PEAKS AB Software

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PEAKS AB - De Novo Antibody Sequencing Software

Key Features:

  • Automated de novo antibody sequencing
  • Quantification of modifications and variants
  • QC/QA of antibody production
  • Comprehensive report generation

Automated de novo Antibody Sequencing

PEAKS AB Software - de novo Antibody Sequencing


Monoclonal antibodies have a wide range of applications in biochemical analyses, medical research, diagnostics and therapeutics. The protein sequence of an antibody (Ab) encodes critical information for its structure and function. When cDNA or the hybridoma cell line is not available, de novo protein sequencing of an antibody can help.

PEAKS AB Software is a platform for de novo antibody sequencing and the characterization of modifications and sequence variants by using liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS). PEAKS AB software also supports characterization of post-translational modifications (PTMs) and variants for research discovery and quality control purposes.

Software Overview

 

 

Antibody protein sequences were obtained from the antibody de novo peptide sequences. The confident de novo sequence tags, which have direct fragment ion proof, were assembled into antibody sequences. The de novo View shows the map of de novo peptide sequence tags.

de novo View

PEAKS AB Software - de novo Antibody Sequencing View

 

 

PEAKS AB provides comprehensive peptide maps, including:

  • insight into full sequence information
  • displaying each amino acid with confidence from direct fragment ions
  • post translational modifications (PTMs)
  • amino acid substitutions (sequence variants)

Peptide Mapping View

PEAKS AB Software - Antibody Peptide Mapping

For each sequence position with modifications, the modified and native peptide forms, along with their chromatrogram are listed for quantitative viewing.

Post-translational Modifications (PTMs) Analysis

PEAKS AB Software - de novo Antibody Sequencing PTM Analysis


Sequence Variant View highlights amino acid substitutions and/or truncations which may result from erroneous transcription of complementary DNA.

Sequence Variant View

PEAKS AB Software - de novo Antibody Sequencing Variant Analysis

With the enhanced “Peptide Mapping” function, PEAKS AB Software can compare annotated chromatograms between different samples. Possible sequence variants will be illustrated to facilitate the product quality control or any other related antibody studies.

As shown in the image to the right, blue peaks in the annotated chromatogram denote the signals that can be mapped to peptides from reference proteins, and the red peaks denote sequence variants or any product-related impurities.

PEAKS AB Software - De Novo Antibody Sequencing Potential Variants/Impurities

Algorithm

PEAKS AB software directly sequences the antibody protein using high resolution LC-MS/MS data sets from orthogonal enzyme digests. It performs de novo peptide sequencing first, and assembles the confident sequence tags into antibody sequences.

PEAKS AB Software - de novo Antibody Sequencing Workflow

Report Generation

  1. Antibody Sample Description
  2. Abbreviations
  3. Experimental Procedure
  4. Antibody Heavy Chain
    1. Amino Acid Sequence
    2. Peptide Mapping at 0.1% of FDR at Peptide-Spectrum Level
    3. Typical Peptides Selected for Variable Region
    4. Ile/Leu Differentiation
  5. Antibody Light Chain
    1. Amino Acid Sequence
    2. Peptide Mapping at 0.1% of FDR at Peptide-Spectrum Level
    3. Typical Peptides Selected for Variable Region
    4. Ile/Leu Differentiation

PEAKS AB Software - de novo Antibody Sequencing Report