Proteogenomics: genomic and proteomic data

Scaffold Variants enables the detection of genetic variation directly from your MS/MS proteomic data and will help you identify and confirm which mutations are translated and important to your experiments.

Scaffold Variants currently accepts MS/MS data files from label-free and TMT-labeled studies and supports the identification of missense mutations (from amino acid substitutions.) Scaffold Variants makes an ideal tool for your experiments which may have paired genomic and proteomic data (proteogenomics), providing multi-omics confirmation of a mutation.

Sonme of the main capabilities of the software are listed below:

  • Generation of search databases from user-supplied genomic variant call data in VCF format for sample- or cohort-specific searching, also compatible with COSMICTM (using QUILTS)
  • The use of dbSNP and ClinVar as pre-built search databases
  • Integration of Comet as a search engine
  • The integration of Percolator for FDR re-scoring based on important features of the data
  • A powerful new variant scoring system for discrimination of variant peptide spectra from close homologs
  • Spectrum visualizations for manual validation

FREE Evaluation

To register for a free 14 day trial of Scaffold or to learn more, please visit the Proteome Software web site – Free Trial.

Further Information

See Downloadable Resources for further technical information or visit Proteome Software Documentation.

Please Contact us if you can not find the information your require or would like a quotation.