Innovation with IntegrityMass Spectrometry

Biopharmaceutical Characterization

N/C-TerminalSequencing

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100% Sequence Coverage in 1 Minute

N-terminal sequencing is traditionally performed by Edman Sequencing. However, Edman is a time consuming and expensive technique (3 hours & $ 100’s) for a sequence of 5 amino acids. Edman is also unable to deliver sequence information from blocked N-termini and the C-terminus, which is essential for complete characterization.

ICH Q6B guidelines suggest “new analytical tech-nology and modifications to existing technology are continually being developed and should be utilized when appropriate”.

Top-Down Sequencing (TDS) by mass spectrometry (MS) is a perfect example of the adaption of an already well established characterization technique. TDS delivers up to 100% sequence coverage in 1 minute through fragmentation of the intact species.

Top-Down Sequencing – Key Advantages

C-terminal sequencing Analyze blocked N-termini No protein digestion required Modifications remain in situ Up to 100% sequence coverage from a single analysis

1 minute analysis &

$ 0.10 per sample

Ultra rapid product confimation of 150 kDa (MOPC21) antibodyTDS – Automated Workflow

Analyze Intact /Subunit Mass

Analyze TDS

Compare with

Automated Reporting

An intact mass can be obtained in 5 seconds confirming either the correct mass or the presence of size variants.

Obtain single TDS spectrum from mAb intact or subunit (Fd, Fc/2 or LC)

TDS offers rapid,robust and inex-pensive characterization. It provides extensive N & C terminal sequence information without protein digestion in less than 1 minute.

Reference Standard Sequence

Confirm sequence match Matching residues highlighted

Bruker’s proprietary software

With automated reporting throughBioPharma Compass, TDS quicklyturns data into reliable reports ready for submission to regulatory bodies.

Top-Down Sequencing (TDS)

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Identify and Validate Sequence Variations and Modifications with T3-Sequencing

Selected TDS references and their application

Application of TDS Reference

Antibody primary structure assessment Ayoub D. et al. MAbs. 2013 Sep/Oct;5(5):699-710.

Protein isoform distinction Calligaris D. et al. Anal Chem. 2010; 82(14):6176-84.

PEGylation site determination Yoo C. et al. J Am Soc Mass Spectrom. 2009 Feb;20(2):326-33.

Disulphide bridged venom peptides Quinton L. et al. J.Prot.Res. 2007 Aug; 6(8): 3216-23

De novo protein sequencing Resemann A et al. Anal Chem. 2010 Apr 15;82(8):3283-92.

N&C-terminal verification T3-sequencing Suckau D et al. Anal Chem. 2003 Nov 1;75(21):5817-24.

Commercial TDS Service Provider http://www.alphalyse.com/fileadmin/Alphalyse/PDF/N-_and_C-terminal_protein_sequencing_20090310.pdf

Suspected modifications or sequence alterations can be confirmed with MALDI T3-Sequencing. T3-Sequencing is a Bruker patented technique whereby a fragment ion from the TDS spectra is selected for further fragmentation.

In this example an intact murine IgG was used for targeted sequencing of the HC´s N-term -LC separation was not used!

The c21-ion was fragmented resulting in a series of b and y type ions. A Mascot search of this T3-spectrum identified the N-terminus of the HC´s V region and confirmed pyro-glutamylation.

T3 Mascot search Pyro-QVQLQQSGAELARPGASKLS

The Power of TDS

Applied to real world monoclonal antibodies

MAbs and related products are the fastest growing class of human therapeutics. Characterization of these biotherapeutics is essential due to the inherent variability of bioproduction to ensure drug potency and safety and also to comply with regulatory authorities.

TDS can be applied to the analysis of any protein or peptide based product including mAbs, bi- and multi-specific antibodies, Fab fragments, oligoclonal

antibodies antibody-drug conjugates and alternative protein scaffolds1.

In 1 minute, a single analysis TDS provides extensive N-, C- and internal sequence information which can confirm an expected sequence or elucidate an unexpected size variant which may be due to post translational modifications (PTMs), amino acid substitutions, non cleaved signal peptides or truncation.

Overview: TDS applied to real world mAbs & protein therapeutics

TDS Achievements Sequence Coverage

mAb/Protein (notes)

• Sequence confirmed• N-term pyroGlu• C-term Lysine clipping

LC = 100%Fc = 100%Fd = 80%

Panitumumab(SS bridge heterogeneity)

• Sequence confirmed• Product related species identified• N-term Methionine deletion• C-term peptide truncation

Protein = 100%Recombinant Tau(plus unexpected species)

• Gene sequence translation from public database & papers is incorrect

• IgZERO glycan identified in situ• A213E Light Chain sequence error

LC = 100%Fc = 100%Fd = 80%

Cetuximab(Fd glycosylation not removable)

• Primary sequence established• N-term pyroGlu• C-term Lysine clipping• Glycan identified in situ

LC = 100%Fc = 100%Fd = 100%

Tocilizumab

LC = Light Chain

1Beck A. Characterization of therapeutic antibodies and related products Anal.Chem.2013; 85 (2): 715-36

Pyro-QVQLQQSGAELARPGASKLS

Biosimilar Development

Panitumumab Example

Biosimilar antibodies are generic versions of marketed antibodies produced through different manufacturing processes and from different clones2.

The European Medicines Agency EMA & the FDA require high similarity between

a biosimilar mAb and its reference product for approval.

TDS is an ideal technique to determine the amino acid sequence and PTMs of Biosimilars delivering up to 100% sequence confirmation in 1 minute.

2Beck A. Biosimilar, biobetter, and next generation antibody characterization by mass spectrometry. Anal Chem 2012; 84:4637-46

Automated TDS Analysis of Panitumumab

Panitumumab, provided by Pierre Fabre, was processed with FabRICATOR® (Genovis) enzyme and reduced producing LC, Fd & Fc/2, which were then separated by HPLC. Fifteen sec fractions were spotted and mixed with sDHB matrix followed by automated TDS analysis and comparison with a reference standard sequence.

• > 90% sequence coverage• N-term pyroGlu, C-term Lys clipping

Analyze Sequence Coverage

Light Chain

100%

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Fd

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Intact Light Chain

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Sequence Confirmation

Cetuximab Example

For the development of biosimilars, availability of the complete amino acid sequence of the originator product is essential. Sequence information can be found in the scientific literature. However, sequence errors do exist and errors have already been reported for several blockbuster antibody therapeutics.

TDS rapidly identified an incorrect gene sequence translation from the published patent of cetuximab at A213E near the LC C-term and confirmed an expected HC C-term Lys clipping. This example highlights the potency of TDS to establish correct antibody sequences3.

3Ayoub D et al. Correct primary structure assessment and extensive glyco-profiling of cetuximab by a combination of intact, middle-up, middle-down and bottom-up ESI and MALDI mass spectrometry techniques MAbs 2013; 5(5):699-710

TDS of Cetuximab Light Chain

Cetuximab processed with FabRICATOR® (Genovis) enzyme and reduced producing LC, Fd & Fc which were then separated by LC, 15 sec fractions spotted and mixed with super-dihydroxybenzoic acid matrix (sDHB ) followed by automated TDS analysis and comparison with a reference standard 1. A213E sequence was confirmed via LC-MS/MS of a Glu-C digest.

LC: Sequence error detected, 100% sequence coverageHC: N-term pyroGlu, C-term Lys clipping; > 90% sequence coverage

Acquire Spectrum

A213E Substitution

Sequence Correct

FNRGEC

LC Sequence Incorrect(+58 Da mas shift detected in C-terminal residues)

FNRGAC Modifications considered

Compare to reference sequence+/- C-term Lys

Compare to modified reference sequence

Product Related Species Identified

Tau recombinant protein Example

Peptide mass mapping is a common MS characterization technique whereby a protein is digested with a specific enzyme resulting in a set of peptides which provide a unique fingerprint capable of identifying a protein from a database.

However, it can be challenging to detect and identify those protein species which are truncated at the N- +/- C-terminus.

Intact mass analysis followed directly by TDS rapidly identifies the presence of truncated protein forms and confirms the correct N- & C-terminus, thus offering a complementary technique to peptide mapping.

Sample provided by M.Novak; Institute of Neu-roimmunology, Slovak Academy of Science, Bratislava

Intact & TDS Analysis of Tau Protein

Product Related Substances XC-terminal truncation; 16647 Da

Product Related Substances YN-terminal met truncation; 25284 Da

ProductRecombinant Tau Protein; 25415 Da

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Establish Primary Sequence for Biosimilar Development

Tocilizumab Example

TDS can be utilized to establish initial sequence information for the development of biosimilar therapeutics, through the generation of a de novo protein sequence tag, which is an extended sequence of amino acids.

This amino acid sequence information can be used to identify a protein using the Basic Local Alignment Search Tool (BLAST) algorithm.

The BLAST algorithm compares a query sequence (user obtained amino acidsequence) with the sequences of millions

of proteins in a protein database. If a sequence match is obtained, the entire protein sequence along with the protein identity can be retrieved.

In this example an unknown therapeutic antibody was identified as Tocilizumab following the generation of sequence tags consisting of a stretch of ≈50 amino-acids from the LC & Fd subunits and a subsequent BLAST search. The Tocilizumab sequence was obtained and served as a reference standard, to confirm the complete protein sequence.

Mab FabRICATOR® (Geno-vis) digestion and reduction followed by LC separation of subunits and mixing with DAN and sDHB matrix and subse-quent TDS analysis. Sequence Tag generated by de novo

Acquire LC & Fd TDS spectra

Light Chain

Fd

Data Quality

Zoom in on c48 ion, showing isotopic resolution, essential for de novo TDS. Obtained with DAN matrix.

BLAST search Tocilizumab identified

≈ 50 amino-acid sequence tag generated from LC & Fd

100% sequence coverage

Compare Tocilizumab sequence with intact mass and TDS of LC, Fc, Fd

• Identification of unknown therapeutic• 100% sequence coverage• N-term pyroGlu• C-term Lys truncation• Abundant glycan identified in situ

Identification of Modifications

Glycosylation & Phosphorylation Examples

During TDS analysis modifications such as glycosylation, phosphorylation, acetylation etc., remain intact delivering unambiguous localization of the modi-fication and facilitating the identification of unexpected modifications.

Potential modifications and their location in the amino acid sequence can be included in the reference sequence and their presence reported during the automated workflow.

β-casein5 phosphoserines RNAse B

Man5 structuremAb-FcIgZERO truncated glycosylation

mAb antibody was treated with IgZERO and FabRICATOR ® to produce Fc fragments with cleaved chitobiose core. β-casein, RNAseB and mAb fragments were mixed with either sDHB or DAN matrix and subjected to automated TDS analysis.

TDS automated workflow including modifications

AnalyzeObtain single MS spectrum from mAb subunit

CompareReference Standard Sequence including modifications

Automated ReportingSequence & Modifications confirmed

Essential Tools for Successful Top-Down Sequencing

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Characterization Strategies

5 second Peptide Mass Fingerprints Amino Acid Sequence, Identity Check & PTMs 5 second Intact Protein Mass

Confirm Correct Product & Detect Impurities 1 minute Top-Down Protein

Sequencing N- / C- terminal Sequencing Patented T3-Sequencing

Confirms unexpected variants LC-MALDI MS/MS

Glycopeptide Identification & Quantitative Assignment

Maximize instrument usage with multiple characterization strategies

Fully AutomatedSoftware BioPharma Compass

Automated acquisition and reporting from peptide maps and N- / C- terminal Sequencing ProteinScape

Combine multiple data sets and visualize in one simple report; maximal sequence coverage & certainty GlycoQuest

Automated detection, localization and identification of glycan isoforms

Automated software for ease of use

InnovativeTechnology

MALDI Perpetual Ion Source Self cleaning source providing maximum performance for every analysis PAN Broadband Resolution

Isotopically resolved top-down sequence readout for more than 100 residues from each terminus Flash Detector

Internal calibration <1ppm; sensitive detection of peptides & proteins >500kDa FlatTop smartbeam Laser

2kHz MS acquisition; minimal sample usage, maximum sensitivity

Innovative technology essential for TDS analysis

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Bruker Daltonik GmbH

Bremen · GermanyPhone +49 (0)421-2205-0 Fax +49 (0)421-2205-103 sales@bdal.de

Bruker Daltonics Inc.

Billerica, MA · USA Fremont, CA · USAPhone +1 (978) 663-3660 Phone +1 (510) 683-4300 Fax +1 (978) 667-5993 Fax +1 (510) 687-1217 ms-sales@bdal.com cam-sales@bruker.com

www.bruker.com

For research use only. Not for use in diagnostic procedures.

“The great advantage of this technique is that it is the only technique that can analyze the N- and C-termini directly on the intact protein. This is important for sequence verification and quality control of biopharmaceuticals, especially for monoclonal antibodies with 4 different termini, frequent C-terminal trunca-tions and N-termini that are partially modified by pyroglutamic acid and blocked for Edman sequencing.”

As CRO specialized in mass spectrometric protein analyses, Alphalyse has provided MALDI TDS analysis to hundreds of researchers world wide, says COO Ejvind Mortz.