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Routine Characterization of mAbs and Other Routine Characterization of mAbs and Other Proteins
Patrick Boyce
Biopharmaceutical Marketing Manager
Europe and IndiaEurope and India
©2011 Waters Corporation 1
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Agendag
Why?
What scientific challenges?
Technology
Example application—Sequence confirmationq
—Identification and quantification of glycans & other PTMs
©2011 Waters Corporation 2
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Why the need to confirm sequence, identify PTMs and quantify PTMs?y q y
Regulatory guidelines such as ICH Q6B, and EMEA/CHMP/BWP/49348/2005 k it l th t EMEA/CHMP/BWP/49348/2005 make it clear that the primary structure should be confirmed, heterogeneity defined, product related substances heterogeneity defined, product related substances characterized, and consistency demonstrated.
©2011 Waters Corporation 3
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Scientific challengesg
Confirming primary structure— LC/MS of peptide map complicated by sub-stoichiometric
difi ti d i d l hi h lt i modifications, and missed cleavages, which may result in a very large quantity of peptides.
Detecting, locating & quantifying modificationsQualitative & quantitative analysis of low mass modifications to — Qualitative & quantitative analysis of low mass modifications to high molecular mass samples
— Dynamic range challengeSpecific MS challengesSpecific MS challenges— Multiple charge states, isotope patterns, co-eluting peptides, in-
source fragmentation, data interpretation— Isobaric peptides in peptide mapp p p p p— Detecting the monisotopic ions becomes more demanding as
mass increases.
©2011 Waters Corporation 4
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Overview of Waters Technology for Biopharmaceutical Analysisp y
ACQUITY UPLC H-Class Bio— UV and fluorescence detectors
fXevo G2 QTof MSBiopharmaLynx 1.2Column chemistriesColumn chemistries— AccQTag Ultra BEH C18— BEH130 & BEH300 C18 PST — BEH300 C4 PrST columns— BEH Glycan columns— BEH200 SEC columnsBEH200 SEC columns— Protein-PakTM Hi Res IEX columns— MassPREP Micro Desalting column
©2011 Waters Corporation 5
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ACQUITY UPLC H-Class BioQ
Ultimate chromatographic performance— Low dispersion system sub-2 µm columns
Biocompatible system— Eliminate system corrosion— Best sample recovery
Flexibility, robustnessSuitable for RP IEX SEC HILIC— Suitable for RP, IEX, SEC, HILIC
— Robustness tested for high salt— AutoBlend+ for dial-up buffersp
Needle in flow path design— Low carryover performance
©2011 Waters Corporation 6
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Mass accuracy, resolution and dynamic rangey g
Accurate mass of monoisotopic peptide for identificationidentification
QuanTof technology: Improved quantitation
Enables identification of larger peptides—Disulfide-linked peptides
Missed Cleavage
QuanTofTM
Low ppm MMA over
TOF >20,000 RESOLUTION
QuanTofTM
Low ppm MMA over
TOF >20,000 RESOLUTION
—Missed Cleavage
—Digests: AspN, LysC, GluC
pp>104 Dynamic
Range
pp>104 Dynamic
Range
©2011 Waters Corporation 7
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Xevo G2 Technical Note
2,000
Peptide Mass
31
Monoisotopic peak (% of total)1
93
Relative Monoisotopic Peak
Height2
1.1
Isotopic EnvelopeDynamic Range3
2,000
Peptide Mass
31
Monoisotopic peak (% of total)1
93
Relative Monoisotopic Peak
Height2
1.1
Isotopic EnvelopeDynamic Range3
15,000
10,000
5,000
0.018
0.3
5.7
0.14
2.1
26
714.2
47.6
3.8
15,000
10,000
5,000
0.018
0.3
5.7
0.14
2.1
26
714.2
47.6
3.8
20,000 0.001 0.01 1000020,000 0.001 0.01 10000
~9:1~9:1
The largest peptide in most antibody tryptic peptide maps: HC T15 (DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTK). Mass 6712.3071 Da.
©2011 Waters Corporation 8
Dynamic Range Required ~1400
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UPLC/MSE to Comprehensively Catalog Complex Samples p p
UPLC/MSE comprehensively catalogs complex samples in a single analysis. It delivers high quality, unambiguous exact mass precursor and fragment ion data quickly and easily
©2010 Waters Corporation
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MS
TIMETIME
MSE
©2011 Waters Corporation 10
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What BiopharmaLynx™ Doesp y
Automates data processing
Facilitates comparisons between a reference standard and batches of reference standard and batches of experimental samples. Useful for:
—demonstrating consistency of batch with material used for clinical studies
—demonstrating comparability of reference product with potential new biosimilar
©2011 Waters Corporation 11
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Application - Introduction and Contextpp
Company X is an international company with a powerful track record in small moleculespowerful track record in small molecules.
They wish to expand their product range and plan to make a biosimilar of an antibody
They sent us two samplesThey sent us two samples— The innovator product— Their copy of that product
They wished to verify that they had successfully mimicked the innovator product. http://en.wikipedia.org/wiki
/File:Antibody2.JPG
©2011 Waters Corporation 12
p
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UPLC/MS of Intact Control and Check SamplesUPLC/MS of Intact Control and Check SamplesWith Data Processed by BiopharmaLynx 1.2
©2011 Waters Corporation 13
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Intact Protein Analysis Workflow
Sample Preparation
+ +
UPLC® Xevo QTof MS Bioinformatics
©2011 Waters Corporation 14
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Control and Check Antibodies Processed automatically by BiopharmaLynx 1.2y y p y
CONTROL
Consistent 64 Da difference in antibody masses for each form
CHECK
©2011 Waters Corporation 15
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High Resolution Separation of a Reduced Monoclonal Antibodyy
Mass SpectrumLC
Mass Spectrum HC
LC ChromatogramW t BEH300 C4 1 7 HC Waters BEH300 C4 1.7 µm2.1 x 50 mmA: 0.1% Formic in WaterB 0 1% F i i ACN B: 0.1% Formic in ACN
25-35 %B over 15 min
©2011 Waters Corporation 16
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Automatically Deconvoluted Spectrum of the Light Chains in BiopharmaLynx g p y
The average masses of
CONTROLmasses of the Light Chains of the
Light Chains are identical
antibodies are identical and it is a d t sreasonable to suggest that they share
CHECKthey share the same chemical
©2011 Waters Corporation 17
composition
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Automatically Deconvoluted Spectrum of the Heavy Chains in BiopharmaLynx y p y
The difference between The difference between the CONTROL and CHECK sample is -32.3 D h h iCONTROL Da per heavy chain.
This corresponds to
CONTROL
papproximately -64.6 Da in the intact antibody of the CHECK sample the CHECK sample when compared with the CONTROL antibody.
CHECK
©2011 Waters Corporation 18
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Glycan Characterization
ACQUITY UPLC H-Class Bio with FLR detectionQ
BEH Glycan Column
Released glycans, 2-AB Labelledg y ,
©2011 Waters Corporation 19
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HILIC-FLR-MS analysis of 2-AB labeled released glycansg y
Biosimilar glycans were qualitatively consistent with the innovator mAb therefore differences are not due to glycoforms
©2011 Waters Corporation 20
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Confirmation of SequenceqBy UPLC-MSE of Trypsin Digest of Control and
Check Samples With Data Processed by Biopha maL n 1 2BiopharmaLynx 1.2
©2011 Waters Corporation 21
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Company X Samples and Analysis for Peptide Mapp p
2 samples – CONTROL (reference) and CHECK (copy)
RapiGest-assisted 4-hour tryptic digestion
ACQUITY UPLC separation (BEH130 C18 column)
MSE detection – for simultaneous qualitative & quantitative analysis
Data Interpretation performed by BiopharmaLynx
©2011 Waters Corporation 22
—CONTROL mAb Light Chain (LC) and Heavy Chain (HC) sequences loaded
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Chromatograms of Control and Check Samplesp
CONTROL
CHECK
©2011 Waters Corporation 23
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Sequence CoverageLight Chaing
Coverage Map for Light Chains for CONTROL and
©2011 Waters Corporation 24
g p gCHECK samples is identical (100%)
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Mirror View of HT34-35s in Biopharmalynx Processed MS tracep y
HT34-35 in CONTROL sample
Missing peptide Unknown peak in CHECK
Missing peptide in CHECK sample
©2011 Waters Corporation 25
CHECK sample
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Mirror View of HT35s in Biopharmalynx Processed dataProcessed data
HT35 i C t l S lHT35 in Control Sample
UnknownMissing peptide Unknown peak in Check S l
Missing peptide in CHECK sample
©2011 Waters Corporation 26
Sample
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MSE Spectra of Control mAb HT35 (EEMTK) and HT34-35 (EPQVYTLPPSREEMTK)
T35 (EEMTK) Control Sample Fragment Ion Data
MSE collects all the exact mass precursor and mass precursor and fragment ion data for every peak
( ) l lT34‐35 (EPQVYTLPPSREEMTK) Control Sample Fragment Ion Data
©2011 Waters Corporation 27
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MSE Spectra of Control mAb HT35 (EEMTK) and HT34-35 (EPQVYTLPPSREEMTK)
T35 (EEMTK) Control Sample Fragment Ion Data
( ) l l
BiopharmaLynx automatically interprets the T34‐35 (EPQVYTLPPSREEMTK) Control Sample Fragment Ion Datainterprets the MSE data and provides
sequence confirmation
©2011 Waters Corporation 28
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MSE Spectra of Check mAb HT35 (DELTK) and HT34-35 (EPQVYTLPPSRDELTK)
T35 (DELTK) Check Sample
T34 35 (EPQVYTLPPSRDELTK) Check SampleSequence confirmation T34‐35 (EPQVYTLPPSRDELTK) Check Sample confirmation of unknown peaks in peaks in CHECK sample
©2011 Waters Corporation 29
p
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Conclusions regarding Datag g
Primary amino acid sequence is different between CONTROL and CHECK
3-amino acid stretch where two amino acids are different and resultant mass difference is 32Dadifferent and resultant mass difference is 32DaEEMTK vs DELTK
Clone appears to have been manufactured using the sequence indicated in Drugbank which is different to the CONTROL mAbdifferent to the CONTROL mAb
A simple LCMSE peptide map saved much time and mone in a oiding scale p fo that clone
©2011 Waters Corporation 30
money in avoiding scale-up for that clone
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Simultaneously Confirming Sequence, Identifying y g q y gPTMs and Quantifying PTMs with UPLC-MSE of
Trypsin Digest of Control and Check Samples With D t P d b Bi h L 1 2 Data Processed by BiopharmaLynx 1.2
©2011 Waters Corporation 31
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Identifying PTMs with BiopharmaLynxy g p y
Scrambled disulfidesdisulfides
©2011 Waters Corporation 32
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Identifying PTMs with BiopharmaLynxy g p y
List of allowed fixed
List of available
or variable modifiers
modifiers –custom
d f
©2011 Waters Corporation 33
modifiers can be added
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Chromatograms of Control and Check Samplesp
CONTROL
CHECK
©2011 Waters Corporation 34
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Automated PTM identification & quantification of PTMs e.g. HT21 (DTLMSIR) g ( )
CONTROL: 9% M-oxidized HT21Unmodified
CHECK: 18% M-oxidized HT21
Unmodified HT21
©2011 Waters Corporation 35
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Summaryy
Routine CharacterizationRoutine Characterization
— UPLC/MS on intact and reduced proteins
— UPLC with FLR detection on released glycans
— UPLC/ MSE analysis of peptide map
S ti f tid ACQUITY UPLC o Separation of peptide map on ACQUITY UPLC
o MSE data acquisition mode to get the exact mass precursor and fragment ion data on every p g ydetectable peak across an entire chromatogram with a single analysis
A t t d d t i ith Bi h L
©2011 Waters Corporation 36
— Automated data processing with BiopharmaLynx
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Search www.waters.com for:
— Rapid comparison of a candidate biosimilar to an innovator monoclonal antibody with advanced LC and MS techniques
— Development of Mass Spectrometric and Informatics Workflows for the Development of Mass Spectrometric and Informatics Workflows for the Automated Assessment of Biosimilarity for a Candidate BiosimilarAntibody
— Fast and Automatic Mapping of Disulfide Bonds in a Monoclonal A tib d i SYNAPT G2 HDMS d Bi h L 1 3 Antibody using SYNAPT G2 HDMS and BiopharmaLynx 1.3
— Comprehensive and Routine Characterization of Proteins and Peptides using an Integrated Waters LC/MS Workflow
— High Sequence Coverage Peptide Mapping of a Monoclonal Antibody High Sequence Coverage Peptide Mapping of a Monoclonal Antibody with UPLC/MSE
— Application Solutions for Biopharmaceuticals: A Focus on Protein Therapeutics
— RapiGest SF— ACQUITY UPLC H-Class Bio— BiopharmaLynx
X G2 QT f
©2011 Waters Corporation 37
— Xevo G2 QTof
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Acknowledgementsg
Scott Berger
Asish Chakroborty
Weibin Chen
St John SkiltonSt John Skilton
©2011 Waters Corporation 38