PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization

We describe PGTools,
an open source software suite for analysis
and visualization of proteogenomic data. PGTools comprises applications,
libraries, customized databases, and visualization tools for analysis
of mass-spectrometry data using combined proteomic and genomic backgrounds.
A single command is sufficient to search databases, calculate false
discovery rates, group and annotate proteins, generate peptide databases
from RNA-Seq transcripts, identify altered proteins associated with
cancer, and visualize genome scale peptide data sets using sophisticated
visualization tools. We experimentally confirm a subset of proteogenomic
peptides in human PANC-1 cells and demonstrate the utility of PGTools
using a colorectal cancer data set that led to the identification
of 203 novel protein coding regions missed by conventional proteomic
approaches. PGTools should be equally useful for individual proteogenomic
investigations as well as international initiatives such as chromosome-centric
Human Proteome Project (C-HPP). PGTools is available at http://qcmg.org/bioinformatics/PGTools.