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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
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
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
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
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
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
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
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
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
HCPHCP
Current Methods for Host Cell Current Methods for Host Cell Protein AnalysisProtein Analysis
©2009 Waters Corporation | COMPANY CONFIDENTIAL
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
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
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
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
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
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
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
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
HCPHCP
Summary of Waters Host Cell Summary of Waters Host Cell Protein MethodologyProtein Methodology
©2009 Waters Corporation | COMPANY CONFIDENTIAL
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
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
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
HCPHCP
The Application of 2D The Application of 2D nanoAcquity ChromatographynanoAcquity Chromatography
©2009 Waters Corporation | COMPANY CONFIDENTIAL
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
MSMSEE Alternating High/Low Alternating High/Low Energy AcquisitionEnergy Acquisitiongy qgy q
MSPrecursor
MSE
Fragments
©2009 Waters Corporation | COMPANY CONFIDENTIAL 25
Fragments
Retention Time
Yeast Enolase
MSEnolase
TIMETIME
MSE
©2009 Waters Corporation | COMPANY CONFIDENTIAL 26
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
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
Comprehensive Peptide Ion Comprehensive Peptide Ion Accounting Accounting gg
1 2 3 4 5
©2009 Waters Corporation | COMPANY CONFIDENTIAL 29
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.
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
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
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)
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)
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)
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.
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
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
HCPHCP
Example Results from Example Results from Biosimilar of TrastuzumabBiosimilar of Trastuzumab
©2009 Waters Corporation | COMPANY CONFIDENTIAL
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
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
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
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
©2009 Waters Corporation | COMPANY CONFIDENTIAL 43
Comprehensive Info from PLGSComprehensive Info from PLGSpp
Sequence Information available even on low level proteins
©2009 Waters Corporation | COMPANY CONFIDENTIAL 44
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
©2009 Waters Corporation | COMPANY CONFIDENTIAL 45
OPTIMISED TARGET PROTEIN ANALYSIS UPLC/MRM
VERIFYVERIFYEE
……ProteotypicProteotypic Peptide Review Peptide Review …Generation of MRM Methods…Generation of MRM Methods
©2009 Waters Corporation | COMPANY CONFIDENTIAL 46
VerifyVerifyEE to find appropriate peptidesto find appropriate peptidesyy pp p p ppp p p p
©2009 Waters Corporation | COMPANY CONFIDENTIAL 47
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
©2009 Waters Corporation | COMPANY CONFIDENTIAL 48
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
©2009 Waters Corporation | COMPANY CONFIDENTIAL 49
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
©2009 Waters Corporation | COMPANY CONFIDENTIAL
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
©2009 Waters Corporation | COMPANY CONFIDENTIAL 51
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
©2009 Waters Corporation | COMPANY CONFIDENTIAL 52
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
©2009 Waters Corporation | COMPANY CONFIDENTIAL 53
The combination of 2D-LC/MSE and Xevo TQ MS provides a total system solution for HCP analysis
AcknowledgmentsAcknowledgmentsgg
Waters Biopharmaceutical Development:
Catalin Doneanu
Hongwei Xie
Keith Fadgen
Martha Stapels
Jim Kehoe
Weibin ChenWeibin Chen
Scott Berger
©2009 Waters Corporation | COMPANY CONFIDENTIAL 54