Antibody CDR3 Sequences from timsOmni Mass Spectrometry

A prototype timsOmni mass spectrometer enabled full CDR3 sequence annotation for paired IgG heavy and light chains using electron-based fragmentation. The dataset, 14.8 KB in size, was created by Simon Ollivier and published on figshare in April 2026. It serves as proof-of-concept data for protein-centric proteomics.

Use Cases

• Benchmark CDR3 sequence annotation algorithms using the provided electron-induced dissociation fragment ion data.
• Analyze the performance of low- and high-energy electron fragmentation on native-like Fab precursor ions.
• Study the generation of (a, x) and (c, z) fragment ion pairs for enhancing sequence coverage in antibody analysis.

Strengths

• Data demonstrates a proof-of-concept for a novel prototype instrument (timsOmni).
• Focus on a specific, critical immunological feature: the hypervariable CDR3 regions of IgG antibodies.

Limitations

• The dataset is very small at 14.8 KB, indicating limited scope for model training.
• Data is derived from a single prototype instrument, limiting generalizability.
• Specific sample size (row count) and column details are unknown.

Provenance

Source

figshare, authored by Simon Ollivier.

Collection Method

Generated using a prototype timsOmni mass spectrometer with electron-induced dissociation (EID) at ~35 eV on native-like Fab ions.

Freshness

Last updated April 2026.