Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework

Proteogenomics combines large-scale
genomic and transcriptomic
data with mass-spectrometry-based proteomic data to discover novel
protein sequence variants and improve genome annotation. In contrast
with conventional proteomic applications, proteogenomic analysis requires
a number of additional data processing steps. Ideally, these required
steps would be integrated and automated via a single software platform
offering accessibility for wet-bench researchers as well as flexibility
for user-specific customization and integration of new software tools
as they emerge. Toward this end, we have extended the Galaxy bioinformatics
framework to facilitate proteogenomic analysis. Using analysis of
whole human saliva as an example, we demonstrate Galaxy’s flexibility
through the creation of a modular workflow incorporating both established
and customized software tools that improve depth and quality of proteogenomic
results. Our customized Galaxy-based software includes automated,
batch-mode BLASTP searching and a Peptide Sequence Match Evaluator
tool, both useful for evaluating the veracity of putative novel peptide
identifications. Our complex workflow (approximately 140 steps) can
be easily shared using built-in Galaxy functions, enabling their use
and customization by others. Our results provide a blueprint for the
establishment of the Galaxy framework as an ideal solution for the
emerging field of proteogenomics.