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Proteomics Computational Tools

To advance precision medicine by understanding aspects of the molecular complexity of cancer, the CPTAC program develops novel approaches to process large-scale proteogenomic data sets.

An important part of the CPTAC mission is to make data and tools available and accessible to the greater research community. Here, OCCPR has curated a collection of computational tools developed and/or utilized by CPTAC for processing and analysis of proteogenomic data. Although NCI does not endorse any specific tool, this list gives researchers a gateway to access bioinformatic tools that are useful for analyzing and/or visualizing large-scale proteomic and proteogenomic datasets generated through high-throughput screens and other approaches.

Data Access

  • GDC
    Harmonizing DNA sequences from CPTAC whole genome sequencing, whole exomes sequencing, and RNAseq using GDC pipelines.
  • PDC
    Making cancer-related proteomic datasets easily accessible to the public and facilitating multi-omic integration through interoperability with other resources.
  • TCIA
    Hosting both the radiology and pathology imaging data generated by CPTAC samples.

Data Processing and QC

  • CDAP
    The CPTAC Common Data Analysis Platform for LC-MS/MS data.
  • 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.
  • MS-PyCloud
    MS-PyCloud is a cloud computing-based pipeline for proteomic and glycoproteomic data analysis. The major components of this pipeline include data file integrity validation, MS/MS database search for spectral assignments to peptide sequences, false discovery rate estimation, protein inference, quantitation of global protein levels, and specific glycan-modified glycopeptides as well as other modification-specific peptides such as phosphorylation, acetylation, and ubiquitination.
  • MSInspector
    MSInspector is a Python program for quality evaluation of the five assay characterization experiments outlined by CPTAC Assay Portal guidance document. MSInspector enables researchers to test their Skyline files for statistical calculation and data visualization through the built-in R scripts. The report file describes the details of any errors.
  • OmicsEV
    Comparing and evaluating data matrices generated from the same omics dataset using different tools, algorithms, or parameter settings.
  • Panorama
    Panorama is a web application for storing, sharing, analyzing, and reusing targeted assays created and refined with Skyline. Panorama allows laboratories to store and organize curated results contained in Skyline documents with fine-grained permissions, which facilitates secure sharing of published and unpublished data via a web-browser interface.
  • Philosopher
    A complete toolkit for shotgun proteomics data analysis. Philosopher is part of FragPipe.
  • Skyline
    Skyline is a freely available, open-source Windows client application for building Selected Reaction Monitoring (SRM) / Multiple Reaction Monitoring (MRM), Parallel Reaction Monitoring (PRM), DIA/SWATH and targeted DDA quantitative methods and analyzing the resulting mass spectrometer data. Its flexible configuration supports All Molecules.

Data Analysis

Databases and Web Portals

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