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CHROMATOGRAPHY

TECHNIQUES FOR
BIOMOLECULE
PURIFICATION

Dr. Chester, Che-Chia Hu


July 29, 2016
Outline

Principles of chromatography

Retention mechanisms in chromatography

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What is biochromatography?

Purification of biological macromolecules (DNA, Proteine) with maintaining the biological function.

Aim is to obtain the target compound as pure as possible.

The separate steps are carried out predominantly (at low temperatures) in aqueous buffer systems.

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What are proteins?

Proteins have a very complex three-dimensional structure, which is important for the biological function and which must
remain unchanged as far as possible during purification steps.

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Amino acids I

An amino acid is the basic molecule of any protein.

Using correct terminology, it is an amino carbonic acid which contains an amino group (-NH2) and a carboxylic group (-
COOH).

Amino acids have a common basic structure, different amino acids vary from each other only by their side chain (R).
Most proteins are build from different combinations of only twenty different amino acids. This pool of twenty amino acids
can be classified according to:

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Amino acids II

Nonpolar amino acids:


Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine

Polar amino acids :


Serine, Proline, Threonine, Cysteine, Asparagine, Glutamine

Aromatic amino acids:


Phenylalanine, Tryptophan, Tyrosine

Negatively charged amino acids:


Aspartate, Glutamate

Positively charged amino acids :


Lysine, Histidine, Arginine

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Amino acids II

Source:
Principles of Biochemistry

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Structure of proteins

Primary Secondary Tertiary Quaternary


structure structure structure structure

Amino acid α Helix Polypeptide chain Assembled


residues subunits

Source:
Principles of Biochemistry

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Structure of proteins

The characteristics imparted to the protein by the amino acid side chains serve as bases for purification process, and
include solubility, charge, hydrophobicity and intermolecular binding.

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Separation methods in protein biochemistry

Chromatography
 Column liquid chromatography
 Thin layer chromatography
 Partitioning chromatography

Electrophoresis
Precipitation
Microfiltration/Dialysis
Extraction
Crystallisation
Centrifugation

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Chromatography

Chromatography is the collective term ... for the separation of mixtures. It involves passing a mixture dissolved in a
mobile phase through a stationary phase, which separates the analyte to be measured from other molecules in the
mixture based on differential partitioning between the mobile and stationary phases.

Source:
Wikipedia
Principles of Biochemistry

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Chromatography

chromatogram
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Chromatogram

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Chromatography system

data acquisition

sample
pump detector
A B load

fraction collector

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Chromatography system

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Elution

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Chromatography basics

+ +
+ +
++
+
+
+
+
++ +
+ ++

Equilibrate Load Wash Elute Regenerate


17
Chromatographic techniques

Adsorptive Polarity
 Ion exchange chromatography  Normal phase chromatography
 Affinity chromatography  Reversed phase chromatography
 Hydrophobic interaction
chromatography

Non-adsorptive
 Size exclusion chromatography
(Gel filtration)

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Ion exchange chromatography

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Ion exchange chromatography

Ion exchange chromatography is based on the ionic attraction


between molecules of opposite electric charge.

There are two main types of resins


 anion exchange, used to separate negatively charged targets.
 cation exchange, used to separate positively charged targets.

The electrostatic interactions are short distance phenomena - and as a


result the separation is based on the total number of accessible
charges – negative or positive on their surface.

Source:
Principles of Biochemistry
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Ion exchange chromatography

Charge of the sample may be strongly effected by the pH


 Charged amino acid side chains are weak ion exchange groups
 The charge / pH dependency is highly non-linear BUT in all cases the molecules will become more positively charged at
lower pH values and more negatively charged at higher pH values.

One important characteristic of biomolecules is the iso-electric point or pI, this is the pH at which the total number of
positive and negative charges are equal and the net charge on the molecule is zero.

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Protein charge depends on pH value

COOH pI = isoelectronic point

NH3+ < pI
net charge: positive

COO-
NH3+ = pI
net charge : neutral

R
COO-
NH2 > pI
net charge: negative

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Choice of the right ion exchange system

Fractogel® EMD SO3, SE Hicap, COO


Eshmuno® S, CPX

isoelectric point
of the antibody

pH

Fractogel® EMD TMAE, TMAE Hicap, DEAE, DMAE


Eshmuno® Q
charge

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Classes of ion exchangers

Strong ion exchangers


 keep their charge independent of the pH value of the used buffer

Weak ion exchangers


 keep their charge only within a smaller pH range

The term „strong“ and „weak“ does not correspond to the strength of binding of proteins!

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Ion exchanger binding mechanism

Matrix Ligand Protein

- -
- - - -
- + - - +- + +
+ - -
- -

Counter ion (Salt) Charged


areas

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Properties of tentacle ion exchangers
Fast mass High selectivity
transport High
Flexibility DBC

tentacle resin

convent. resin

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Outstanding binding capacities
Fractogel® media

Batch capacity experiments for CEX

All data from: Generic purification processes for monoclonal


35 antibodies and Fc fusion proteins; Abhinav Shukla, Peter Hinckley,
capacity (mg/ml)

Eva Gefroh, Priyanka Gupta and Brian Hubbard, Amgen, IBC


meeting 2002, San Diego, USA
25

15

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Eshmuno® CPX: Superior mAb binding capacity

Static mAb07 post-protA pool binding capacities*

Eshmuno® CPX Competitor 1 (Agarose) Competitor 2 (Polymer)


12 12 12
90 50 20 80
120 130 120 60 70 50 30
130 100 80 80 60 80 70 60
70 40
11 110 80 11 11
70

130 130 90 10 50 80
10 10 90
120 100 80

Conductivity [mS/cm]
70
Conductivity [mS/cm]

70 80 60

Conductivity [mS/cm]
120 90 80 90
130 110
9 9 70
9
90
130
80
120 50 90
8 8 80 8
130 90 60
120 140 70 80 80 90
110 70
140 90
7 130 7 7
90
80
6 140 6 6
130 140 90
120 70 80 90 80 90
110 100 100
5 5 5
4,00 4,25 4,50 4,75 5,00 5,25 4,00 4,25 4,50 4,75 5,00 5,25 4,00 4,25 4,50 4,75 5,00 5,25
pH pH pH

* in mg/mL settled resin

Eshmuno® CPX shows highest mAb binding capacities.

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Start & elution conditions in ion exchange chromatography

Binding conditions Elution conditions Cleaning step

Highest salt concentration Lowest ionic strength Higher salt concentration


at which the target protein is still which allows elution of the target than the one used for elution
well bound. protein.

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Elution options in ion exchange chromatography

Increasing salt concentration


 step-wise
 as linear gradient

pH gradient (or step)


 with weak ion exchangers

(Caution: Protein must not precipitate at the IEP!)

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Weak vs. strong CEX resins – mAb 1
Selectivities of different functional groups

Fractogel® EMD COO- (M) Eshmuno® CPX Fractogel® EMD SO3- (M)

Weak CEX (COO-) vs. strong CEX resins (SO3-, CPX):


Better separation of mAb aggregates from monomer
Fractogel® EMD COO- (M) > Eshmuno® CPX > Fractogel® EMD SO3-(M) media
Experimental:
Column size: 200 mm L x 5 mm i.d. (CV = 3.9 mL)
Binding capacity of Fractogel® EMD COO- (M) resin may be lower Operating buffer:
compared to strong CEX, but selectivity is often higher 50 mM acetate + 24 mM NaCl, pH 5.0 (ca. 6 mS/cm)
Linear gradient elution: 0 - 1 M NaCl in 40 CV
Load: 40 mg/mL CV
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Weak vs. strong CEX resins - mAb 1
3.8% initial aggregate level
Fractogel® EMD COO- (M) resin Eshmuno CPX resin Fractogel® EMD SO3- (M) resin
6.0
mAb pool aggregate level (%)

5.0

initial mAb aggregate level: 3.8% initial mAb aggregate level: 3.9% initial mAb aggregate level: 3.8%
4.0

3.0

2.0
87% mAb yield at target ≤ 1.5% aggregates 75% mAb yield at target ≤ 1.5% aggr. 68% mAb yield at target ≤ 1.5% aggr.

1.0

0.0
0 20 40 60 80 100 0 20 40 60 80 100 0 20 40 60 80 100
cumulative mAb pool yield (%) cumulative mAb pool yield (%) cumulative mAb pool yield (%)

Experimental:
Fractogel® EMD COO- (M) resin: 87% mAb yield at target ≤ 1.5% aggr. Column size: 200 mm L x 5 mm i.d. (CV = 3.9 mL)
Operating buffer: 50 mM acetate + 24 mM NaCl, pH 5.0
Eshmuno® CPX resin: 75% mAb yield at target ≤ 1.5% aggr. (ca. 6 mS/cm)
Linear gradient elution: 0 - 1 M NaCl in 40 CV
Fractogel® EMD SO3- (M) resin: 68% mAb yield at target ≤ 1.5% aggr. Flow rate: 200 cm/h
Starting level of aggregates: 3.8%
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Load: 40 mg/mL CV
Comparison of elution profiles

mAb monomer

Eshmuno® CPX
competitor (agarose)
Elution peak width
%B Eshmuno® CPX: 11.4 CV
Conductivity Competitor (agarose): 14.3 CV

Conductivity at peak max.


Eshmuno® CPX: 21.4 mS/cm,
17.2% B, approx. 0.16 M NaCl
Competitor (agarose): 16.1 mS/cm
12.0% B, approx. 0.11 M NaCl

mAb aggregates

Feed: mAb06 (post-ProtA pool), aggregate level 2.9 %


Column size: 8 mm i.d. x 100 mm; Column vol. : 5.0 ml; Linear flow rate: 250 cm/h
Buffer A: 25mM sodium acetate + 50mM sodium chloride, pH 4.75, 8 mS/cm
Buffer B: 25mM sodium acetate + 1M sodium chloride, pH 4.75
Gradient: 0 to 50 %B, 20 CV; Load: 50 mg/mL
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Ion exchange chromatography: Pros and Cons

Advantages
 High protein binding capacity
 Independent of sample volume
 Target is concentrated
 Easy scale-up

Drawbacks
 High salt concentration interfers with binding
 Eluate contains salt

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Affinity chromatography

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Affinity chromatography

The method is based on the specific interaction between biological


counterparts (e.g. enzyme substrate).

Ligands with specific biological affinities are immobilized on Fractogel


via polymer chains. The ligand, which has a highly specific structure is
capable of binding complementary protein molecules in a "lock and
key" type mechanism. (Hydrogen bonds and polarizable molecules)

Source:
Principles of Biochemistry
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Affinity chromatography

Only the protein of interest is bound to the specific ligand; other sample components are eluted from the column in the
washing buffer or during the loading.

Elution of the sample protein may either be specific (e.g. using an enzyme substrate) or non-specific using salt or a
change in pH.

Affinity chromatography is the most powerful purification technique for the isolation of proteins.

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Separation mechanism of affinity chromatography

Matrix Ligand Protein

- - - - Impurities
- -
+
- - - -
Complex
Binding region

- - -
- - -
+ +
- - - -
Purified protein
Affinity molecule for elution

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Ligands for affinity chromatography

Dyes
Immobilised metal ions (IMAC)
Lectins
Biospecific ligands

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Protein A affinity chromatography
Protein A media Clarified feedstock from the
e.g. ProSep®, Eshmuno® A fermenter containing mAb

Clarified feedstock from the fermenter containing mAb


passed over column, product binds, impurities pass through

Intermediate wash to remove any remaining


impurities but leave mAb bound to protein A

Elution of mAb by reducing the pH of buffer


(typically pH 3.5-4.5)
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Breakthrough curves at 3 min residence time
Dynamic binding capacity of protein A affinity resin

 Equilibration Buffer: 50 mM Tris, 25 mM NaCl, 5 mM EDTA, pH 7.0


 Intermediate wash: 0.1 M Citric Acid, pH 5.5
 Elution buffer: 0.1 M Acetic Acid, pH 3.0
 Column dimension: 10 mm i.d. x 50 mm bed height
 Feedstream: A purified monoclonal antibody is used for this test.
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Dynamic binding capacities at different residence times

 Equilibration Buffer: 50 mM Tris, 25 mM NaCl, 5 mM EDTA, pH 7.0


 Intermediate wash: 0.1 M Citric Acid, pH 5.5
 Elution buffer: 0.1 M Acetic Acid, pH 3.0
 Column dimension: 10 mm i.d. x 50 mm bed height
 Feedstream: A purified monoclonal antibody is used for this test.

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Eshmuno® A media removes more aggregates

Eshmuno® A Media MabSelect SuRe® resin

Pre-Peak Post-Peak
Monomer in Overall mAb Total Aggregate
Resin % Aggregate % Aggregate
pool (%) Yield (%) Removed (%)
Removed Removed
Eshmuno® A Media 94.6 79.4 25.7 36.9 62.6
MabSelect SuRe® 88.9 80.3 6.1 26.1 32.2

 Equilibration Buffer: 50 mM Tris, 25 mM NaCl, 5 mM EDTA, pH 7.0;


 Intermediate wash: 0.1 M Citric Acid, pH 5.5
 Elution buffer: 0.1M Acetic Acid, pH 3.0;
 Column dimension: 6.6 mm i.d. x 14 cm bed height
 Feedstream: A purified monoclonal antibody is used for this test. With a loading of 12mg/ml and a max loading of
aggregate of 40mg/ml.; Initial mAb feed aggregate: 13.5 %; Gradient elution using citrate buffer, pH 6 – 3 over 20 CV
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Elution & intermediate wash conditions in protein A affinity
chromatography

Intermediate Wash step Elution conditions Cleaning step

low pH, salt, solvent and lower pH acidic solution or akaline


detergent solution depends on the based
which allows elution of the mAb
matrix and ligand stability
which removes the impurities
6 M Urea, 6 M guanidine HCl,
20% ethanol/0.5 M acetic acid,
20% ethanol can be sufficient for
removing strongly bound
material

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Protein A affinity chromatography: Pros and Cons

Advantages
 A powerful tool in capture step for mAb
 Very specific - high purity (> 90%) in one step
 Easy operation

Drawbacks
 Resin cost is high
 Protein A ligand leaching

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Metal chelate affinity chromatography

Retention accomplished by the coordination of electron donor groups


on the protein surface with immobilised transition metal ions

IMAC is widely used for the purification of native or recombinant


proteins.

Commonly Cu (II), Ni (II), Co (II) or Zn (II) ions are immobilised onto


 Chelating ligands which are covalently attached to a support.

The binding is based on the electron-pair acceptor properties of the


 Metal ion (Lewis acid) and the electron-pair donor properties of
 Histidine containing side chains of the protein (Lewis base).

The existence of surface accessible histidine residues is necessary for


the binding of a protein.

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Metal chelate affinity chromatography: PROS & CONS

Advantages
 High capacity compared to other affinity techniques
 Good selectivity
 Flexibility due to the immobilization of different metal
ions
 High stability of the ligand
 Supported by molecular techniques (expression vectors!)
 Identification of histidine residues on the protein's
surface
 Scalability/cleanability

Drawbacks
 Necessity of histidine residues on the surface
 More steps for column preparation are necessary
 Bleeding of metal ions

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Hydrophobic interaction chromatography

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Hydrophobic interaction chromatography

In hydrophobic interaction chromatography binding is achieved under high salt concentration

The eluent of choice is an inverse gradient with ammonium or sodium sulphate to buffer or water

Binding is the result of permanent dipoles of water molecules conferring an ordered structure on the water and thus
increasing the association of the hydrophobic patches of the target compound and the hydrophobic regions of the
stationary phase (increased entropy in the system).

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Separation mechanism of hydrophobic interaction chromatography

Matrix Ligand Protein

- -
- - - -
+ - +
-
- -
- -
„Ordered“ „Disordered“
water molecules Hydrophobic patches water molecules

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Terminology

Hydrophilic = “loves water”


 Hydrophilic molecules are well water-soluble

Hydrophobic = “rejects water”


 Hydrophobic molecules behave like oil and are badly water-soluble

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Start & elution conditions in hydrophobic interaction chromatography

Binding conditions Elution conditions Cleaning step

Lowest salt concentration Highest salt concentration Low salt concentration


at which the target protein is which (already) allows elution of (water or organic solvent is the
(already) well bound. the target protein. best)

 decreasing salt concentration


 linear gradient/step

 decreasing salt concentration


with simultaneously increasing
ethylene glycol concentration
(40%)

 detergents for membrane


proteins
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Hydrophobic interaction chromatography: PROS & CONS

Advantages
 Sample binding occurs in the presence of salt.
 During elution salt concentration can be reduced.
 Very good separation efficiency (isoenzyme separation)

Drawbacks
 High salt load.
 Denaturation of proteins.

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Size exclusion chromatography

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Size exclusion chromatography

Also referred to as gel permeation chromatography or gel filtration. It is an easy


technique for the purification of proteins and other compounds according to their
molecular size and shape.

In contrast to other chromatography methods no adsorption effects should be


involved during the separation. Therefore the packing material has to be
strongly hydrophilic. To avoid hydrophobic interactions between biopolymers and
the matrix, 100 mM salt (or more) should be added to the mobile phase. Elution
of the sample can be performed under isocratic conditions without any gradient
mixer.

Since the separation mechanism is independent from the buffer, the most
suitable buffer conditions for each protein can be used.

Source:
Principles of Biochemistry

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Separation mechanism in size exclusion chromatography

Yellow = large protein


Green = medium sized protein
Red = small protein

Different migration
distances depending on the
molecule’s size and shape

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Important parameters in size exclusion chromatography

Flow rate (must not be too high)

Retention time (min)


90
Sample volume
80

Appropriate salt concentration 70

60
Column dimensions (length: 40-100 cm)
50

40
Optimal column packing
30 BSA
Ovalbumin
20 Cytochrome c

10

0
0 50 100 150 200 250 300
[sodium chloride] (mM)

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Separation efficiency

A280

Column: Superformance 1000-100, packed with Fractogel ® EMD BioSEC (S)


Bed height: 95 cm (7.46 Liter of packed gel)
Buffer: 20 mM Na-citrate, pH 7.4, 200 mM NaCl, 2 mM CaCl2
Flow rate: 6.2 ml/min (5 cm/h)
Sample: IgM, thyroglobulin, ovalbumin, myoglobin, vitamin B12
(each 10 mg) dissolved in 50 ml of running buffer

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Size exclusion chromatography: PROS & CONS

Advantages
 No adsorptive interaction between stationary phase and
sample.
 Free choice of the buffer system (optimal conditions for
the target protein).
 Predictable elution behavior.

Drawbacks
 Loading volume is limited and large columns are
required.
 Technique is unsuitable for sample molecules of similar
size.

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Biochromatography media

... an excellent investment for your process economy!

Ion exchange Affinity Size exclusion


media media media

Fractogel® EMD Eshmuno® Fractogel® EMD Fractogel® EMD


– TMAE Hicap – Q – Chelate – BioSEC
– TMAE Medcap – S
– TMAE – HCX ProSep®
– DEAE – CPX
– DMAE – ProSep Ultra Plus
– SE Hicap – ProSep-vA Ultra
– SO3- – ProSep-vA High
– COO- Capacity
Eshmuno® A

RoboColumn
RoboColumn
MiniChrom Column
MiniChrom Column
Chromabolt® Chromabolt®

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Silica gel and high performance sorbent

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Separation based on polarity

Normal Phase Column (Si)

N Mobile phase
P NP P POLAR SORBENT NON-POLAR
P

Like attraks like


Reversed Phase Column (RP18)

N Mobile phase
PSample
NP NON-POLAR SORBENT P POLAR
P

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Separation based on polarity

Analyte Stationary phase


Mobile Phase
Functional Group
polar non-polar polar

Salts Hexane
Silica
Acids
Alcohols THF
Ketones
CN
Ethers

C4
Hydrocarbons: Acetonitrile
halogenated
C8
aromatic Alcohol
aliphatic
C18
fluorinated Water

non-polar polar non-polar

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Separation based on polarity

-C18 low polarity

Reversed phase -C8

-C2

-Phenyl > 90% of all applications

Medium polar phase -CN

(dep. on the seperation -NH2


problematic and the
used eluent) -Diol

Normal phase -Si high polarity

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Preparative chrom product range

Preparative Chromatography

PharmPrep® P spherical
Performance

LiChroprep®
irregular

Silica Gel 60 / Geduran Si 60

10 12 20 25 40 63 200 500 µm
Particle size

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Influence of particle size on resolution

LiChrospher (5 µm) and LiChroprep RP-18 sorbents


Mobile phase: Buffer/ACN 68.5/31.5, flow rate 1 ml/min, UV 220 nm
Samples (1) Thymine (2) Tropic acid (3) Phenol (4) Cinnamic acid (5)
Acetophenone (6) Naphthol (7) Benzene

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Silica gel and high performance sorbent

... an excellent investment for your process economy!

Silica Gel LiChroprep® PharmPrep® Others

Silica gel 60 LiChroprep® PharmPrep® P Cellulose micro-crystalline


Silica gel 60 silanised – Si 60 – Si 100 Avicel®

Geduran 60 – RP-8 – 100 RP-18e Florisil®


– RP-18 – 100 RP-8e Aluminium Oxide
– NH2 – AlOx 60, active, basic
15 - 25 μm – DIOL 10 μm – AlOx 90, active, basic
15 - 40 µm – CN 20 μm
– AlOx 90, active,
25 - 40 μm neutral
35 - 70 µm 15 - 25 μm – AlOx 90, active, acidic
40 - 63 μm 25 - 40 μm HIBAR®
– AlOx 90, st. Brockm.
63 μm 40 - 63 μm
– AlOx 150, basic
63 - 100 μm
63 - 200 μm Geduran AlOx 90
200 - 500 μm HIBAR® st. Brockm.

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upgrade potential productivity
Improve your process economics

Protein A
VI UF IEX UF VRF IEX UF
Soft gel

time reduction
Protein A -44%
IEX
VI UF UF VRF IEX UF
rigid

for increased productivity rigid media are advantageous


Higher bed height = more column capacity = less re-cycling

From: An evaluation of Protein A and Non-Protein A methods for the recovery of monoclonal
antibodies and considerations for process scale-up by Martin Smith, LONZA, Presented
at“Scaling-up of Biopharmaceutical Products”, 26/27thJanuary 2004, The Grand, Amsterdam

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Strictly controlled production and quality

Long term track record of successful audits by regulatory authorities

Safety stock can be held in all geographies close to customer sites

Flexible and extra manufacturing capacity supporting customer demand changes

Business contingency plans

Definition of critical product quality attributes and strict adherence in manufacturing

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Strictly controlled production and quality

Rigorously controlled producton from start to finish

In accordance with cGMP

Excellent batch-to-batch reproducebility


 Ensures long-term consistency for your product quality

Outstanding regulatory support


 Assists in fullfilling regulatory requirements

Unrivalled expertise
 Over a century of experience in providing quality solutions

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Chromatography training

Experiences biopharm course at Mannheim, Germany

THREE-DAY COURSE

THREE-DAY COURSE

Operation chromatography training at Singapore and Shanghai

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Thank you

2498 members…

Is now on

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