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...

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Bibliographic Details
Published in:Journal of proteome research 2015-05, Vol.14 (5), p.2255-2266
Main Authors: Nagaraj, Shivashankar H, Waddell, Nicola, Madugundu, Anil K, Wood, Scott, Jones, Alun, Mandyam, Ramya A, Nones, Katia, Pearson, John V, Grimmond, Sean M
Format: Article
Language:English
Subjects:
Cell Line, Tumor
Chromosomes, Human - chemistry
Colorectal Neoplasms - genetics
Databases, Protein
Humans
Mass Spectrometry
Molecular Sequence Annotation
Open Reading Frames
Pancreatic Neoplasms - genetics
Proteome - genetics
Proteomics - methods
Proteomics - statistics & numerical data
Sequence Analysis, RNA
Software
Transcriptome
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Description
Summary: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.
ISSN:1535-3893
1535-3907
DOI:10.1021/acs.jproteome.5b00029