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Validation of Free Flow Electrophoresis as a novel plasma and serum
processing and fractionation method in biobanking
Gwenaelle Gaillard1, Jean-Pierre Trezzi2, Fotini Betsou*2
1Biobanque de Picardie, avenue René Laennec, 80480 Saleux, France
2Integrated Biobank of Luxembourg, 6 rue Ernest Barble, L1210, Luxembourg
Short title: Free Flow Electrophoresis validation in biobanking
Keywords: proteomics, free flow electrophoresis, fractionation, validation, plasma, biobank
*Integrated Biobank of Luxembourg, 6 rue Ernest Barble, L1210 Luxembourg. Tel 003532744641, Fax
0035227446464, [email protected]
Abstract
Free Flow Electrophoresis (FFE) is a fractionation method, based on isoelectric focusing (IEF). We
validate the reproducibility of the method and show that it can be applied by biobanks in order to
efficiently and reproducibly fractionate fluid biospecimens and facilitate downstream proteomic
applications. We also propose a simple method allowing to assess the reproducibility of each FFE run.
Introduction
Despite important advances in the use of genomics and transcriptomics for the identification of
clinically relevant biomarkers, circulating proteins or peptides remain the most sought-after
candidate biomarkers because of ease of blood sampling and biological meaningfulness. Their initial
identification in biological fluids requires proteomic analysis, usually performed on well annotated
fluid samples (e.g., serum, plasma) from biobanks.
One of the most important technical difficulties in this approach is linked to the dynamic range of
plasma proteins which is of the order of magnitude of 1010 (1). The most abundant protein in human
plasma is serum albumin which is present at 40-50 mg/ml while some cytokines and tissue leakage
proteins are present at levels approximating 10 pg/ml. To overcome this problem, two usual
strategies are followed: depletion of high-abundance proteins and/or fractionation. Depletion of
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albumin and IgG may increase sensitivity for detection of remaining proteins, but many proteins may
get irreversibly and non-specifically bound during the process. Previous fractionation of the biological
fluid is an alternative or can be combined to subsequent abundant-protein depletion. One of the
least explored sample fractionation methods is FFE.
Free Flow Electrophoresis, first described by Hannig (2, 3), is a prefractionation method enabling the
resolution and identification of low abundant proteins and the reduction of protein mixture
complexity. The method is performed with fractionation equipment that continuously streams a
sample into a carrier ampholine solution flowing between two plates, as a thin laminar film (0.3-
1mm). An electrical field is applied perpendicular to the direction of flow and proteins and peptides
are separated by IEF according to their pI values and >70 fractions are collected in a microplate. Each
fraction is separated by ~0.02-0.1 pH units depending on the pH gradient created. Using this method,
proteins with extreme physical-chemical properties can be detected. Free Flow Electrophoresis has
been used for pre-fractionation of samples because of two main advantages: improved sample
recovery due to absence of gel media and high sample loading capacity. Although FFE is not
automatable and samples can only be processed one by one, the typical turn-around time for one
sample fractionation is only 10-15 min. It has previously been shown that FFE is fit for purpose for
different downstream proteomic analyses, including both targeted ELISA (Enzyme-Linked
Immunosorbent Assay) and high throughput proteomic 2D-electrophoresis or mass spectrometry (4,
5, 6). However, in order for biobanks to be able to use FFE as a routine fluid biospecimen processing /
fractionation method, it is important to confirm and be able to assess the reproducibility of the
method in terms of pH gradient and consequently, protein contents in each fraction or pool of
fractions obtained.
Reproducibility of 2D FFE-IEF/RP-HPLC (Reversed-Phase High-Performance Liquid Chromatography)
system has previously been studied (7). In that study, reproducibility was assessed from the
downstream analysis point of view : RP-HPLC chromatograms, where Standard Deviation (SD) of
retention times and of microplate well numbers were calculated across three replicates for nine
peaks located between wells 13 and 87. The SD for uncorrected FFE well numbers was 0.83 (when
the FFE well numbers were adjusted by pH, the SD was 0.62). This corresponds to 0.05pH units within
FFE pools. However, this study was performed with standard cellular protein preparations. The
objectives of our study were to assess the reproducibility of FFE in human plasma samples, and to
identify internal quality control markers that can be used to define acceptance criteria for FFE
fractionation reproducibility. Therefore, we validated the reproducibility of FFE fractionation of
human serum and plasma, by showing that the position of proteins in a given range in a 96-well plate
can be reliably predicted, enabling post-fractionation protein analysis.
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Materials and Methods
FFE
FFE was applied as previously described (8, 9, 10).
Preparation of the FFE buffers
Deionised and overnight degassed water was used. For the Stripe test, which ensures homogeneity
of the applied electrical current, a specific dye (SPADNS; 2-(P-sulfophenylazo)-1,8-dihydroxy-3,6-
naphthalene disulfate) was diluted to 0.01% in distilled and degassed water. The three separation
buffers, the two stabilisation buffers and the electrode buffers were prepared according to the
manufacturers’ instructions for the QC2 test (BD protocol, IEF-GH 3-10, native). The 6M urea (Serva,
ref 24524) separation buffer was also prepared according to manufacturers’ instructions (BD
protocol, IEF 3-10, 6M urea, denaturating conditions). The separation buffer 1 was composed of
30,3g IEF Buffer 1, 69,7g distilled water and 54g urea, the separation buffer 2 contained 100g IEF
buffer 2, 100g distilled water and 108g urea and the separation buffer 3 contained 37g IEF buffer 3,
63g distilled water and 54g urea. The three IEF buffers, the SPADNS and the pI mix were included in
the BD kit (ref 441118). The pH and conductivities were measured after each buffer preparation. The
separation buffers contained glycerol, urea, hydroxyl prolyl methyl cellulose (HPMC), H2SO4, Prolyte1,
Prolyte 2, Prolyte 3, NaOH. The counterflow buffer contained glycerol and urea. The anodic and
cathodic circuit electrolytes were H2SO4 and NaOH respectively.
Plasma and serum samples
Plasma samples and serum samples from BD Vacutainer EDTA and SST collected whole blood
specimens respectively, were prepared from two different healthy donors. The blood was
centrifuged, one hour after collection, at 2000g for 10 min at room temperature, and 0.5 ml of serum
or plasma was aliquoted in 1.5ml microtubes and stored at -80°C. One aliquot for each separation
was thawed on the separation day and diluted 1 to 4 in Separation buffer 2 for the IEF 3-10, 6M urea,
denaturating protocol. Final protein concentration, measured by Biorad Bradford assay, was
approximately 15 mg/ml.
FFE performance test
The FFE was set up on each of five different separation days according to the manufacturer’s
instructions. The volume of the chamber, the media and sample pumps flow rates were measured. A
running Stripe test (QC1) and a running performance test with separation media (QC2, with pI mix)
were run. The absorbance of the microplates was then measured at 405nm to locate the SPADNS dye
and the pI markers, in addition to their visual inspection. Residence time in the separation chamber
was ~30min. Fractions of approximately 200 l were collected in 96-well polypropylene plates. BD
polypropylene 96-well microplates and BD polypropylene covers were used in order to avoid protein
adsorption.
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Validation of the method reproducibility: Five FFE separations in 6M urea, pH3-10
Five plasma aliquots from the same sample (plasma A) were used for the five separations to test the
technical reproducibility in denaturing conditions. One aliquot of a second sample (plasma B) was
used to test the biological reproducibility. The five separations were performed on five different days
with all buffers freshly prepared. The microplates containing the FFE fractions were stored at -80°C
for further analysis. Two serum aliquots were also used on two different days in the same separation
conditions to compare plasma to serum fractionation profiles. One plasma aliquot was run in 8M
urea denaturing conditions to test for robustness of the method to composition of the separation
buffer.
Electrophoretic analysis of FFE fractions
Serum and plasma FFE microplate contents were electrophoretically analysed with the Agilent 2100
Bioanalyzer in order to detect marker peaks for assessment of FFE fractionation reproducibility. The
Agilent Protein 230 Kit (in denaturating conditions) was used for the electrophoresis of the fractions
according to the manufacturer’s instructions. Preliminary analyses of microplate fractions showed
that the most abundant protein, presumably corresponding to albumin, was detected in at least two
fractions in the fraction range 4F-5G. Therefore, for each of the five separations, the microplate
fractions 4F to 5G were analysed on the same chip. Collected electrophoretic data revealed six
markers, each of which corresponded to a specific molecular weight and isoelectric point. For each of
these protein markers, detected by Agilent electrophoresis in the fractions 4F to 5G, data including
the molecular weight in kDa, the relative concentrations in ng/µl and the percentage of total protein
were analyzed. The total relative concentrations of each fraction were also measured. Two different
calculations were made, with or without alignment to the fraction with the highest protein
concentration (presumably albumin).
Identification of internal QC protein markers
FFE separations of two plasma and two serum 96-well microplates were used for pooling and
Western blotting (Wb) analysis. For each plate, three pool series were prepared: Pool 1 (wells 4F, 4G,
4H, 5A), pool 2 (wells 5B, 5C, 5D 5E), pool 3 (wells 5D, 5E, 5F, 5G). Each pool was made up of identical
volumes of fractions from each individual well and stored at -20°C. Positive controls were prepared
of plasma and serum extracted from fresh blood tubes after centrifugation at 2000g for 10 min at
room temperature and supernatant dilution with PBS 1X (1/500 and 1/100 dilution for serum and
plasma respectively).
SDS-PAGE
Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) was performed using the
PhastSystemTM (GE Healthcare). Pooled samples and positive controls were diluted 1:5 in reducing
SDS-PAGE sample buffer (5 ml glycerol, 0.5 ml 2-mercaptoethanol, 1 g SDS, 0.38 g Tris/HCl, 0.25 mg
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Bromophenol Blue, 4.5 ml H2O, pH6.8). Samples were heated at 95°C for 2 min before
electrophoresis. One μl of each pooled sample was separated on 8-25% gradient SDS polyacrylamide
gels. Molecular weight markers used were the Pierce Chemiluminescent Blue Prestained Peroxidase-
labeled Protein Molecular Weight Marker. SDS-PAGE settings were 15°C gel bed temperature, 75 Vh
at 250V, 10 mA, 3 W.
Western blotting
Western blotting (Wb) was performed using the BioRad Trans-Blot SD Semi-Dry Transfer Cell.
Western Blot setup was 20 mA (constant), 20V for 25 minutes. Transfer buffer contained 3.94 g
Tris/HCl, 14.4 g glycine, 200 mL methanol per L, pH7.5. After electrotransfer, the Hybond ECL
nitrocellulose membrane was incubated with ECL (chemiluminescence) Blocking Agent (GE
Healthcare) for 1h. Primary antibodies used and corresponding dilutions in Blocking Reagent were
the following: anti-serum albumin, ABCAM, ab10241 (1/1000), anti-alpha-1-antitrypsin, ABCAM,
ab49088 (1/500), anti-ceruloplasmin, ABCAM, ab48614 (1/250), anti-apolipoprotein A-I, Cell
Signaling Technology, 3350S (1/500). Membranes were incubated overnight at 18-22 °C room
temperature (RT), three 10 minutes washing steps were made in TBS1x/Tween 0.05%. Secondary
antibodies used were anti-mouse IgG, Horseradish peroxidase-linked, NA931 (1/5000), and anti-
rabbit IgG, Horseradish peroxidase-linked, NA934 (1/25000). These were diluted in TBS1x/Tween
0.05% and incubated for 1h at RT, followed by three 10 minutes washing steps. Membranes were
finally incubated in detection reagent (ECL plus Western blotting detection System) for 5 minutes and
detection was performed using the ImageQuantTM LAS 4000 (GE Healthcare).
Results
FFE performance tests
The QC1 results for each separation showed three distinct peaks of approximately the same width,
14 to 17 wells, which correspond to successful Stripe tests according to the manufacturer’s guide
(Figure 1, Figure 2). The QC2 results also showed successful results, with seven distinct peaks
corresponding to markers of specific pI (data not shown). The gradient indicated by the distribution
of the pI markers of the QC2 tests, was approximately pH 5 for fractions 4F to 5G, which were
analysed with the Agilent system. The pH of all FFE buffers was stable across different preparations
and separation days with separation buffers 1, 2 and 3 having pH 4, 7 and 9 respectively (Figure 3).
Electrophoretic profiles of the FFE fractions
Total initial plasma protein concentration was approximately 60 to 80 g/L. Comparison between total
protein concentration across fractions 3A to 6G from plasma separated in 6M urea and 8M urea
separation buffer showed similar patterns (Figure 4). Bioanalyzer data from plasma and serum
separated in 6M urea buffer revealed six protein markers separated in three consecutive fraction
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pools (Figure 5). Pool 1 (fractions 4F to 5A) showed a high percentage (28 %) of a 23 kDa protein and
a lower percentage (8 %) of a 154 kDa protein. Mean measured protein concentrations, based on
comparison of protein peak areas with kit standards, were 18.2 and 5.3 ng/µl respectively (Figure 6A,
6F). Pool 2 (fractions 5B to 5E) analysis revealed a very high concentration (84 %) of a 64 kDa protein
and a very low concentration (1 %) of a 119 kDa protein. The respective concentrations were 569.3
and 6.5 ng/µl (Figure 6C, 6E). Pool 3 (fractions 5D to 5G) showed peaks corresponding to a 58 kDa (15
%) and a 93 kDa (12 %) proteins with respective concentrations of 12.5 and 16.9 ng/µl (Figure 6B,
6D).
Therefore, six candidate internal fractionation quality control protein markers were identified at 23,
58, 64, 93, 119, 154kD. Figure 7 shows the concentrations and percentages of total protein in each of
the three consecutive fraction pools from either plasma or serum. Results are shown in microwells
non-adjusted by pH (and consequently by highest protein concentration fraction), because this
approach was more relevant to validation purposes. When microwells were adjusted by pH, the
uncertainty was lower (results not shown). ExPaSy database searches, limited to the Homo sapiens
plasma protein map, and corresponding to each molecular weight, as detected by Agilent Bioanalyzer
electrophoresis, and corresponding pI ranges, as detected by the FFE separation, showed one to
seven possible protein matches, corresponding to each molecular weight. For each molecular weight,
we selected the protein corresponding to the highest concentration in plasma, as being the most
probable match. These selected protein markers were apolipoprotein A-I (23 kDa, pI~5, expected
concentration in plasma 900-2100 mg/L), alpha-1-antitrypsin (58 kDa, pI~4.7, expected concentration
on plasma 1900-3500 mg/L), serum albumin (67 kDa, pI~5.8, expected concentration in plasma
35000-55000 mg/L), secretory immunoglobulin chain alpha (93 kDa, pI~5.3, expected concentration
in plasma 900-4500 mg/L), ceruloplasmin (119kDa and 126 kDa, pI~5.1, expected concentration in
plasma 150-600 mg/L).
Identification of FFE internal quality control markers
Western Blot results (Figure 8) confirmed the initial hypothesis on the identity of the potential FFE
internal quality control markers except secretory immunoglobulin chain alpha. Albumin was well
separated, showing bands in pool 2 and 3, in both plasma and serum samples. These pools have two
fractions in common. Pool 3 contained monomeric alpha-1 antitrypsin. Higher molecular weight
alpha-1 antitrypsin bands may be due to serine proteinases binding. A free alpha-1 antitrypsin
gradient was observed comparing the 3 pools for both plasma and serum samples. Pool 1 contained
most self-aggregated alpha-1 antitrypsin whereas pool 2 and especially pool 3 contained less self-
aggregated alpha-1 antitrypsin. Pool 3 showed very efficiently separated monomeric alpha-1
antitrypsin. Pool 1 contained free, monomeric apolipoprotein A-I. At low concentrations,
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apolipoprotein A-I can be found in a monomeric state whereas at higher concentrations it tends to
aggregate, giving rise to higher molecular weight complexes (11). Pool 1 contains the most free
apolipoprotein whereas pools 2 and 3 show minor apolipoprotein A-I detection in either plasma or
serum samples. Ceruloplasmin was mainly detected in two forms: abundant glycosylated (154 kDa)
and low-concentration non-glycosylated (119 kDa) form. It was detected in higher concentration in
pool 1 (154 kDa) and lower concentration in pool 2 (119 kDa).
Based on the above results, a quality control assay for serum/plasma FFE fractionation
reproducibility can thus be based on Western blotting detection of apolipoprotein A-I and/or
ceruloplasmin in microwell pool 4F-5A, albumin in microwell pool 5B-5E and alpha-1 antitrypsin in
pool 5D-5G.
Discussion
FFE is matrix-free electrophoresis; the molecules are separated according to their charge and
electrophoretic mobility in a continuous laminar flow of buffer solutions in an electric field. The
laminar flow is collected in 96 capillaries at the end of the separation chamber and allows continuous
fractionation in collection plates.
Microwell fractions were analyzed based on our hypothesis that the fractions 4F to 5G can be
grouped into three pools, each containing two of the six reproducible markers indicated by Agilent
Bioanalyzer (Figure 5). Western Blot results confirmed our hypothesis.
Variation in the molecular weights of the markers may be attributed to different post-translational
modifications and/or different pre-processed status of the same protein.
All of the proposed internal quality control markers were reproducibly detected in their
corresponding fraction pools, with the exception of the 58 and 93 kDa markers which were absent in
the 20090805 microplate. This might be due to a relatively higher flow rate of the media pump on
the day of this fractionation (Figure 9).
Whereas one single ~60kDa form was detected for albumin, and found predominantly in pool 2,
different MW forms than the expected ones were observed for the other proteins. Protein pre-
processed forms may explain these different molecular weight (MW) forms observed on Western
blots.
Apolipoprotein A-I may aggregate with other lipid components of HDL (11, 12). Pool 1 contained the
expected, lower MW apolipoprotein A-I in higher concentrations than pool 2 and 3. This might be
due to free apolipoprotein A-I being eluted into pool 1 wells whereas lipid-aggregated apoA-I is
eluted into other pools. This finding proves that plasma and serum fractionation by FFE is efficient
and could, for example, be used for apolipoprotein A-I purification.
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In ceruloplasmin Western blots, a band over 220 kDa was observed. This might be due to
ceruloplasmin (122 kDa) binding to myeloperoxidase (MPO) (140 kDa) (13). Furthermore,
ceruloplasmin auto-aggregation has previously been observed (14). Pool 1 contained a 150kDa and
the >220kDa forms, pool 2 contained the 150kDa and a lower 60kDa form while pool 3 contained
only the lower 60kDa form. Ceruloplasmin contains a number of potential glycosylation sites and this
may explain the higher molecular weight form of 150kDa. The lower MW form may correspond to
ceruloplasmin fragments.
Alpha-1-antitrypsin was expected to be found in higher concentrations in pool 3 than in pool 1 and 2
but this was not the case. Monomeric alpha-1-antitrypsin was detected in pool 3 but higher MW
forms were also detected in pools 1 and 2. Residual binding of alpha-1 antitrypsin (52 kDa) to serine
proteinases (66-75 kDa) (15) may be at the origin of the higher alpha-1 antitrypsin molecular weight
bands, observed in pool 1 and 2.
Free-flow electrophoresis shows powerful pre-fractionation capacities enabling fast and accurate
analysis of a given protein mixture from a biological fluid specimen, compared to chromatography or
isotachophoresis. We showed that the FFE fractions are obtained following a reproducible separation
scheme. Fractionation reproducibility could be confirmed, not at a single fraction level, but at a four-
fraction pool level. We propose a simple internal QC method to assess reproducibility of
fractionation; this is Western Blotting detection of apolipoprotein A-I and/or ceruloplasmin in
fraction pool 4F-5A, albumin in fraction pool 5B-5E and alpha-1 antitrypsin in fraction pool 5D-5G.
Confirmation of the reproducibility of the fractionation pattern, allows the biobank to sub-collect,
store and distribute specific FFE fractions or fraction pools.
Acknowledgements
We are grateful to the Conseil Régional de Picardie for supporting this work.
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Figure 1
A. The FFE apparatus with horizontal separation chamber. B. Stripe test (QC1) showing straight flow
of the pH gradient.
A B
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Figure 2
QC1, Stripe test on six different fractionation days.
Figure 3
Plot showing stability of the different FFE buffer pH on different days. BD Ref corresponds to values
obtained upon IQ/OQ of the equipment.
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Figure 4
Plasma separation in 6M and 8M urea separation buffer. Total protein distribution across fractions
shows the same pattern.
Figure 5
Validation hypothesis based on 6 protein markers separated in 3 different microwell pools
4F 4G 4H 5A 5B 5C 5D 5E 5F 5G
23 kDa = pI~5 154kDa= pI~5,2
64 kDa = pI~5,6 119kDa = pI~5,1
58kDa = pI~5,3 93kDa = pI~5,3
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Figure 6
Total protein concentrations (A) and distribution of each of the internal QC protein markers in
microwells 4F to 5G (B, C, D, E, F). Average and standard deviation of concentration in ng/l is shown
for each of the five plasma A separations. Concentration in ng/l is shown for plasma B separation.
Well numbers were not adjusted by highest protein concentration fraction.
A
14
B
C
15
D
E
16
F
G
17
Figure 7
Concentration and total percentage of internal QC proteins in each of the three target pools, in
plasma (A) and in serum (B)
A
4F 4G 4H 5A 5B 5C 5D 5E 5F 5G
18
4F 4G 4H 5A 5B 5C 5D 5E 5F 5G
4F 4G 4H 5A 5B 5C 5D 5E 5F 5G
B
4F 4G 4H 5A 5B 5C 5D 5E 5F 5G
19
4F 4G 4H 5A 5B 5C 5D 5E 5F 5G
4F 4G 4H 5A 5B 5C 5D 5E 5F 5G
20
Figure 8
Representative W. blots of albumin (A), alpha-1-antitrypsin (B), apolipoprotein A-I (C) and
ceruloplasmin (D) in plasma and serum FFE pools. 1, plasma pool of fractions 4F to 5A ; 2, plasma
pool of fractions 5B to 5E; 3, plasma pool of fractions 5D to 5G; 4, plasma positive control; 5, serum
pool of fractions 4F to 5A; 6, serum pool of fractions 5B to 5E; 7, serum pool of fractions 5D to 5G; 8,
serum positive control.
A
B
220 k
104 k
76 k
45 k
1 2 3 4 5 6 7 8
220 k
104 k
76 k
45 k
1 2 3 4 5 6 7 8
21
C
D
1 2 3 4 5 6 7 8
220 k
104 k
76 k
45 k
104 k
76 k
45 k
33 k
18 k
1 2 3 4 5 6 7 8
22
Figure 9
Effective flow rates of sample pump (l/h, right ordinate), media pump (ml/h) and separation
chamber volume (ml, left ordinate), measured on every one of the five plasma fractionation days.