Bioanalytical

Sample Preparation
White Paper
 

CONTENTS

3 What are the Benefits of Sample Preparation? You analyze a lot of biological samples. You deliver
4 Options for Sample Preparation of Biological Fluids accurate, reliable data, consistently. You use
4  Dilute and Shoot (D&S) sophisticated, vhigh-end analytical techniques such
4  Filtration
4  Protein Precipitation (PPT) as LC-MS/MS or GC-MS. And the pressure is always
6  Phospholipid Depletion (PLD) there to do it faster, with greater sensitivity and, if
7  Dual Mode Extraction (DME) possible, at lower cost. Sample preparation can be
8  Liquid-Liquid Extraction (LLE)
8  Supported Liquid Extraction (SLE)
critical for success.
9  Solid Phase Extraction (SPE) and Micro-SPE
Sample preparation enables more reliable identification and
12 Matrix Considerations in Sample
quantification of an analyte from a biological sample. The
Preparation for Bioanalysis
analyte is extracted (and often concentrated), from sample
12  Liquid Samples
constituents that might interfere with the subsequent analysis.
12  Solid Samples
This can sound simple, but consider the basic challenges:
12  Common Matrix Types
14 Optimizing, Streamlining and » Extracting an analyte without introducing variability.
Automating Sample Preparation » Handling a wide variety of sample matrices,
such as urine, blood, oral fluid, tissue, or hair,
14  Format and Equipment
etc. with their different challenges.
15  Eliminating Steps
16  Automation
» Handling large numbers of samples
with limited lab resources.
17 Do You Need Lower Detection Limits? » Achieving low detection limits despite
17  Evaporation Headaches introducing extra steps for clean-up.
18  Using Micro-SPE to Achieve Low Detection Limits » Maintaining simplicity and controlling
19 Sample Preparation for Bioanalysis: Conclusions costs despite the extra steps.
19  References Choosing a sample preparation approach can have far-reaching
consequences for your results as well as for the overall perfor-
mance of your lab.
Let’s take a look at the issues that you should consider and the
options that are available for sample preparation.

Sample Pre-Treatment Sample Evaporation Analysis

Preparation

Figure 1. An analytical workflow for LC-MS/MS or GC-MS can include several steps prior to the actual analysis.

2 Bioanalytical Sample Preparation | © Biotage 2020

 What are the Benefits of Sample Preparation?

What are the Benefits

of Sample Preparation?
Sample preparation is often considered a necessary inconve-
nience in the analytical process. You might want to disregard
it as just extra work prior to the more glamorous analytical
technique that delivers the result. Yet there are definite benefits
you can gain from carefully chosen, appropriate, sample prep.
» Higher quality data. It makes good sense to ensure that
samples are presented in a form that enables the best
performance from sophisticated analytical equipment. This
helps meet the demand for accurate and consistent results.
» Lower costs. By avoiding ‘dirty’ samples, you
minimize downtime and maintenance of expensive
equipment, as well as avoiding reruns.
» Better sensitivity. Clean samples, concentrated
and without interfering matrix components,
help you to achieve low detection limits.
» Greater robustness. By ensuring consistency in
the treatment of samples applied to downstream
analytical steps, you control variability (for example,
protecting the subsequent analysis from extremes
in matrix composition that can impact results
through interference or masking of analytes).
However, sample prep does add to the complexity of the
analytical workflow and, unfortunately, there is no ‘one size fits
all’. Extra steps take time and an incorrect choice of method can
introduce errors rather than reducing them. So, what are your
options and how do you choose between them?

3
 Options for Sample Preparation of Biological Fluids

Options for Sample Preparation

of Biological Fluids

There is a whole range of sample preparation or phospholipids) are still present, they might reduce liquid
chromatography (LC) column lifetime, build up on the mass
techniques and each one has its place. Loosely, spectrometer (MS) source, or suppress ionization of the target
methods can be divided into ‘matrix scavenging’, analyte (if co-eluting with analyte from the liquid chroma­
designed to remove specific matrix components, and tography column).
‘targeted extraction’ where the characteristics of If you can live with reduced sensitivity, afford the potential
the analyte of interest directly impact the choice of instrument downtime, accept costs for replacing LC columns
more frequently, and accept having to regularly clean the MS
sample prep technique and, frequently, components source, then D&S is itself cheap, fast, and simple.
within the chosen technique.
Filtration
Matrix Scavenging Techniques tend to be quicker, cheaper
and simpler, whilst they usually require little or no method Another simple technique is to pass the sample through a 0.45
development compared with targeted extraction. However, they or 0.2 µm filter. Clearly, this will remove particulates that could
might not provide sufficiently high recovery or concentration to clog an LC column, but won’t remove dissolved matrix compo-
provide satisfactory detection limits. nents that can interfere in other ways. Commonly, filtration
will be followed by dilution then injection. This method is also
Targeted Extraction Techniques, such as supported liquid typically applied to urine although it may be appropriate for
extraction (SLE) and solid phase extraction (SPE) can be other biofluids. As with D&S, it is simple, quick and relatively
tailored more effectively to exploit analyte characteristics. They cheap.
are often more complex, require more method development,
and can be more expensive per analyzed sample. However, this
is compensated for by delivering cleaner extracts with higher Protein Precipitation (PPT)
recoveries and potentially higher analytical sensitivity (lower This is a matrix scavenging technique usually based on the
detection limits). familiar ‘acetonitrile crash’ approach. Simply add excess
acetonitrile to the sample and either filter or centrifuge away the
These techniques are applicable to liquid samples as well as
precipitated proteins.
solid or semi-solid biological samples (such as tissue, hair
or fingernails). For solid and semi-solid samples, additional PPT is primarily used for blood, serum or plasma samples that
sample pre-treatment is normally required to transfer analytes carry a heavy protein load (Figure 2).
into a liquid phase before clean-up.
It is available in a 96-well microtiter plate format where precipi-
tation occurs in the wells and the clear protein-free samples
Dilute and Shoot (D&S) are collected after passage through bottom filters (induced
Before we look at more complicated approaches to sample by pressure or vacuum). This format is particularly suited to
preparation, let us consider the simplest. There are situations automated high-throughput assays, whereas using test tubes
where the sample can be diluted then injected directly into, for and a centrifuge is more appropriate for manual handling of
example, an LC-MS/MS instrument. This is most often exploited small sample numbers (Figure 3).
with urine samples, which can be simply diluted 1:10 with water PPT demands little method development, but it will not be
or buffer. suitable in all situations because it only removes proteins
Clearly, there will be a direct negative impact on the limit (not phospholipids) and doesn’t target any specific analyte.
of detection, but this might be acceptable. Furthermore, Nevertheless, the method is quick, simple and relatively
because all matrix components (such as salts, urea, proteins inexpensive.

4 Bioanalytical Sample Preparation | © Biotage 2020

 Options for Sample Preparation of Biological Fluids

Plasma Components
0.8% 0.3% 0.1%
Albumin 41.5% Fibrinogen 3%
0.6%
5.8%
3.5% Glycoprotein 1.4% IgG, A, M, D 12.8%
HS Glycoprotein 0.6% Inorganic Substances 3.5%
41.5%
12.8% Antitrypsin 1.5% Nitrogenous Substances 0.6%
Antichymotrypsin 0.5% Amino Acids 0.8%

Globulins 22.5% Lipids 0.8%

22.5%
3%
1.4% Ceruloplasmin 0.4% Prealbumin 0.8%
0.2%
0.7% 0.6% Haptoglobilin 4% Vitamins 0.1%
4% 1.5% Hemopexin 0.7% Peptides 0.0%
0.4% 0.5%
Transferin 0.2% Carbohydrates 0.0%

Protein Precipitation
Figure 2. Plasma is one protein-rich biological sample you might be analyzing1.

Dispense crash solvent Dispense sample matrix Apply low vacuum/

(e.g. plasma, blood) positive pressure

Protein

Analyte

Mix as required

Precipitated proteins
retained by depth filter

Collect purified analytes

Bottom frit prevents dripping

Figure 3. Schematic PPT procedure used in 96-well microtiter plates with bottom filters.

5
 Options for Sample Preparation of Biological Fluids

Phospholipid Depletion (PLD)

Removal of phospholipids is extremely important in LC-MS/
MS of biological fluids, particularly blood-based samples.
Phospholipids are a family of compounds that can elute at
various points throughout the chromatogram in LC and cause
significant ion suppression in subsequent MS (Figure 4).
Phospholipids can be conveniently removed following acetoni-
trile PPT using a scavenging adsorbent (Figure 5).
PLD is another example of a matrix scavenging technique that Figure 4. Total ion chromatograms (TICs) from a post column infusion
experiment. Top trace shows phospholipid species monitored by specific
does not target specific analytes. Although samples are rather multiple reaction monitoring (MRM) transitions. Bottom trace shows
clean after PLD, the technique might not be suitable for some a simultaneous fixed concentration flow of propranolol (specific MRM
transition) added after the column, but before the MS source. Note that
kinds of analyses. However, method development is normally the signal decreases in the lower trace due to ion suppression by the
minimal, and PLD is simple and quick with relatively low costs. phospholipid peaks.

Dispense crash solvent Dispense sample matrix Apply low vacuum/

(e.g. plasma, blood) positive pressure

Depth Filter

Upper Frit

Phospholipid
Scavenger Sorbent

Lower Frit
Precipitated proteins
retained by depth filter

Phospholipids retained
Phospholipids

Protein
Collect purified analytes
Analyte(s) Mix as required

Figure 5. Schematic procedure for PPT with isopropanol crash solvent, followed by PLD using a scavenging adsorbent. Available in column or 96-well
microtiter plate formats.

6 Bioanalytical Sample Preparation | © Biotage 2020

 Options for Sample Preparation of Biological Fluids

ISOLUTE HYDRO DME+ with Hydrolysis step

In-Well
Hydrolysis Add Acetonitrile Elute

HYDRO Frit
Scavenging Sorbent Apply low vacuum/
Middle Frit positive pressure
Hygroscopic Sorbent Mix as
required
Lower Frit

Collect purified
Matrix components analytes

Analytes of interest

Hydrolysis enzyme

Figure 6. Schematic DME procedure using in situ hydrolysis followed by acetonitrile precipitation and matrix removal by elution through separate
scavenging and hygroscopic sorbents. Available in column or 96-well plate formats.

Dual Mode Extraction (DME)

This is a matrix scavenging technique designed principally for a hydrolysis step and possibly proteins from the urine itself),
urine sample preparation. It is available commercially in column are removed by acetonitrile treatment followed by elution
and 96-well plate formats. Matrix components such as urea, through two different sorbents. These steps can be performed
salts, pigments, creatinine, and proteins (residual enzyme from in situ without any need for sample transfer (Figure 6).

Urine Hydrolysis
In the body, most drugs are metabolized prior to excretion in rates. So, you will have to optimize hydrolysis conditions for your
urine or feces. Many drugs and metabolites are conjugated as a analytes of interest. Once hydrolyzed, the sample will contain not
glucuronide or sulfate to increase water solubility and improve only pre-existing matrix components (for urine these include salts,
their elimination. Hydrolysis of urine specimens using a beta- urea, creatinine, and pigments), but also excess enzyme, which
glucuronidase (and/or sulfatase) converts such analytes to their can:
‘free’ form (de-conjugation) to increase analytical sensitivity, and » foul the analytical LC column leading to impaired analyte
improve chromatographic characteristics. separation, requiring frequent replacement
Urine sample hydrolysis involves incubating the sample (usually at » lead to increased system back pressure
elevated temperature) with an appropriate enzyme prior to cooling » interfere with derivatization steps (particularly important in GC-
and quenching to stop the reaction. The enzyme is abundant in living MS analysis).
systems because it is an essential part of carbohydrate metabolism. For these reasons, sample clean-up after hydrolysis is particularly
Widely used laboratory sources of beta-glucuronidase include snails important.
(Helix pomatia), abalone, and various recombinant forms.
In conclusion, being a matrix scavenging technique, DME may
Factors such as enzyme type and concentration, incubation not be suitable for certain analytes, but method development is
temperature and time, and pH conditions will all affect hydrolysis minimal, and the method has a straightforward, pass-through
efficiency, and different drug conjugates will hydrolyze at different workflow.

7
 Options for Sample Preparation of Biological Fluids

Liquid-Liquid Extraction (LLE)

LLE is still widely used as a targeted sample preparation
technique in bioanalysis, even if other approaches have
partially replaced it. For low volume biofluid samples it can
be performed in small vials, with manual shaking and use of a
lab pipette to remove the unwanted layer – rather than using
a separation funnel (which is easier for large samples such
as drinking water or waste water, Figure 7). Large numbers of
small-volume samples can be handled in a 96-well plate format,
although it is challenging to do several steps in parallel.
LLE is effective and useful, particularly if you only have a few
samples. It is also relatively cheap (if you don’t count labor
costs). The issues come if you need to process large numbers
of samples. Capping/shaking/settling of layers and pipetting
can be challenging. It is difficult (although not impossible) to
automate.
These issues have led to an increase in the popularity of
alternative techniques, in particular supported liquid extraction
(SLE), which works according to similar principles but is much
easier to automate, avoids the risk of emulsion formation, and
often provides a more efficient extraction process (i.e. with
higher recovery).
Figure 7. Classic LLE funnel setup.

Supported Liquid Extraction (SLE)

Supported Liquid Extraction (SLE) is a targeted extraction support (a form of diatomaceous earth). The aqueous sample
technique for sample preparation before LC-MS/MS or GC-MS forms a thin layer over the support to create a ‘stationary
analysis. This extraction technique is based on the same phase’.
chemistry as liquid-liquid extraction. However, instead of using
The water-immiscible organic extraction solvent is then passed
a separation funnel and partitioning between two immiscible
through the column/plate. As it passes over the thin layer of
liquids – one aqueous and one organic – the extraction is
SLE+ Load Wait Elute
performed on a solid support. Using SLE, an aqueous sample
aqueous sample, analytes partition into the organic solvent,
which is collected (Figure 8).
is loaded onto a 96-well plate or column containing an inert

Step 1 Step 2 Step 3

Load Wait Elute

Analyte

Matrix components
e.g. phospholipids, salts
and proteins

SLE Support
material (diatoms)

Aqueous sample flows Analytes partition

onto extraction bed, into elution solvent
and is dispersed and are collected
in small droplets.

Figure 8. Schematic SLE procedure available in 96-well plates or columns.

8 Bioanalytical Sample Preparation | © Biotage 2020

 Options for Sample Preparation of Biological Fluids

Clean-up is based on an analyte’s ability to partition into the SPE uses a solid phase to bind the analyte of interest under
water-immiscible organic extraction solvent. The method can be defined conditions. Matrix components are removed by one or
tailored to deliver high recovery of a specific analyte. Proteins, several washing steps and the target is recovered by eluting
phospholipids, salts, pigments, etc., that might interfere with under conditions that discourage binding.
subsequent analyses tend not to be very soluble in the organic
The solid phase consists of modified silica or polymer particles
phase, so they are left behind in the aqueous phase on the
that are packed in columns or 96-well plates. There is a wide
column.
choice of media offering many retention mechanisms and it
The outcome of SLE will always net an organic solvent, which is this wide choice that makes method development rather
one can direct inject or derivatize (for GC/MS analysis). If LC/ complex.
MS analysis is used, then the solvent must be dried down and a
compatible reconstitution solution must be employed, because Silica-based SPE media characteristics
LC-MS/MS normally uses reversed phase chromatography Non-polar modified silica: a wide range of hydrophobic bonded
(RPC), which is incompatible with immiscible organic solvents. silicas are available, for example, C18, C8, C2, and PH.

Method development is required, but it is relatively simple. Key Polar modified silica: these are not often used for biofluid
variables are: extraction. However, non-bonded silica and amino- or diol-
bonded silicas are available.
» the pH of the sample (just like in LLE, you acidify
to increase recovery of acidic analytes, or add Cation exchange modified silica: cation exchangers can
base to increase recovery of basic ones) contain strong or weak acidic groups that give them different
» the choice of extraction solvent. charge-carrying characteristics over a range of pHs. A strong
cation exchanger, such as one containing sulfonic acid groups,
will be negatively charged over a wide pH range. A weak cation
Solid Phase Extraction (SPE) and Micro-SPE exchanger, such as one containing carboxylic acid groups, will
SPE is a very powerful targeted extraction technique that can be negatively charged at high pH values but will lose its charge
combine sample clean-up and analyte concentration with gradually as pH values are reduced.
high recoveries and low matrix effects (Figure 9). Micro-SPE
combines these benefits with optimized small-scale formats Anion exchange modified silica: In a similar fashion, a strong
Metal Mitigation
to achieves high concentration analyte recoveries in small anion exchanger is one substituted with strong basic groups,
elution volumes. such as quaternary amines, that are positively charged over a
wide pH range. Weak anion exchangers typically contain amine
However, method development in SPE is often more challenging groups that are positively charged at low pH but gradually lose
than for the other techniques, and the overall greater their charge as pH is raised.
complexity, both regarding solid phases and reagents, is
Condition Equilibrate Load Wash Elute
reflected in higher costs per analysis.

Step 1 Step 2 Step 3 Step 4 Step 5

Condition Equilibrate Load Wash Elute

Figure 9. Schematic SPE procedure. The silica or polymer particles can be packed in columns or a
96-well plate format.
Interferences
Interferences
Analyte of interest
Analyte of interest

9
 Options for Sample Preparation of Biological Fluids

Mixed-mode modified silica: These types of media combine Mixed-mode polymeric SPE particles combine the charac-
non-polar or hydrophobic characteristics with anion- or cation teristics of a non-polar (hydrophobic) polymer backbone
exchangers. The hydrophobic- and charge-based retention (usually containing some polar/wettable groups) and an ionic
mechanisms result in solid phases that can retain most drugs functional group. In other words, they have mixed-mode binding
and other small molecules. They have proved very useful for SPE characteristics, but this is achieved in a different way than with
of biological fluids since the combined retention mechanisms silica-based media.
together with strong washes and selective elution solvent
A mixed-mode silica-based stationary phase tends to have
choices offer highly effective removal of matrix components,
lower hydrophobicity than the equivalent mixed-mode
such as phospholipids, and good recovery of the specific
polymeric sorbent. Consequently, the non-polar retention
analyte of interest.
mechanism provided by the silica-based C8 or C18 is generally
The most common mixed-mode silica types are cation less strong (less retentive) than that provided by a polymeric
exchangers with either C8 or C18 non-polar groups. They are backbone. This can mean that cleaner extracts are possible
widely used in forensic toxicology applications to extract basic from silica-based materials, because solvent washes can
drugs from urine samples. more effectively remove the weakly bound matrix interference
components.
Why use Polymeric SPE?
Polymeric SPE phases are often described as being more robust Polymeric SPE media
and are increasingly chosen in favor of silica-based media for Typically, polymeric SPE stationary phases are available in 5
biofluid extraction. This is because of a couple of drawbacks types:
common to silica-based media:
» Non-polar water wettable polymer: the primary retention
pH Stability: silica-based media are not very stable above pH 8 mechanism is through non-polar interactions
and should only be used at higher pHs (up to pH 10) for very » Mixed-mode - strong cation exchange +
short exposure times. In contrast, polymeric stationary phases, non-polar water wettable polymer
usually based on modified divinyl benzene (DVB) polymers, are » Mixed-mode - weak cation exchange +
stable over the pH range 1–14. non-polar water wettable polymer
Conditioning: silica-based solid phases need to be ‘condi-
» Mixed-mode - strong anion exchange +
non-polar water wettable polymer
tioned’ (usually by a wash with methanol) to ensure that the
functional groups are active prior to use, and because of this,
» Mixed-mode - weak anion exchange +
non-polar water wettable polymer
they can be sensitive to drying out. Polymeric SPE based on
DVB are modified with polar monomers or functional groups to Pore size considerations
make them easily wettable without conditioning, and they are The high surface area of SPE phases makes it possible to extract
unaffected by drying out. analytes using small amounts of media. The particles used in
SPE, whether silica- or polymer- based, are highly porous, giving
Polymer-based SPE media characteristics them a high surface area.
Polymeric SPE particles consist of a backbone, typically a DVB
modified with polar groups to make the polymer beads water The size of the pores can influence extract cleanliness, particu-
wettable. These beads are then modified by substitution with larly regarding proteins. With wider pores, more protein can
ion exchange groups. penetrate inside of the particles, giving high binding capacity
not only for the analyte but also for protein components that can
interfere with the subsequent analysis.
Table 2. Retention mechanisms of silica-based SPE media.

Sorbent type Retention mechanism Typical functional groups Used to extract

Neutrals, acids and/or bases, with

Non-polar Hydrophobic C18, C8, C2, PH
some hydrophobic character

Analytes with polar character (from

Polar H-bonding, dipole-dipole or π-π -NH2, DIOL
non-polar solvents)
Strong: -NR4+ Acidic analytes with a negative
Anion exchange Ion exchange
Weak: -NH3+/-NH2 charge
Strong: -SO3-
Cation exchange Ion exchange Basic analytes with a positive charge
Weak: -COO-/-COOH
Combination of hydrophobic and ion C8 + SO3- Analytes with hydrophobic and ionic
Mixed-mode
exchange C8 + -NR4+ functional groups

10 Bioanalytical Sample Preparation | © Biotage 2020

 Options for Sample Preparation of Biological Fluids

In the experiment illustrated by the electrophoresis gel (see

Figure 10), an SPE sorbent with nominal 40 Å pore diameter is
compared with one that has nominal 100 Å pores. Very little
protein is extracted with the smaller pore size media.

220
120
70
40
30

20

10
10

Ra

M
40

w
0

w
Å

tM
Å

Se ze
Po ize
Po

ar
ru
re
re

ke
m
Si
S

Figure 10. Comparison of extracted protein using 40 Å and 100 Å pore

diameter SPE media.

11
 Matrix Considerations in Sample Preparation for Bioanalysis

Matrix Considerations in Sample

Preparation for Bioanalysis

Liquid Samples
Biofluids are often diluted (usually 1:1 to 1:3, v:v) before the » grinding and homogenization
clean-up technique in order to: » solvent or buffer extraction
» reduce viscosity so they flow through the
» saponification to remove fats
extraction device more easily.
» adjust sample pH (using buffer) to improve the Common Matrix Types
extraction or adapt for the subsequent extraction. Here we briefly summarize the special issues related to a few
This pH will vary depending upon the analyte, sample specific biofluids.
prep technique, and analytical technique.
Urine
Dilution in this way brings more consistency to samples that
Urine contains urea, salts, creatinine, enzyme from hydrolysis,
may vary considerably in viscosity — for example, urine samples
and sometimes other proteins associated with certain illnesses
can vary depending on how hydrated the patient is. Dilution will
(Figure 11).
improve standardization, which is especially important when
you are batch-processing or using 96-well plate formats. Hydrolysis to deconjugate drugs has been described in the
section “Dual Mode Extraction (DME)” on page 7. It
improves detection limits for parent drugs. Removal of post
Solid Samples hydrolysis enzyme or other proteins is an important safeguard
All the sample preparation described, and the subsequent and, as described in the Optimization and Streamlining section
analytical techniques of LC-MS/MS or GC-MS, require liquid (page 14), a step in the workflow can be avoided using an
samples. Solids or semi solids must be pre-treated to get the in-well approach. Alternative hydrolysis approaches such as
analytes into the liquid state before clean-up. This is a very large acid or base hydrolysis are also commonly used, and their
area that we don’t cover here, but, for example, it can include: impact on the sample prior to extraction (such as the effect of a

Urine Composition

Urea 56.1% Sodium 8%

Uric acid 1.3% Ammonia 1%

Phospholipids 0.5% Calcium 0.3%

Amino acids 6% Sulfate 4%

Creatinine 2% Chloride 14%

Others 0.2% Phosphate 3.6%

Potassium 3%

Figure 11. Components in urine, excluding water (% values can vary considerably)1.

12 Bioanalytical Sample Preparation | © Biotage 2020

 Matrix Considerations in Sample Preparation for Bioanalysis

changed pH) needs to be considered when developing sample

preparation methods.

Whole blood/serum/plasma
Challenges with these types of samples can be divided into:
» endogenous: including proteins,
phospholipids, red blood cells
» exogenous: including dosing vehicles from
therapeutic drug formulations
Lipid content can vary greatly depending on dietary differences
and timing after meals.
Viscosity variations can also cause issues, for example related
to vacuum manifolds, mentioned in the next section.
Some analytes, such as many drugs, are transported in blood
bound to proteins and must be released prior to extraction
using techniques such as SLE or SPE. Steps can include pH
adjustment to denature the protein and addition of solvent to
break the analyte – protein bond.

Oral fluid and associated collection devices

Things to consider here are if the sample is simply neat saliva
or if it is collected with an oral fluid collection device that can
introduce buffers and surfactants. These can impact on analyte
recovery, or cause matrix effects in LC-MS/MS.

Others (hair/nails/meconium/tissue)
These solid or semi-solid samples introduce another level of
matrix complexity that we will not address in detail here.
Collection of hair and nails is a non-invasive operation which
is seeing growing popularity in drugs-of-abuse (DoA) analysis
and workplace testing because sampling can be done in ’public’
(unlike with urine).
Other examples are meconium, which is used for monitoring
DoA exposure in the womb, and liver tissue which is particularly
useful in forensic postmortem cases where blood or urine may
not be available.

13
 Optimizing, Streamlining and Automating Sample Preparation

Optimizing, Streamlining and

Automating Sample Preparation

As in any method development process, the first per batch, the volume of sample to be extracted, and your
overall lab throughput. Choosing a micro-SPE plate format may
thing you should do is consider your lab’s purpose, be governed by you having very small sample volumes, or by
your goals, and the measurable objectives that your need to achieve small and concentrated elution volumes –
define achievement and good performance. thereby gaining sensitivity in the subsequent analysis.
To induce flow, the simplest manual method is to connect an
Scenarios can be very different in research, forensic and clinical SPE column to a syringe barrel and, by depressing the barrel,
environments. Ask the questions: force the liquid (solvent or sample) through the SPE column.
This is cheap and effective, but not convenient for processing
» What is the ideal output from my lab?
multiple samples.
» What is the incoming sample load, in
qualitative and quantitative terms? Vacuum manifolds are often used to process samples in parallel
For example, incoming sample quality can be high and consis- (for example 10-20 columns or 96 samples in a plate format).
tent, or low and variable. Liquids can be manually added by the operator, who also
controls the vacuum, although automated systems are also
Numbers of samples to be analyzed per day or week will steer available (see ”Automation” on page 16).
the need for automation and the use of different formats and
approaches. Vacuum manifolds (Figure 12) are low cost and easy to use but
there are challenges, such as plugged wells/columns due to
Accuracy, precision and sensitivity are all important parameters particulate materials in the samples that can result in the faster-
for analytical work, but they might be prioritized differently flowing wells/columns running dry and creating free-flow paths
depending upon the application. Normally you can’t have it all, for the vacuum to pull through.
and there will be a trade-off between simplicity, speed and cost.
A similar challenge with vacuum-induced flow is that as
less-viscous samples vacate their wells quickly, the pressure
Format and Equipment
For many sample preparation methods, there is a basic choice
between columns (or test tubes) and 96-well plates, the former
allowing larger sample volumes, the latter offering greater
opportunities for improved throughput and automation, with
lower elution volumes and, usually, smaller sample volumes.

PPT
In devices with a bottom filter, flow can be induced by positive
pressure or vacuum to remove the precipitate. Precipitate can
also be spun down by centrifugation, although the workflow for
multiple samples is difficult to automate.

LLE and SLE

LLE is a very hands-on procedure, with equipment varying
from large, traditional separation funnels, through disposable
capped tubes and micropipettes, to 96-well plates. In addition,
LLE can often be replaced by SLE, which has greater potential for
automation.

SPE
SPE is available in columns, standard 96-well plates- or micro-
SPE plate formats. Your choice of column or 96-well plate format
depends on the typical number of samples you want to process Figure 12. Vacuum manifold for manual processing of SPE columns.

14 Bioanalytical Sample Preparation | © Biotage 2020

 Optimizing, Streamlining and Automating Sample Preparation

Eliminating Steps
drop over all the wells decreases, and this can leave more- Every additional step:
viscous samples still on the plate, resulting in variable analyte
recoveries.
» adds time,
» adds complexity (increasing the probability of human
These problems can be avoided by using positive pressure errors, and requiring more training and skills), as well as
systems to process multiple samples in parallel (Figure 13). » potentially decreasing the recovery of analyte
Common formats are 96, 48 or 24 columns, depending on » potentially decreasing the precision of the method
the column size, or 96-well plate devices. Again, liquids can Lean operation principles are applicable in sample preparation,
be manually added by the operator, who also controls the just as they are when considering total lab functions, or automo-
pressure. Alternatively, fully automated systems operating with bile manufacturing!
positive pressure are available.

Figure 13. Positive pressure manifolds for 96-well plate and column processing.

15
 Optimizing, Streamlining and Automating Sample Preparation

Looking at table 1 again, we see that many sample preparation It is important to consider the whole workflow so that automa-
techniques can be steered to allow direct injection into the tion of sample preparation or even a single step within sample
analytical system, without extra steps — the exceptions being preparation, doesn’t simply lead to a bottle neck at some other
LLE and SLE. point.
Also, evaporation and reconstitution can be avoided if sample There are 2 major choices in automation of sample prep:
prep can be achieved with SPE.
» An automated sample preparation
And, of course, if applicable, D&S and filtration require fewer system can be stand-alone
steps than other sample preparation techniques, but they » Sample prep can be integrated with the
neither eliminate matrix effects nor ‘extract’ the analyte. analytical platform, so that a sample is loaded,
prepared, and analyzed within one device.
A smart example of step elimination is ‘in-well hydrolysis’
during DME or SPE, which eliminates a sample transfer step. Both approaches have their advantages.
This is achievable with the help of special hydrophobic frits
Vacuum versus positive pressure processing
that hold up the sample during hydrolysis but allow it to pass
in automated sample preparation
through when pressure is applied after hydrolysis. Hydrolysis
Flow-through sample preparation techniques such as SPE, PPT,
efficiency is not affected by performing the hydrolysis in this
SLE and filtration are often automated. A high throughput lab
way.
will prefer to do parallel processing automatically.
In SPE, the use of a water-wettable polymer-based media
The choice between a positive pressure or vacuum SPE system
eliminates a conditioning step that is required with silica-based
is particularly important for automated processing. With 96-well
media (compare Figure 14 with Figure 9 on page 9).
plates and for micro-SPE a blocked well or a well with remaining
sample may not be detected. Vacuum manifolds for columns
Automation can have the option of individual column control, so that you
Automation will reduce the risk for human errors and allow a can ‘switch off’ the vacuum for columns that have run dry, BUT
higher throughput in your lab, but it will require investment in this requires constant monitoring and is not conducive to high
equipment. However, running costs per analysis should be less throughput, and can’t be easily automated.
after automation and highly trained staff can be used for more Positive-pressure based automation systems eliminate these
Load Wash Elute
demanding tasks than repeated manual operations. issues.

Figure 14. Using a wettable polymer-based SPE adsorbent eliminates the conditioning and equilibration steps that are required with silica media.

16 Bioanalytical Sample Preparation | © Biotage 2020

 Do You Need Lower Detection Limits?

Do You Need Lower Detection Limits?

Sample prep helps you clean-up biological samples Matrix scavenging methods and LLE/SLE usually dilute the
analyte and, if additional sensitivity is needed, you must
before analysis, but it doesn’t automatically improve evaporate and reconstitute to achieve high concentrations. In
sensitivity. Sometimes, only small amounts of contrast, SPE inherently concentrates the analyte.
sample are available. High-sensitivity analysis by Although evaporation followed by reconstitution in a smaller
LC-MS/MS demands the injection of small volumes volume of solvent is a standard approach, it has several
of sample extract. High concentrations of the analyte challenges.

that is sometimes in short supply are needed to

achieve low detection limits. So, the lower the extract Evaporation Headaches
The evaporation step can take time and increases the
volume the more concentrated the extract, and the
complexity of sample preparation. Some analytes are also prone
lower the detection limit that can be achieved. to losses during evaporation, which can reduce sensitivity, and
make it difficult to achieve the required detection limits. This is
Table 3 indicates sample prep techniques that allow convenient particularly problematic for:
direct injection into an LC-MS/MS system, the ones that dilute
the analyte and need to be combined with evaporation and
» ‘sticky’ peptides, and other hydrophobic molecules, which
can bind irreversibly to the walls of the evaporation vial/
reconstitution, and the ones that offer potential concentration.
plate, or be difficult to solubilize after evaporation.
The table shows where you might lose or gain sensitivity.
» highly volatile analytes such as amphetamines.
» analytes that are sensitive to thermal degradation.

Table 3. Sample prep characteristics that impact detection limits and workflow streamlining opportunities.

Evaporation +
Technique Inherent concentration? Direct injection possible?
reconstitution?

D&S No, sample is diluted Yes N/A

Filtration No Yes N/A

Yes, but dilution with mobile phase may be necessary

PPT No, sample is diluted Yes, for low detection limits
for compatibility with LC-MS/MS conditions

Yes, but dilution with mobile phase may be necessary

PLD No, sample is diluted Yes, for low detection limits
for compatibility with LC-MS/MS conditions

Yes, but dilution with mobile phase may be necessary

DME No, sample is diluted Yes, for low detection limits
for compatibility with LC-MS/MS conditions

No, extraction solvent is incompatible with reversed

LLE & SLE No, sample is usually diluted Yes. Essential
phase LC-MS/MS

Yes, but dilution with mobile phase may be necessary

SPE Usually Yes, for low detection limits
for compatibility with LC-MS/MS conditions

Yes, but dilution with mobile phase may be necessary

Micro-SPE Yes No
for compatibility with LC-MS/MS conditions

17
 Do You Need Lower Detection Limits?

Using Micro-SPE to Achieve

Low Detection Limits
Micro-SPE devices are essentially miniature versions of the
traditional 96-well SPE plate that contain tiny amounts of
sorbent. However, this is not enough to assure high concentra-
tions of eluted analyte with small samples. This is achieved by
eliminating dead volumes and using relatively long and narrow
columns of SPE stationary phase, rather than short wide ones
(Figure 15).
Micro-SPE can help avoid evaporation and reconstitution, SPE Bed Micro-SPE Bed
saving time and offering high recovery of analytes in small Dimensions Dimensions
elution volumes — ready for high sensitivity LC-MS/MS
Figure 15. Micro-SPE bed dimensions are taller and narrower than
(Figure 16).
standard SPE.

Standard SPE 8888

8860
8888
8860

1:1 dilution

3 ng analyte in 300 μL 3 ng analyte in Evaporate and 3 ng analyte in 10 µL injection =

300 µL sample matrix elution 300 µL extract re-con in 30 µL 30 µL sample 1000 pg on column

Typical SPE method – 10 x concentration (WITH evaporation step)

Micro-SPE

1:1 dilution

3 ng analyte in 30 μL 3 ng analyte in
10 µL injection =
300 µL sample matrix elution 30 µL extract 1000 pg on column

Micro-SPE method – 10 x concentration (NO evaporation step)

biomark113.2

Figure 16. Low elution volumes in micro-SPE can help avoid evaporation steps

18 Bioanalytical Sample Preparation | © Biotage 2020

 Sample Preparation for Bioanalysis: Conclusions

Sample Preparation for Bioanalysis: Conclusions

Sample preparation offers significant benefits if you

are using sophisticated analytical techniques such as
LC-MS/MS and GC-MS but finding the right solution to
meet your needs can be complex. This brief overview
hopefully illustrates the range of challenges and the
choices available. You should speak with your peers
and talk to manufacturers of sample preparation
consumables and systems, who often have a deep
understanding of the issues. Arrange to see various
options in action, especially if you are thinking
of high throughput situations and automation.
Understand how equipment will operate in practice
and note the difficulties as well as the benefits. In
the end, your lab and your colleagues will benefit
from a good choice of this ‘necessary inconvenience’.

References
1. http://www.chromedia.org/chromedia?waxtrapp=wptlvLsHi
emBpdmBlIEcCKDnC

19
 Title Truncated if Neccessary... | Page 20

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