Proteogenomics uses mass spectrometry data to experimentally validate gene products and to assist in the process of genome annotation and comparison. We develop tools and methods to facilitate use of proteomics data for this application.


  • Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome.

    Brosch M, Saunders GI, Frankish A, Collins MO, Yu L et al.

    Genome research 2011;21;5;756-67

  • Accurate and sensitive peptide identification with Mascot Percolator.

    Brosch M, Yu L, Hubbard T and Choudhary J

    Journal of proteome research 2009;8;6;3176-81

  • Interrogating the human genome using uninterpreted mass spectrometry data.

    Choudhary JS, Blackstock WP, Creasy DM and Cottrell JS

    Proteomics 2001;1;5;651-67