This document outlines the critical role of sample preparation in metabolite identification for bioanalytical workflows, emphasizing techniques like liquid-liquid extraction, protein precipitation, and solid phase extraction. It details various methods and protocols for sample collection and preparation aimed at ensuring accurate metabolomics analysis, including in vivo sampling techniques and modern extraction approaches. Additionally, it highlights the importance of choosing appropriate sample preparation methods to enhance metabolite coverage and maintain biological relevance in the data obtained.

1. SAMPLE PREPARATION AND PROTOCOLS IN
METABOLITE IDENTIFICATION
PRESENTED BY
DURGADEVI.G
1ST M.PHARM(2ND SEM)
DEPT. OF PHARMACEUTICAL ANALYSIS
PSG COLLEGE OF PHARMACY.

2. SAMPLE PREPARATION
Sample preparation is a primary
step of any bioanalytical workflow,
especially in metabolomics analysis
where maximum information has
to be obtained without spoiling
the analytical instrument.

3. Sample preparation includes all procedures and operations applied
to the sample prior to its analysis.
This step is essential when MS-based techniques are used.
It is implemented to
(i) stabilize the sample,
(ii) remove the sample contaminants,
(iii) enable sample enrichment,
(iv) improve the analysis selectivity,
(v) avoid fouling of the mass spectrometer.
Sample preparation approaches can be divided into two groups,
namely sample pretreatment and sample extraction methods.

4. CHOICE OF SAMPLE PREPARATION
The choice of sample-preparation method is extremely important in
metabolomic studies because it affects both the observed metabolite
content and biological interpretation of the data.
An ideal sample-preparation method for global metabolomics
should
(i) be as non-selective as possible to ensure adequate depth of
metabolite coverage;
(ii) be simple and fast to prevent metabolite loss and/or degradation
during the preparation procedure and enable high-throughput;
(iii) be reproducible; and
(iv) incorporate a metabolism-quenching step to represent true
metabolome composition at the time of sampling.

5. SAMPLE PREPARATION
Sample collection
Quenching by liquid nitrogen or cold methanol
(stops metabolism)
Extraction of intracellular metabolites
Concentration
(evaporation under vacuum, lyophilization, SPE)

6. SAMPLE PREPARATION METHODS
Dilute-and-Shoot:
The most commonly employed method for global metabolomics
of urine is the “dilute-and shoot” strategy.
Solvent Precipitation:
Preferred Method for Plasma, Serum, and Other Biofluids.
The most commonly employed method for global metabolomics
of blood and cerebrospinal fluid (CSF) is protein precipitation
with organic solvent.

7. LIQUID LIQUID EXTRACTION (LLE)
Liquid-liquid extraction (LLE) is a very common sample preparation method
used primarily in targeted metabolomics analysis.
LLE was also successfully employed in a recent study of CSF after solvent
precipitation, whereby the samples were separated into lipid and polar phases
using the combination of water and ethanol/dichloromethane followed by GC-
MS and LC-MS analysis.
Delipidation of serum samples before other treatment was also tried by
Liquid–Liquid Extraction (LLE) with a non-polar solvent.
1 mL of serum sample was vortex-mixed with 500 µL of n-hexane, for 1 min.
Centrifugation followed at 6000 g for 5 min and the upper layer was
discarded.
Then 100 µL of the lower aqueous layer were vortex-mixed with 300 µL of
ACN for one minute and finally centrifuged again at 7000 g, 4 ◦C for 10 min .
Five µL of the clear supernatant were injected into the system.
The same procedure was followed for spiking serum samples in order to
construct a five point calibration curve for standard addition approach.

8. PROTEIN PRECIPITATION
Protein precipitation (PP) is simple and straightforward
method widely used in bioanalysis of plasma samples.
It is accomplished by using organic solvent (typically
acetonitrile or methanol) or an acid (typically perchloric or
trichloroacetic acid).
Addition of 300µl of ACN in 100µl of upper phase and
centrifuge.
Addition of 200µl sample addition of 500 ACN-MEOH-H2O
and centrifuge.

9. DISPERSIVE SOLID PHASE
EXTRACTION
Dispersive solid phase extraction (DSPE) has been used as a pretreatment
technique for the analysis of several compounds. This technique is based
on the dispersion of a solid sorbent in liquid samples in the extraction
isolation and clean-up of different analytes from complex matrices.
A dispersive SPE (d-SPE) protocol was applied with a QuEChERS(quick
easy cheap effective rugged safe ) dispersive Kit.
The approach includes two steps: (1) a buffering and initial extraction step
with acetonitrile where protein precipitation also takes place in the case of
serum and (2) a second clean-up step with MgSO4 and a sorbent to remove
water and undesired co-extracted lipids, respectively.
From the 2 mL tubes containing 50 mg PSA and 150 mg MgSO4, 10 mg
were transferred to a 1.5 mL vial where 100 µL of serum were added and
mixed with 300 µL ACN, vortexed for 1 min and finally centrifuged at
7000 g and 4◦C for 10 min

10. HYBRID SPE
Solid Phase Extraction with a novel Zirconia coated silica based material
(HybridSPE®-Phospholipid Technology) for the removal of phospholipids
and proteins was alternatively applied.
Hybrid SPE Phospholipid cartridges were used under various conditions.
Based on manufacturer guidelines three different modifiers can be used to
aid protein precipitation and hinder the retention of analytes for the Zr-Si
sorbent together with the phospholipids: formic acid (FA), citric acid (CA)
and ammonium formate (AmF).
As the set of analytes comprises both acidic, basic and zwitter ionic
compounds, a combination of modifiers was expected to be required. Initial
trials used the minimum sample volume (100 µL) and protein precipitation
on the SPE cartridge with acetonitrile (ACN) acidified with (a) 0.5% and
1% formic acid (FA); (b) 0.5% and 1% citric acid (CA) or (c) by buffering
with 1% ammonium formate (AmF) in methanol (MeOH). It was found
that recoveries of the target metabolites on HybridSPE cartridges were in
general low in comparison to conventional PPT

11. IN VIVO SAMPLING
In vivo sampling and sample preparation are particularly
attractive for global metabolomics, because the process of
sampling and removing the sample from its biological is likely
to disturb the metabolite profile by exposure to oxygen,
solvents, and pH changes, and can activate a variety of
biological processes.
Two techniques are:
1. Micro dialysis
2.Solid phase micro extraction

12. 1.Micro dialysis:
 Micro dialysis is the recommended technique for sampling low-molecular-
weight metabolites directly in vivo from both blood and tissue samples. Its
utility has been established for tissue metabolomics, without the need for
biopsy, in combination with NMR , GC–MS , and electrochemical
detection .
2.Solid phase micro extraction:
 In vivo solid-phase micro extraction (SPME) as recently shown for direct
sampling of the circulating mouse blood metabolome in awake animals .
This method is directly compatible with LC–MS injection, and is suitable
for hydrophilic and hydrophobic metabolites, thus addressing some of the
limitations of micro dialysis in the context of untargeted studies. The use
and detailed theory of in vivo SPME in combination with GC–MS and
LC–MS for global metabolomics has been discussed

13. DRIED BLOOD SPOT
One emerging technique in the field of bioanalysis and drug discovery is
the dried bloodspot (DBS) analysis, which is also successfully used for
neonatal screening of inborn errors of metabolism using targeted
metabolomics.
The dried blood spot (DBS) sampling that was once used to screen inborn
errors of metabolism has emerged as a new method in metabolomics study.
The major steps of DBS metabolomics were listed in Figure.
Briefly, the blood sample is directly soaked on a paper, and then measured
by modern analytical systems after extraction of the punched spot. Several
advantages of DBS technique such as simple, inexpensive, minimal
volume requirements and ease of transport, make it being one of the most
appropriate blood sampling techniques for large population analysis.
A small drop of whole blood or other bio fluid is placed on filter paper and
allowed to air-dry for several hours.
This spot is subsequently extracted in a solvent such as methanol prior to
analysis.

14. LASER MICRO DISSECTION
Laser microdissection (LMD) is a method for isolating specific cells of interest
from microscopic regions of tissue/cells/organisms.
It has been widely used in genomics, transcriptomics and proteomics studies.
A variety of samples can be performed on LMD, such as blood smears,
cytologic preparations, cell cultures and tissue.
LMD in metabolomics involves sample collecting, fixation, embedding ,
sectioning and harvesting. Due to the nature of metabolites, LMD in
metabolomics is different from a typical protocol.
Specifically, the organic solvent used in the fixation should be avoided in
metabolomics analysis, because metabolites are easily dissolved in these
chemicals and lost in this process.
Cold phosphate buffered saline (PBS) and water can be used for fixation step
in LMD metabolomics.
In addition, freezing medium embedding is recommended to replace paraffin
embedding, because it can decrease delocalization and loss of metabolites.
Finally, the exact amount of dissected samples is calculated by weighting the
collected cap for downstream analysis

15. MICROWAVE-ASSISTED EXTRACTION
When design MAE experiment, several parameters were considered,
including solvent, application time, microwave-power, sample
surface area and temperature.
In general, water is seen as a good substitution of organic solvents
for MAE.
Application time and microwave-power parameters were optimized
built on the properties and composition of samples.
Compared with the customary method, MAE can reduce work time
and improve efficiency 2-3 times.
Currently, MAE has mainly evolved in plant and food metabolomics
as a simple and rapid sample preparation technique.

16. ULTRASOUND-ASSISTED EXTRACTION
Ultrasound-assisted extraction (UAE) is another useful extract technique in
metabolomics study.
In UAE, ultrasonic energy enhances the extraction efficiency by creating
cavitation with high pressures and high temperatures, and then accelerates
the extraction of analytes from matrices.
Stirrer and ultrasound bath is basal apparatus in a UAE device.
Comparing with MAE, a wide range of solvents can be employed in UAE,
such as methanol, ethanol, isopropyl alcohol and their mixture.
UAE can decrease the extraction time (1-2 times), and thus save energy
and costs.
The potential of UAE in metabolomics analysis has been demonstrated in
a few studies, such as imazamox in leaves of wheat plants , boldine in
Boldo Leaves and phenolic compounds in peaches and pumpkins
However, ultrasonic energy should be evaluated previous to UAE, because
high ultrasonic energy and the resulting elevated temperature may cause
the degradation of metabolite

17. ENZYME-ASSISTED EXTRACTION
Enzymes are able to degrade or disrupt cell walls and membranes, thus
increasing extract efficiency.
The application of enzymes in extraction, named Enzyme-assisted
extraction (EAE), can increase the effect of solvent extraction and also
decrease the amount of solvent for microbe extract.
The overall process of EAE was summarized in Figure . In brief, sample
was mixture with buffer or water, and hydrolysis by the enzyme.
The supernatant was sucked to concentrate and analyze after centrifugation
and filtration. EAE has been recently employed in metabolomics study
recently.
For instance, EAE was utilized to extract toxic fungal metabolites from
milk, cheese and sour cream samples.
In some ways, EAE exhibited higher extract effect than UAE and MAE,
such as extraction of colorants and lycopene from plant.
However, it should be noted that EAE introduce metabolite artifacts in
some cases as the used enzyme may induce side reaction.

18. IN-VIVO METABOLITE
IDENTIFICATION
Metabolite identification (Met ID) is important during the early stages of
drug discovery and development, as the metabolic products may be
pharmacologically active or toxic in nature. Liquid chromatography-mass
spectrometry (LC-MS) has a towering role in metabolism research.
Liquid chromatography(LC)-high resolution mass spectrometry (HRMS)
techniques proved to be well suited for the identification of predicted and
unexpected drug metabolites in complex biological matrices.
To efficiently discriminate between drug-related and endogenous matrix
compounds, however, sophisticated post acquisition data mining tools,
such as control comparison techniques are needed. For preclinical
absorption, distribution, metabolism and excretion (ADME) studies that
usually lack a placebo-dosed control group, the question arises how high-
quality control data can be yielded using only a minimum number of
control animals.

19. 8) Repeat steps 1–5 for all samples. Lastly, use the same procedure for the QC
sample. For the extraction blank, perform step 3 (cold ACN without sample)
and use the same procedure thereon.
9) Filter the precipitated samples by centrifuging the plate for 5 min at 700 g at
4 C.
10) Remove the filter plate and seal the 96-well plate tightly with the 96-well
cap mat to avoid sample evaporation.
11) Analyze the samples immediately or store the plate at +4 C for a maximum
of 1 day or at 20 C until analysis.

20. PROTOCOL FOR LC-MS ANALYSIS
Protocol 1: Plasma/Serum Samples
1) Thaw plasma/serum samples in ice water and keep them on wet ice
during all the waiting periods.
2) Place the 96-well plate on wet ice for sample preparation and set the
filter plate on it.
3) Add 400 L of cold ACN to the filter plate well.
4) Vortex a plasma/serum sample 10 s at the maximum speed.
5) Add 100 L of plasma/serum sample to the same well as ACN.
6) To prepare the pooled quality control (QC) samples, collect 10 L
aliquots of each sample and add them to the same clean
microcentrifuge tube and finally, mix properly.
7) Mix ACN and sample by pipetting four times. Use wide orifice Finn
Pipette tips to avoid tip clogging.

21. Protocol 2: Tissue Samples
12) Weigh a maximum of 300 mg frozen tissue into 2-mL OMNI microtube
with beads. Keep the samples on dry ice.
13) Add ice cold 80% methanol in a ratio of 500 L solvent per 100 mg tissue
and keep the tubes on wet ice. Include an extraction blank with solvent only.
14) Optional step: In the case of metabolite-dense sample material (e.g.,
plants), it might be necessary to use a more diluted solvent/sample ratio to
avoid analytical problems, such as saturation of the detector or overloading of
the column.
15) Homogenize samples with a Bead Ruptor 24 Elite homogenizer. For soft
tissues, perform one homogenization cycle at the speed 6 m/s at +/- 2 C for 30
s.

22. 16) Optional step: In case a homogenizer instrument is not available, manual
tissue disruption can be performed using mortar and pestle with liquid
nitrogen.
17) Extract the homogenized samples in a shaker for 5 min at RT.
18) Centrifuge samples for 10 min at 20,000 g at +4 C.
19) Collect the supernatants on a 96-well filter plate and centrifuge for 5 min
at 700 g at 4 C.
20) Optional step: Filter the samples using solvent resistant syringes and
PTFE filters into the HPLC vials.
21) Take aliquots (5–25 L) of filtered samples and combine into one vial to be
used as QC sample in the analysis.
22) Analyze the samples immediately or store the plate at +4 C maximum of 1
day at 20 C until analysis.

23. PROTOCOL FOR HR-MS BASED
APPROACH:
A 10 µM solution of each compound is prepared in DMSO.
Test compound is incubated with pooled liver microsomes (1
mg/mL) (or other samples, like S9, hepatocyte, recombinant
enzymes) and NADPH-generating system in phosphate buffer
(pH 7.4) for a period of 0 or 90 minutes at 37°C.
Microsomes-compound matrix is quenched by addition of
acetonitrile.
After centrifugation, supernatants are transferred to new tubes,
and analyzed by high-resolution mass spectrometry.
Control samples are quenched at time zero.

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