PGTools – a software suite for proteogenomics data analysis and visualization

Researchers from the Queensland Centre for Medical Genomics have developed PGTools, an open source software suite for analysis and visualization of proteogenomic data. PGTools is comprised of 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 datasets using sophisticated visualization tools.

The researchers experimentally confirm a subset of proteogenomic peptides in human PANC-1 cells and demonstrate the utility of PGTools using a colorectal cancer dataset 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).




Availability – PGTools is available at

Nagaraj SH, Waddell N, Madugundu AK, Wood S, Jones A, Mandyam RA, Nones K, Pearson JV, Grimmond SM. (2015) PGTools: a software suite for proteogenomics data analysis and visualization. J Proteome Res [Epub ahead of print]. [abstract]

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