Vermillion et al., J. Proteome Res.  2015, 14, 4792-4804.

  • Hibernation proteogenomics in 13-lined ground squirrel.
  • Study quantified 2007 cardiac proteins and over 350 peptide sequences derived from previously uncharacterized protein products.
  • This allows for improved genomic annotation of this non-model organism, as well as quantification allows insights into novel cardioprotective mechanisms used during hibernation.

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Jagtap et al., J Proteome Res. 2014 13(12): 5898–5908.

  • Extended the Galaxy bioinformatics framework to facilitate proteogenomic analysis.
  • The customized Galaxy-based workflow includes automated, batch-mode BLASTP searching and a Peptide Sequence Match Evaluator tool, both useful for evaluating the veracity of putative novel peptide identifications.
  • 53 peptides corresponding to novel proteoforms were identified.
  • 14 of these peptides were mapped as alternative translating frames in the PRB1 and PRB2 genes on chromosome 12.