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The Identification and Quantification The Identification and Quantification The Identification and Quantification The Identification and Quantification of Residual Host Cell Proteins of Residual Host Cell Proteins (HCPs) (HCPs) (HCPs) (HCPs) Steve Taylor Steve Taylor ©2009 Waters Corporation | COMPANY CONFIDENTIAL

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Page 1: The Identification and Quantification of Residual Host ... · PDF fileThe Identification and Quantification of Residual Host Cell Proteins (HCPs) Steve Taylor ©2009 Waters Corporation

The Identification and Quantification The Identification and Quantification The Identification and Quantification The Identification and Quantification of Residual Host Cell Proteinsof Residual Host Cell Proteins

(HCPs)(HCPs)(HCPs)(HCPs)

Steve TaylorSteve Taylor

©2009 Waters Corporation | COMPANY CONFIDENTIAL

Page 2: The Identification and Quantification of Residual Host ... · PDF fileThe Identification and Quantification of Residual Host Cell Proteins (HCPs) Steve Taylor ©2009 Waters Corporation

OverviewOverview

In purified product there product there is a high concentration of ‘p od ct’ of ‘product’ proteins low concentration of ‘host’ proteins

Waters can Identify and

©2009 Waters Corporation | COMPANY CONFIDENTIAL 2

Quantify these with UPLC-MSE

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HCPHCP

Background to HCPs and the Background to HCPs and the Guidelines of the EU Regulatory Guidelines of the EU Regulatory

AuthorityAuthority

©2009 Waters Corporation | COMPANY CONFIDENTIAL

Page 4: The Identification and Quantification of Residual Host ... · PDF fileThe Identification and Quantification of Residual Host Cell Proteins (HCPs) Steve Taylor ©2009 Waters Corporation

Host Cell Proteins (HCPs)Host Cell Proteins (HCPs)( )( )

Recombinant Proteins produced in host cells

Proteins from cells can co-purify with therapeutic protein of interest

Chi H t O (CHO) ll —e.g. Chinese Hamster Ovary (CHO) cell proteins in recombinant monoclonal antibody therapeutics

Purification steps should remove contaminants. Low levels can remain because ofbecause of

—Poor process control

—Process changes: can affect HCP

©2009 Waters Corporation | COMPANY CONFIDENTIAL 4

Process changes: can affect HCP pattern and abundances

Biopharm International, Volume 13, Number 6, pp. 38-45, May 2008

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Guidelines Governing HCPsGuidelines Governing HCPsgg

Safety drives the need for removal/minimization

Link between HCPs and immunogenicity—Link between HCPs and immunogenicity

European regulations in effect since 2007

‘6 2 Validation of the purification — 6.2 Validation of the purification procedure - …. The ability of the purification process to remove other specific contaminants p psuch as host-cell proteins … should also be demonstrated’

—ICH Guidelines: 2009 review in progress(http://www.emea.europa.eu/pdfs/human/bwp/BWPworkprogramme.pdf)

©2009 Waters Corporation | COMPANY CONFIDENTIAL 5

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Importance of HCPs Importance of HCPs –– approvalapprovalpp pppp2008: approval of follow-on biologic/ biosimilar (EU; USA)

Initially the application was turned

Diagramatic representation of amino acid sequence of human

growth hormone— Initially the application was turned down due to a potential immunogenetic effect due to HCPs

Issue was resolved before drug

growth hormone

— Issue was resolved before drug release – positive opinion given

— ‘The cause of immunogenicity was linked to excess host cell was linked to excess host cell protein contamination, which was resolved by the

f t ith dditi l manufacturer with additional purification steps’.(http://www.pubmedcentral.nih.gov/articlerender.fcgi?

artid=2638545)

©2009 Waters Corporation | COMPANY CONFIDENTIAL 6

artid 2638545)

Image source: http://www.rxlist.com/omnitrope-drug.htm

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Importance of HCPs Importance of HCPs –– failurefailurepp

HCPs and approval problems for some Biosimilars: — Application by biosimilar company for Interferon Alfa 2a (HepC)pp cat o by b os a co pa y o te e o a a ( epC)

— Marketing permission rejected 2006:

—“The reasons for the rejection by the EMEA included quality and clinical differences between [the biosimilar product] and and clinical differences between [the biosimilar product] and the reference product, … inadequate validation of the process for the finished process and insufficient validation of immunogenicity testing ”validation of immunogenicity testing.”

Liver Damage

©2009 Waters Corporation | COMPANY CONFIDENTIAL 7

Image Source : Copyright © 1996, 1997 University of Pittsburgh http://tpis.upmc.edu/tpis/HB/H00030m.html

Liver Damage from Hepatitis

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Challenges of HCP AnalysisChallenges of HCP Analysisg yg y

Thousands of possible protein contaminants

HCPs can be present at extremely low levelsHCPs can be present at extremely low levelso Typically ppt to ppm (relative to biotherapeutic)

o Guidelines suggest monitoring to ppm (1-100ppm)

Developing methods is expensive and time consuming

Business Impacts of Failure to identify and remove contaminants:

o Can reduce drug efficacy

o May lead to adverse events

o Drug development and introduction delayso Drug development and introduction delays

o Longer cycle to introduce process improvements

o Perceived product quality issue = competitive disadvantage

©2009 Waters Corporation | COMPANY CONFIDENTIAL 8

o Kill a promising candidate

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Main Goals of Waters Host Cell Main Goals of Waters Host Cell Protein AnalysisProtein Analysisyy

Develop a methodDevelop a method— To identify,

— Quantify and

Monitor HCPs from recombinant means— Monitor HCPs from recombinant means

Results must have a means of validating the results (e.g. peptide sequence; concentration confirmation)

Needs to be complementary/ compatible with existing methods

Needs to provide improvements compared to existing Needs to provide improvements compared to existing methods (generality; efficiency; speed)

Needs to provide cost-effective benefits for process improvements for Waters customers

©2009 Waters Corporation | COMPANY CONFIDENTIAL 9

improvements for Waters customers

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HCPHCP

Current Methods for Host Cell Current Methods for Host Cell Protein AnalysisProtein Analysis

©2009 Waters Corporation | COMPANY CONFIDENTIAL

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Comparison of current HCP MethodsComparison of current HCP Methodspp

Narrow dynamic range (<100)

©2009 Waters Corporation | COMPANY CONFIDENTIAL 11

Biopharm International, Volume 13, Number 6, pp. 38-45, May 2008

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SPEEDSPEEDEFFICIENCYEFFICIENCYSignificantly shorter Significantly shorter

development time for assaydevelopment time for assayAbility to provide high Ability to provide high

Simultaneous i.d. and Quan Simultaneous i.d. and Quan of proteinsof proteinsEfficient assay and use of Efficient assay and use of

h C/ Sh C/ SEE f C ?f C ?

throughput/ flexible monitoring throughput/ flexible monitoring assay assay

resourcesresources

Why UPLC/MSWhy UPLC/MSEE of HCPs?of HCPs?

ACCURACYACCURACY GENERALLY APPLICABLEGENERALLY APPLICABLEAccurate quan of HCPs in Accurate quan of HCPs in

complex mixturecomplex mixtureQuan over > 4 orders of Quan over > 4 orders of

HCPs do not need to be known HCPs do not need to be known prior to analysisprior to analysisCan be widely applied and easily Can be widely applied and easily

©2009 Waters Corporation | COMPANY CONFIDENTIAL

Quan over > 4 orders of Quan over > 4 orders of magnitudemagnitude

Can be widely applied and easily Can be widely applied and easily modifiedmodified

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Attributes Needed for Analysis of Attributes Needed for Analysis of HCPs HCPs –– User ExpertiseUser Expertisepp

User Expertise Needed for Routine UseUser Expertise Needed for Routine Use

LC/MS TofHigh

LC/UVLow

ELISA:Very Low

Gel and Blot: LowLow

LC/MS Quad

©2009 Waters Corporation | COMPANY CONFIDENTIAL 13

LC/MS QuadReasonably Low

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Attributes Needed for Analysis of Attributes Needed for Analysis of HCPs HCPs -- QuantitationQuantitationQQ

Ability to Quantify over wide dynamic rangeAbility to Quantify over wide dynamic range

LC/MS4 orders

Good

ELISA:Poor

LC/UV2 - 3 orders

Good Good

Gel and Bl t

Good

Blot:Poor

©2009 Waters Corporation | COMPANY CONFIDENTIAL 14

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Attributes Needed for Analysis of Attributes Needed for Analysis of HCPs HCPs -- SensitivitySensitivityyy

Ability to Detect at very low levelsAbility to Detect at very low levels

LC/MSGood (ppm)

ELISA: Excellent

(ppt)

LC/UV:Acceptable (high ppm)

Gel and

(ppt)(high ppm)

Gel and Blot:

Variable

©2009 Waters Corporation | COMPANY CONFIDENTIAL 15

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Attributes Needed for Analysis of Attributes Needed for Analysis of HCPs HCPs -- InterpretationInterpretationpp

User Interpretation required for AnalysisUser Interpretation required for Analysis

LC/MSHighly

Objective

LC/UVObjective by

RT Objective

Gel and ELISA:

RT

Blot: Subjective

ELISA:Subjective

©2009 Waters Corporation | COMPANY CONFIDENTIAL 16

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Attributes Needed for Analysis of Attributes Needed for Analysis of HCPs HCPs -- CertaintyCertaintyyy

Unambiguous Identification of HCPsUnambiguous Identification of HCPs

LC/MSExtremely

High

LC/UV: High with

SOP High

Gel and Blot: ELISA:

SOP

Gel and Blot: Acceptable

ELISA:Low

©2009 Waters Corporation | COMPANY CONFIDENTIAL 17

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Attributes Needed for Analysis of Attributes Needed for Analysis of HCPs HCPs -- CertaintyCertaintyyy

Method FlexibilityMethod Flexibility

LC/MSExtremely Flexible

LC/UV: Flexible Flexible

Gel and Blot: ELISA: Gel and Blot: FlexibleVery

Inflexible

©2009 Waters Corporation | COMPANY CONFIDENTIAL 18

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HCPHCP

Summary of Waters Host Cell Summary of Waters Host Cell Protein MethodologyProtein Methodology

©2009 Waters Corporation | COMPANY CONFIDENTIAL

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Comparison to ProteomicsComparison to Proteomicspp

Similarity to proteomics applications

- Similar tools can be used with minor changes- Similar tools can be used with minor changes

- Complex Samples by tryptic digest

- Same data mining and rules for identifyingg y g

- Databases used

- MSE acquisition

Differences:

- Greater need for dynamic range (>4)

d h h h d d- Need to cope with high product concentration and a small amount of HCP (ppm)

- Not normally sample limited

©2009 Waters Corporation | COMPANY CONFIDENTIAL 20

Not normally sample limited

- Databases can be tailored because Host is known

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Tools Available for HCP AnalysisTools Available for HCP Analysisyy

InformaticsPLGS and IdentityE: validated protein identification

d i f l iti reducing false-positive space.BiopharmaLynx 1.2 for automated sequence coverage and confirmation of primary structure of biomolecules (intact mass; peptide mapping)(intact mass; peptide mapping)VerifyE for the determination of the most appropriate peptides for quantification (by MRM)

InstrumentationNanoUPLC with 2D RP-RP – more reproducible chromatography (greater sensitivity)Synapt/ XevoQtof – accurate mass MSMSTQD/ Xevo TQ – high dynamic range quantitation

ChemistryRapigest: aids tryptic digestion

©2009 Waters Corporation | COMPANY CONFIDENTIAL 21

PST/ BEH: Peptide Separation ColumnsHILIC (‚normal phase‘); Glycan columns

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General MethodologiesGeneral MethodologiesggIdentityE to discover proteins- Peptide sequences matched (dB)- Confidence ranking of identification

BiopharmaLynx to- Compare samples vs control

M it / difi ti

ExpressionE to quantify proteins- Measure of amount

E t bli h d t l

- Monitor/ quan modifications- (e.g. glycoforms)

- Confirm peptide sequence with MSE

- Established protocol- Generally applicable

VerifyE for ‘signature’ peptides

©2009 Waters Corporation | COMPANY CONFIDENTIAL 22

Verify for signature peptides- Relevant Peptides obtained for MRMs- Output of MRM method for Tandem Quad

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HCPHCP

The Application of 2D The Application of 2D nanoAcquity ChromatographynanoAcquity Chromatography

©2009 Waters Corporation | COMPANY CONFIDENTIAL

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Optimisation of 2D ChromatographyOptimisation of 2D Chromatographyp g p yp g p y

FIRST DIMENSION:

1 mm x 0.5 cm X-Bridge packed with BEH130, 5 1 mm x 0.5 cm X Bridge packed with BEH130, 5 µm; 10 µL/min at pH 10 to elute all peptides.— HIGH RESISTANCE to extreme pH

Trap col mn fo this esea ch p oject 500 m Trap column for this research project 500 µm x 2 cm packed with Symmetry C18, 5 µm— High loading capacity

SECOND DIMENSION:

300 µm x 15 cm with BEH130 1 7 µm; 4 300 µm x 15 cm with BEH130, 1.7 µm; 4 µL/min

Standard ESI probe with narrow bore capillary

©2009 Waters Corporation | COMPANY CONFIDENTIAL 24

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MSMSEE Alternating High/Low Alternating High/Low Energy AcquisitionEnergy Acquisitiongy qgy q

MSPrecursor

MSE

Fragments

©2009 Waters Corporation | COMPANY CONFIDENTIAL 25

Fragments

Retention Time

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Yeast Enolase

MSEnolase

TIMETIME

MSE

©2009 Waters Corporation | COMPANY CONFIDENTIAL 26

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TimeTime--Aligned Aligned Precursor/Product Ion listPrecursor/Product Ion list//

ss MH+ Ret.Time Volume

Charge-Stat

e

15 Seconds Chromatographic Window

curs

or M

a

1189.5802 46.71 78430 1.98

765.3742 46.67 449 1

522.2606 46.67 554 1

Pre

c 800.4481 46.67 3754 1

963.5187 46.69 3658 1

515.3250 46.70 2325 1

687.3742 46.70 2351 1

ct M

ass

1100.5773 46.71 1112 1

822.4154 46.71 436 1

781.4823 46.71 163 1

896 5183 46 72 675 1

Prod

u

retention time

896.5183 46.72 675 1

685.3210 46.72 862 1

1009.6112 46.74 125 1

498.3296 46.75 709 1

©2009 Waters Corporation | COMPANY CONFIDENTIAL 27

432.2357 46.75 356 1

906.5477 46.76 364 1

Precursor/Product Ion List

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Waters IdentityWaters IdentityEE High High Definition Proteomics SystemDefinition Proteomics Systemyy

‘C il ’ l Ch t h Mass Spectrometry

SynaptTM HDMSTM

‘Capilary’ scale Chromatography Mass Spectrometry

nanoAcquity UPLC system

with 2D Technology

Informatics

with 2D Technology

©2009 Waters Corporation | COMPANY CONFIDENTIAL 28

IdentityE Software ProteinLynx Global Server

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Comprehensive Peptide Ion Comprehensive Peptide Ion Accounting Accounting gg

1 2 3 4 5

©2009 Waters Corporation | COMPANY CONFIDENTIAL 29

Page 30: The Identification and Quantification of Residual Host ... · PDF fileThe Identification and Quantification of Residual Host Cell Proteins (HCPs) Steve Taylor ©2009 Waters Corporation

HCPHCP

h d l f ll ih d l f ll iMethodology for Host Cell Protein Methodology for Host Cell Protein MonitoringMonitoring by Tandem Quadrupoleby Tandem Quadrupole

Once HCPs have been established a high-throughput method can be

©2009 Waters Corporation | COMPANY CONFIDENTIAL

a high throughput method can be developed for process monitoring.

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VerifyE flow diagramVerifyE flow diagramy gy g1 0 0

2 3 .8 04 1 8 .7

2 2 .4 54 5 8 .7

3 3 .1 34 8 4 .7

2 7 .3 74 2 2 .2

2 6 .9 95 4 0 .2

2 4 .9 34 5 9 .7

2 9 .1 26 2 6 .3

2 9 .9 34 0 7 .7

3 0 .7 35 8 2 3

Discovery phase LC-MSE data

Acquisition as above

VerifyE data processing(N) proteotypic pep

(X) trans per peptide

%

1 9 .4 04 0 6 .2

1 8 .7 45 5 1 .2

1 7 .4 75 7 5 .21 6 .9 3

4 8 8 .5

1 7 .9 64 1 9 .9

2 0 .8 74 1 1 .7

2 0 .2 23 7 3 .2

2 1 .6 07 2 2 .2

2 2 .8 64 4 7 .2

2 4 .5 44 6 1 .7 2 6 .7 7

4 1 6 .7

2 6 .2 64 3 5 .2

2 6 .1 65 3 1 .7

2 5 .8 95 5 9 .2

2 8 .2 24 0 7 .7

2 8 .2 95 3 6 .7

5 8 2 .3

3 0 .3 56 2 5 .3

3 1 .3 55 2 7 .2

3 1 .9 07 2 1 .8

3 2 .2 86 6 9 .7

3 3 .2 47 2 4 .3

3 3 .4 45 9 8 .3

3 5 .8 47 9 0 .9

3 3 7 6 3 6 9 0

T im e1 6 .0 0 1 8 .0 0 2 0 .0 0 2 2 .0 0 2 4 .0 0 2 6 .0 0 2 8 .0 0 3 0 .0 0 3 2 .0 0 3 4 .0 0 3 6 .0 0 3 8 .0 0 4 0 .0 0 4 2 .0 0

0

3 5 .7 07 8 9 .8

3 3 .7 67 4 0 .3

3 6 .9 07 0 0 .3

3 9 .1 14 9 9 .2 4 1 .7 9

7 8 2 .3

Automatically generated Xevo TQ MRM exp file

©2009 Waters Corporation | COMPANY CONFIDENTIAL 31Verification- MRM transition monitoring

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MRM development for Targeted MRM development for Targeted MonitoringMonitoringgg

Use MSE data to develop MRM assay

Use in high-throughput monitoring and absolute quantification of HCPs

Xevo TQMSTM Xevo TQ with selected MRMs

MS1 Collision Cell MS2

©2009 Waters Corporation | COMPANY CONFIDENTIAL 32

StaticStatic

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Applying Proteomics Workflows Applying Proteomics Workflows to HCP Analysisto HCP Analysisyy

Workflow Overview:

—Shotgun enzymatic digestion of sample into peptides

1D or 2D LC/MSE with IdentityE to DISCOVER—1D or 2D LC/MSE with IdentityE to DISCOVERcontaminant proteins

—2D for more loading capacity2D for more loading capacity

—Develop proprietary host cell protein database

—(Hi3 for absolute quantitation, label-free)(Hi3 for absolute quantitation, label free)

—Data mined for MRMs

—Transfer to Tandem Quad for absolute

©2009 Waters Corporation | COMPANY CONFIDENTIAL 33

Qquantitation (e.g. labeled peptides)

Page 34: The Identification and Quantification of Residual Host ... · PDF fileThe Identification and Quantification of Residual Host Cell Proteins (HCPs) Steve Taylor ©2009 Waters Corporation

2D Chromatography Factors2D Chromatography Factorsg p yg p y

2D Chromatography requires optimisation because:—Column loading is non-linear (more loading Column loading is non linear (more loading

does not equate to more dynamic range)—Product is present in much higher concentrations

2D app oa h means lo le el imp ities - 2D approach means low-level impurities quantifiable despite disparity in concentrations

Gilar M. et. al, J. Sep. Sci. 2005, 28, 1694-1703

Chemistries specifically selected for RP/RP 2D approach:—Retention time models applied (based on Retention time models applied (based on

hydrophobicity scale of tryptic peptides)—All Chemistries readily available (but dimensions

adapted)

©2009 Waters Corporation | COMPANY CONFIDENTIAL 34

adapted)

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Host Cell Protein Analysis of Host Cell Protein Analysis of Biopharmaceutical ProductBiopharmaceutical Productpp

1D Chromatography (75 um scale)— 0.05 ug of product digest loaded for peptide mapping0 05 ug o p oduct d gest oaded o pept de app g

— 90 min gradient (5-40% acetonitrile)

2D RP-RP (High/Low pH) Chromatography5 (80 l) f d t di t ( )l d d + 100 f l ADH

Gilar M. et. al, J. Sep. Sci. 2005, 28, 1694-1703

— 5 ug (80 pmol) of product digest (over)loaded + 100 fmol ADH

+ 1 fmol BSA

— 1st Dimension (pH 10): 5 or 10 step gradient (0 - 45% acetonitrile)

— 2nd Dimension (pH 2.6): 90 min gradient (5 - 40% acetonitrile)

UPLC: nanoACQUITY® 2D UPLC®

QTof: SYNAPT MS (MSE mode)

D t PLGS 2 4 (Id tit E)

©2009 Waters Corporation | COMPANY CONFIDENTIAL 35

Data: PLGS 2.4 (IdentityE)

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Diagram of 2D setup at higher scaleDiagram of 2D setup at higher scaleg p gg p g

Online dilution of 1D flow to Trap column – change

pH and therefore selectivity

2D pH=2.4. 0.3 mm x 150 mm BEH C18 1.7 µm, Flow at 4 µL/min. 90

min gradient from 3 to 40% t it il (0 1% FA f i id)p a d t e e o e se ect ty acetonitrile (0.1% FA-formic acid).

1D pH=10. flow 10 µL/min. XBridge high resistance to pH regime. Mobile phase

Trap: 5-µm Symmetry C18 trap -peptides

©2009 Waters Corporation | COMPANY CONFIDENTIAL 36

resistance to pH regime. Mobile phase 20 mM ammonium formate in water

(Solvent A) and ACN (Solvent B). Five Fractions (to 50.0% B).

washed on to 2D column.

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2D HPLC using High/Low pH RPLC2D HPLC using High/Low pH RPLC

pH 10.020 mM ammonium formate

0-42% acetonitrile in 5 or 10 steps of 15 min0 42% acetonitrile in 5 or 10 steps of 15 min

100 TIC4.37e8

18 95

pH 10

%

18.95

15.79

8.53

6.775.705.214.10

14.0310.38

9.64

13.2111.73

16.41

18.58

18 21

25.68

22.39

21.0419.89 24.20

29.41

29.0025.92

41.26

35.85

35.48

37.65

39.5841.92

0-56% B in 70 minutes 20 mM NH4OH pH 10

100Bovine_Hemoglobin_Digest_Stored_091803_1 1: Scan ES+

TIC4.51e9

28.55

18 75

2.50 5.00 7.50 10.00 12.50 15.00 17.50 20.00 22.50 25.00 27.50 30.00 32.50 35.00 37.50 40.00 42.50 45.00Time1

18.21

pH 2.6

neutral acidic

basicacidic

basic

pH 2.60.2% Formic acid

0-42% acetonitrile in 90 min

%

18.75

17.36

16.3010.99

8.91

4.70 6.29

11.4013.24

23.86

22.79

22.39

19.61

27.0026.68

26.51

35.0530.68

31.41

©2009 Waters Corporation | COMPANY CONFIDENTIAL 37

Gilar M. et. al, J. Sep. Sci. 2005, 28, 1694-1703

1

4.29 11.9314.09

19.93 26.06 34.27 36.19

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2D Chromatograms2D Chromatograms10 Fractions, 5 10 Fractions, 5 μμg Loadedg Loaded,, μμgg

45% ACN

One peptide may appear in multiple Ch hi

20 8% ACN

45% ACN

23.6% ACN

Chromatographic steps - ‘merge’ step to create coherent

fractions20.8% ACN

17.4% ACN

18.9% ACN

14.5% ACN

15.9% ACN

11.7% ACN

13.0% ACN

©2009 Waters Corporation | COMPANY CONFIDENTIAL 38

8.2% ACN

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HCPHCP

Example Results from Example Results from Biosimilar of TrastuzumabBiosimilar of Trastuzumab

©2009 Waters Corporation | COMPANY CONFIDENTIAL

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HCPs from Biosimilar of TrastuzumabHCPs from Biosimilar of Trastuzumab(Non European Production)(Non European Production)( p )( p )

Methodology for Greater Confidence:

R d id dd d D Random peptide sequences added as Decoy strategy to ensure identified peptides real = Total 27,216 entries in database created— 13,600 entries from Swissprot for Golden Hamster and Mouse

(homologs)

— 6 protein sequences from spiked in proteins: LA, ADH, PHO, BSA, ENL, porcine trypsin,

— 2 sequences from TrastuzumAb (heavy and light chains)

— Equal number of random sequences as known entries (13,608)q q ( )

False Positive Rate of Protein Return: 5% (user adjustable)

Concentration range found here was 10 to 50 ppm relative to therapeutic

©2009 Waters Corporation | COMPANY CONFIDENTIAL 40

therapeutic

Lower confidence hits (nearing random) not reported

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HCPs from Biosimilar of TrastuzumabHCPs from Biosimilar of Trastuzumab(Non European Production)(Non European Production)( p )( p )

Host cell: Chinese Hamster Ovary (CHO)

Database with combination of all the mouse and Database with combination of all the mouse and hamster protein sequences listed in the Swiss-Prot database (http://www.expasy.ch/sprot/)

—Chinese Hamster database held privately so homology database used (Golden hamster; M )Mouse)

©2009 Waters Corporation | COMPANY CONFIDENTIAL 41

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HCPs from Biosimilar of Trastuzumab HCPs from Biosimilar of Trastuzumab ––confident assignments, 10confident assignments, 10--50ppm range50ppm rangeg ,g , pp gpp g

©2009 Waters Corporation | COMPANY CONFIDENTIAL 42

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PLGS Project view of proteins id’dPLGS Project view of proteins id’dj pj p

Listing of ProteinsListing of Proteins— Accession details

— Names and sequences

generated

— Confidence ranking

Spectral overview (can be zoomed)

Sequence information for identified protein

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Comprehensive Info from PLGSComprehensive Info from PLGSpp

Sequence Information available even on low level proteins

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VERIFYVERIFYEE

…Data Work…Data Work--FlowFlow

Proteotypic Peptide Filters Efficient

IDENTITYE (Discovery Data) Input .csv/.txt

Transition Filters

UPLC/MRM (& TargetLynx) Method File Creation

Retention Time Optimization

Scouting Run UPLC/MRM

Targeted (DDA) .exp Targeted (MRM) UPLC/MRM FileQuanpedia dB

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OPTIMISED TARGET PROTEIN ANALYSIS UPLC/MRM

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VERIFYVERIFYEE

……ProteotypicProteotypic Peptide Review Peptide Review …Generation of MRM Methods…Generation of MRM Methods

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VerifyVerifyEE to find appropriate peptidesto find appropriate peptidesyy pp p p ppp p p p

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Reproducibility of the MRM assay: MIX-5 protein digestp g

RSD = 3%

1 picomole BSA digest on 1 picomole BSA digest on column

Reproducible Chromatography

R d ibl RTReproducible RTs

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Reproducibility of MRM assay: MIX-5 proteins spiked in Trastuzumab and digestedp g

RSD = 3%RSD 3%

1 picomole BSA digest on column

R d ibl Ch t hReproducible Chromatography

Reproducible RTs

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Reproducibility of the MRM assay:

MIX-5 protein digest

RSD = 8%

200 fmoles ENL digest on column200 fmoles ENL digest on column

Reproducible Chromatography

Reproducible RTs

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Reproducibility of MRM assay: MIX-5 proteins spiked in Trastuzumab and digestedg

RSD = 13%

200 fmoles ENL digest on column

Reproducible Chromatography

R d ibl RTReproducible RTs

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Summary of Workflow advantages Summary of Workflow advantages for HCP Analysisfor HCP Analysisyy

Workflow Models:— UPLC-MSE is well-established

— Proteomics tools already exist and are developing (e.g. HDMSE)

Applications Benefits:— Confident Identification of individual HCPs – with ranking of Confident Identification of individual HCPs with ranking of

confidence

— Quantitation of each identified HCP

o Label free with discovery stage (Synapt/ XevoQT)o Label-free with discovery stage (Synapt/ XevoQT)

o Using isotopically labelled peptides (XevoTQ/ TQD)

— Much faster development time than immunoassay

— Provide a multi-purpose platform for many other tasks

— Sensitivity levels comparable to ELISA (low ppm)

— Also applicable to subunit (recombinant) Vaccines

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Conclusions

The 2D-LC/MSE setup is able to identify low abundance protein contaminants present in biopharmaceuticals over p p pmore than 4 order of magnitude

The 2D LC setup using the second chromatographic The 2D-LC setup using the second chromatographic dimension provides the sensitivity and robustness required for HCP analysis

A high-throughput MRM assay on the Xevo TQ MS can quantify these protein impurities (absolute quantification q y p p ( qcan be done using isotopically labeled peptides)

The combination of 2D LC/MSE and Xevo TQ MS provides a

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The combination of 2D-LC/MSE and Xevo TQ MS provides a total system solution for HCP analysis

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AcknowledgmentsAcknowledgmentsgg

Waters Biopharmaceutical Development:

Catalin Doneanu

Hongwei Xie

Keith Fadgen

Martha Stapels

Jim Kehoe

Weibin ChenWeibin Chen

Scott Berger

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