Antibody Protein Analysis with Valens™
Direct protein analysis is critical to antibody characterization, including determining the primary amino acid sequence and any post-translational modifications that are present. Valens™ is a mass spectrometry-powered service to provide direct information about the antibody protein. We offer two services using Valens™; antibody protein sequencing to recover the full antibody sequence when no source cell is available and antibody sequence confirmation to determine if the produced antibody matches the intended gene sequence.
Valens™ builds upon two patented technologies developed at the University of California – San Diego.
Valens™ uses the patented spectral networking paradigm, which proposes that any single mass spectrum contains incomplete information and interpreting many spectra in concert results in higher antibody sequencing accuracy. We’ve seen the principles of spectral networking in action for nearly 10 years. The approach allows us to recover the sequence of antibodies from any species and any level of divergence from the germline.
For antibody sequence confirmation, Valens uses the generating function approach to score mass spectrum matches to protein sequences.
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Resources and Publications
Valens builds on over a decade of algorithm development including ideas invented at the University of California – San Diego Center for Computational Mass Spectrometry. For background on our methods check out these publications:
- Guthals, et al. (2012). Shotgun protein sequencing with meta-contig assembly. Mol Cell Proteomics, 11, 10:1084-96.
- Castellana, NE, et al. (2011). Resurrection of a clinical antibody: template proteogenomic de novo proteomic sequencing and reverse engineering of an anti-lymphotoxin-α antibody. Proteomics, 11, 3:395-405.
- Castellana, NE, et al. (2010). Template proteogenomics: sequencing whole proteins using an imperfect database. Mol Cell Proteomics, 9, 6:1260-70.
- Bandeira, N, et al. (2007). Shotgun protein sequencing: assembly of peptide tandem mass spectra from mixtures of modified proteins. Mol Cell Proteomics, 6, 7:1123-34.