Scaffold Variants

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Proteogenomics: genomics and proteomics

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