Tag: Proteogenomic

QUILTS 2.0 – Proteogenomic Data Integration tool

QUILTS 2.0

:: DESCRIPTION

QUILTS is a tools for creating sample specific protein sequence databased. It uses genomic and transcriptomic information to create comprehensive sample specific protein database that supports the identification of novel proteins, resulting from single nucleotide variants, splice variants and fusion genes.

::DEVELOPER

Laboratory of Computational Proteomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2015 Dec 2. pii: mcp.M115.056226.
An analysis of the sensitivity of proteogenomic mapping of somatic mutations and novel splicing events in cancer.
Ruggles KV et al.

Peppy – Proteogenomic, Proteomic search tool

Peppy

:: DESCRIPTION

Peppy: a fully integrated, proteogenomic mapping software tool. Peppy generates a peptide database from genome files, tracks peptide loci, matches peptides to MS/MS spectra, assigns scores to those matches, and tracks score distributions to find E-Values. To determine false discovery rate thresholds, Peppy automatically generates a decoy database from the original genome files and repeats the entire search process.

::DEVELOPER

The Giddings Lab at Boise State

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 Peppy

:: MORE INFORMATION

Citation

Peppy: proteogenomic search software.
Risk BA, Spitzer WJ, Giddings MC.
J Proteome Res. 2013 Jun 7;12(6):3019-25. doi: 10.1021/pr400208w.