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COMPARATIVE WORKFLOW INTRODUCTION Sequence variants (SV) are unintended amino

acid substitution in the primary structure of proteins, and are classified as product-related impurities. The presence of sequence variants may pose concerns regarding bioactivity, stability, and immunogenicity.

Sequence variants are usually present at very low-level in a therapeutic protein. From an analytical stand point, the detection and characterizing SV in a complex digest mixture that is several orders of magnitude more concentrated, remains a significant challenge.

A comparative analytical strategy is presented for the identification of SV peptides among multiple samples. The strategy was developed and tested by analyzing monoclonal antibody samples which contain spiked synthetic peptides with amino acid substitutions.

An additional strategy is being developed to identify SV peptides in a single sample by using UNIFI 1.8 sequence variants workflow. The Biopharmaceutical Platform Solution with UNIFI provides a dedicated DDA peptide mapping workflow, which streamlines data acquisition, processing, and report generating for routine peptide mapping as well as SV analysis.

IDENTIFYING SEQUENCE VARIANTS BY INTEGRATED MASS SPECTROMETRIC AND INFORMATICS WORKFLOWS

Liuxi Chen1; Henry Shion1; Stephane Houel1, Ying Qing Yu1; Barry Dayson2; Rose Lawler1; Weibin Chen1 1Waters Corporation, Milford, MA 01757, USA, 2Waters Corporation, Stamford Avenue, Altrincham Road, Wilmslow, SK9 4AX, UK

METHODS Sample Preparation: For comparative workflow: Three tryptic digests of Trastuzumab (Digest A, B or C) were prepared separately, each at a final concentration of 2.40 pmol/µL. In digest C, two synthetic peptides of T14 containing substituted amino acid residues (see Table 2) were spiked at 2.40 fmol/µL. For single sample workflow: two synthetic peptides containing substituted amino acid were spiked in to Trastuzumab digests (1.65 pmol/µL) at various level (0.5%, 1%, 2.5%, 5%, 10%)

LC/MS: LC: ACQUTIY UPLC H-Class System Column: ACQUITY UPLC BEH C18, 300Å, 1.7 μm, 2.1

x 100 mm (p/n 186003686) Column temperature: 65 oC Mobile phase: A. 0.1% Formic acid in water B. 0.1% Formic acid in acetonitrile MS: Vion IMS QTof /Synapt G2-Si Data Acquisition: LC/MSE Mode: ESI positive mode Capillary Voltage: 2.5 kV Cone Voltage: 80 V Source Temperature:100 °C Desolvation Temperature: 250 °C Scan Rate: 0.5 sec Mass Range (m/z): 100-2000 Informatics: UNIFI 1.8 Progenesis QI

CONCLUSION Comparative workflow: Progenesis QI can detect and quantify low abundance sequence variant

peptides (0.1%) in a monoclonal antibody digest. HD-DDA spectra of sequence variant peptides loaded on a 2.1 mm column at

7 femtomoles provides enough information to pin-point the substitution. UNIFI single-sample workflow: An integrated workflow is developed in UNIFI 1.8 to identify and quantify SV

peptides; Two SV peptides spiked in a Trastuzumab digest at 0.5% level were

successfully identified.

• Impact clinical safety and efficacy• Product related impurity• Present in every recombinant

biotherapeutics• Critical for cell line development,

process optimization, quality control• Need to be closely monitored

Val

ues

• Present at very low level• Sensitivity and dynamic range• Relatively high number of false

positive match• Manual data evaluation needed

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Peptide Sequence1:T14 (N9S) VDNALQSGSSQESVTEQDSK2:T37 (N14S) GFYPSDIAVEWESSGQPENNYK

UNIFI WORKFLOW FOR A SINGLE SAMPLE

Data AcquisitionPeptide Mapping MSE or

FastDDA MS/MS

Data ProcessingPeptide Mapping with

Defined Error Tolerance

Review and Reporting Peptide Mapping with SVSAu

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ated

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UNIFI 1.8 Peptide Mapping & Sequence Variant Workflow

Scoring Bayes’theorm Best match returned

Fragment Ion ConfirmationIn-silico fragmentation CID or ETD Define fragment match tolerance

parameter

Sequence Variant SearchingMass match Define peptide match tolerance

Sequence Variant GenerationBlosum 62 matrix Define substitution likelihood Define max variants per peptide

Source Peptide Component Generation Digest products Missed cleavages Semi-digest products Fixed and variable mods

Sequence Variant Search Algorithm in UNIFI 1.8

Sequence Variant Search - Method Setup in UNIFI 1.8

UNIFI Search Review

Sequence variant peptides identified from the work-flow are provided in compo-nent summary and labeled (highlighted) against the protein sequence

1:T14 (N9S)

2:T37 (N14S)

1:T14 (N9S) 2:T37 (N14S)

Extracted ion chromatogram of the identified sequence variant peptides overlay with LC/MSE chromatogram of the entire run.

0.5%1.0%

2.0%

5.0%

10%

0.5%1.0%

2.0%

5.0%

10%

Summary plots of MS intensity of SV peptides at different spiked-in levels track the abundance variation of SV peptides among samples.

1:T14 (N9S) 2:T37 (N14S)