
2
4
6
8
10
Fluoride
0 5 10 15
t (min)
µS/cm
Adsorbable organic fluorine (AOF) by combustion
ion chromatography
Analyzing for adsorbable organically-bound fluorine is used to
determine if the mass of fluorine present in the sample exceeds
that in the targeted screen. If the total amount is higher, then other
PFAS may be present in the sample which were not on the target list.
The use of this technique is well documented for the determination
of other adsorbable organic halogen-containing components (AOX).
Unknown
Screening by
LC-HRAM MS
Could other PFAS
be present?
Greater mass of fluorine
present than accounted
for in target list
No significant increase in total fluorine, all
mass accounted for in targeted screen
Discover compounds
contributing to total mass
of fluorine
Quantify the amount of
each compound on the
target list
OF
Total Fluorine (TF)
Inorganic
Fluorine
(IF)
Organic Fluorine (OF)
Adsorbable
Organic
Fluorine
(AOF)
Targeted PFAS analysis
Extractable
Organic
Fluorine
(EOF)
Could other PFAS molecules be present?
Automated combustion ion chromatography (CIC) provides a
complimentary screening method indicate the possible presence
of non-targeted PFAS or other fluorine containing compounds.
Targeted
screening by
LC-MS/MS
Fluorine mass
balance
PFAS
Combustion Ion Chromatography System
AOF by combustion ion chromatography
For complex samples with unknown amounts of
other PFASs, utilization of Compound Discoverer
software can reduce the data processing time and
quickly show results.
Workflow example in Compound Discoverer software.
Flow-chart style elements can be easily dragged and
dropped into place for easy customization.
Thermo Scientific™
Orbitrap Exploris™ 120
mass spectrometer
• Ultra high-resolution capability
• Removes concerns over false
positives/negatives
• Eliminates matrix interferences
• High mass accuracy to generate
reliable results
• Significantly accelerates the path to
confident results for both expert and
novice MS users
Orbitrap Exploris 120
0 HPIC system
face
Dionex ASE 350
Accelerated Solvent
Extractor
AutoTrace 280
H 27 x W 23
A UCMR3 sample shown having trace hits for a non-targeted compound (PFDS). Post-run
identification was performed by looking at the isotopic pattern recognition, accurate mass and
retention time for confirmation. Note the real-world water sample chromatogram on the left shows the
linear (RT 17.5) and branched isomers (RT 17.2) of PFDS, vs the linear PFDS isomer standard on the right.
U.S. EPA Method 537 target list
PFAS
compound
Critical Level
(ng/L)
DL
(ng/L)
LCMRL
(ng/L)
PFBS 0.15 0.2 <0.5
PFDA 0.15 0.26 <0.5
PFDoA 0.47 0.73
PFHpA 0.09 0.15 <0.5
PFHxA 0.13 0.19 <0.5
PFHxS 1.7 2.4
PFNA 0.11 0.17 <0.5
PFOA 0.22 0.5
PFOS 0.26 0.5
PFTA 0.15 0.2 <0.5
PFTrDA 0.31 0.55
PFuNA 0.38 1
U.S. EPA Method 537 target list
PFAS
compound
Critical Level
(ng/L)
DL
(ng/L)
LCMRL
(ng/L)
PFBA 0.19 0.64
PFODA 0.55 1
PFDS 0.13 0.19 <0.5
PFHxDA 0.12 0.5
PFPA 0.18 0.19 <0.5
PFAS compounds can be detected and quantitated by using a
triple quadrupole mass spectrometer (MS) in targeted analysis.
However, the identification and quantitation of unknown PFAS uses
LC coupled to high resolution mass spectrometry (HRAM MS).
With significant advances in HRAM MS comes can this move to
the first column to not only increase the range of potential targets
monitored, but to also increase confidence in assignments,
access the power of comprehensive tools to identify unknowns
and emerging contaminants, and retrospectively analyze data
even when the sample no longer exists.
Screening for unknown PFAS
Routine quantitative workflows and non-targeted analysis can be performed in a single analysis.
Input files
Mark
background
compounds
Predict
compositions
Search
mass lists
Search ChemSpider™ database search
Fill gaps
Merge features
Align retention times
Select spectra
Group unknown compounds
Using a full scan approach, required Detect unknown compounds
detection limits or MRLs can be
achieved while interrogating for other
untargeted PFAS compounds.
The compounds highlighted in blue are
additional analytes that are not part of
the original U.S. EPA Method 537 list
but were found in processed drinking
water from the same UCMR3 water
extracts.
10
Search Thermo Scientific™ mzCloud mass spectral library
2 g of soil extracted using the
ASE 350 accelerated solvent extractor
SPE clean up of the extract using
a styrene divinylbenzene (SDVB)
LC-MS/MS analysis using the
Vanquish UHPLC system
and TSQ Quantis mass spectrometer
Data analysis with Chromeleon CDS
and TraceFinder software
01
03
04
02
11
Compound Recovery
(%)
13C3-PFBS 98
13C3-PFHxS 95
13C8-PFOS 91
13C3-HFPODA 56
2
H3-NMEFOSAA 93
2
H3-NETFOSAA 90
13C8-FOSA 92
13C2
-4:2FTS 110
13C2
-6:2FTS 93
13C2
-8:2FTS 98
Thermo Scientific™ TSQ Quantis™ triple
quadrupole mass spectrometer with
the Vanquish UHPLC system fitted
with the PFC free kit
• Superb sensitivity, even in complex matrices
• Outstanding robustness; prolonging instrument uptime
• Reliability and reproducibility improve data quality for every
run and every sample
• Simplicity and ease-of-use allow users of all expertise levels to
acquire high quality data with improved confidence in results
Thermo Scientific™ Dionex™ ASE™ 350
accelerated solvent extractor
• Automates extraction for up to 24 samples
• Saves solvent—Just 50 mL used for PFAS
• Saves time—Only 7 minutes per PFAS extraction
H 26.75 x W 30
TSQ Altis Triple-Stage
Quadrupole
TSQ FoQuadru32.25 H x 21.65 W Vanquish Core
32.25 H x 21.65 W
Vanquish Core
32.25 H x 21.65 W
Vanquish Core
Dionex Integrion HPIC System
24.61 H x 11.8 W
TSQ Quantis Triple-Stage
Quadrupole
27.7 H x 21 W
Orbitrap Exploris 240 Orbitrap Exploris 120
Dionex ICS-6000 HPIC system
with Tablet Interface
Dionex ASE 350
Accelerated Solvent
Extractor
AutoTrace 280
H 27 x W 23
100
80
60
40
20
0
Relative abundance
0 2 4 6 8 10 12 14 16
1.38
Time (min)
2.00
2.72 3.16
3.98 4.95 5.76
6.18
4.31
6.35
7.03 8.03
8.73 9.09
10.20
10.69
11.19
11.59
12.46
11.75 12.59 13.71 14.68 15.55
15.98
16.40
15.34
14.49
13.48
12.30
10.91
9.27
7.41
5.40
3.52
2.17
1.49
9.72
C4 acid
(PFBA)
C14 acid
(PFTeDA)
PFOA
6.18 8.03 4.31 2.72
9.72
PFOS 11.19 12.46
Acids
Sulfonates
Fluorotelomer
Sulfonamides
Chromatogram of various PFAS molecules extracted from soil.
Recovery of the isotopically labeled PFAS compounds.
Compound Recovery
(%)
13C4-PFBA 71
13C5-PFPeA 93
13C5-PFHxA 97
13C4-PFHpA 96
13C8-PFOA 94
13C9-PFNA 104
13C6-PFDA 99
13C7
-PFUdA 95
13C2
-PFDoA 97
13C2
-PFTeDA 108
Data courtesy of Pacific Rim Labs.
The need to analyze PFAS in soil samples is also extremely
important. Soil becomes contaminated with PFAS through runoff
and leachate from landfills and other sources. Any produce or
vegetation growing in this soil is at risk for accumulating PFAS.
PFAS extraction and analysis in soil
Accelerated solvent extraction is an effective method for extracting a wide selection of PFAS, from 4-carbon to 14-carbon
fluoroalkyl chain lengths and five different polar head-groups, from soil over a wide range of concentrations.
PFAS
Find out more at thermofisher.com/pfas-testing
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