Software Tools

The CPTAC program develops new approaches to elucidate aspects of the molecular complexity of cancer made from large-scale proteogenomic datasets, and advance them toward precision medicine.  Part of the CPTAC mission is to make data and tools available and accessible to the greater research community to accelerate the discovery process.

Bioinformatics support is often required for analyses of the massive datasets used and generated through the experimental pipelines employed by CPTAC centers of excellence.  To facilitate the processes of mining, visualizing, analyzing, and using such datasets, OCCPR has curated a collection of analytical tools.  OCCPR/CPTAC does not endorse any specific tool.  However, this list gives researchers a gateway to access many tools that are useful for analyzing and/or visualizing large-scale proteomic and proteogenomic datasets generated through high-throughput screens and other assays.


MassQC
MassQC is an online Quality Control Tool that serves to diagnose liquid chromatography-mass spectrometry instrument hardware to ensure the instrument is running in a reproducible manner.  Using data from CPTAC inter-lab studies, the National Institute of Standards and Technology developed a number of metrics to assess instrument performance and ProteomeSoftware subsequently built a graphical user interface to commercialize this tool.

Key Publication: PMCID: PMC2918158; Journal of Biomolecular Techniques
Access: http://massqc.proteomesoftware.com

MSFragger
MS Fragger is an ultrafast database search tool that uses a fragment ion indexing method to rapidly perform spectra similarity comparisons.  MSFragger empowers the open database search concept for comprehensive identification of peptides and all their modified forms to uncover differences in modification rates across experimental samples and conditions.

Key Publication: PMID: 28394336; Nature Methods
Access: http://www.nesvilab.org/software.html

NetGestalt – Gene Network Browser
NetGestalt is a data integration platform that allows the simultaneous presentation of large scale experimental and annotation data from many sources in the contest of a biological network to facilitate data visualization, analysis and interpretation and hypothesis generation.

Key Publication: PMID: 23807191; Nature Methods
Access: http://www.netgestalt.org

ProteoWizard
ProteoWizard Library and Tools are a set of modular and extensible cross-platform tools and software libraries that facilitate proteomics data analysis.  The libraries enable rapid tool creation by providing a robust, pluggable development framework that simplifies and unifies data file access, and performs standard chemistry and LCMS dataset computations.

Key Publication: PMID: 18606607Bioinformatics
Access: http://proteowizard.sourceforge.net

Skyline
Skyline is an application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM - Targeted MS/MS and DIA/SWATH) and targeted DDA with MS1 quantitative methods and analyzing the resulting mass spectrometer data.

Key Publication: PMID: 20147306; Bioinformatics
Access: https://skyline.ms/project/home/software/Skyline/begin.view