Researchers

If you are on the cutting edge of protein science and proteomics research, Scaffold is for you!

Scaffold validates, organizes, and interprets proteomics search data, so you can more easily manage large amounts of data, compare samples, and search for protein modifications.

  • View patterns of differential expression across samples
  • Display probability scores, spectrum counts, peptide counts and more
  • Search data repeatedly to broaden or refine your findings
  • Examine each spectrum, protein sequence, and fragmentation table
  • Analyze combined results from multiple search engines
  • Protein lists can be sorted and filtered in various ways:
  • Probabilities, number of peptides, FDR
  • Custom filters: peptide sequence, protein name, PTMs
  • Filter by taxonomy and Gene Ontology
  • Hide, star, and sort proteins
  • Extensive export options
  • View GO term pie charts by GO domain
  • Compare GO expression across sample categories
  • Sort and filter protein list by GO terms
  • Annotate with custom Ontologies
  • Customize to highlight GO terms of interest
  • Use nested tree for greater detail
  • Access detailed protein information with direct link to NCBI
  • Examine expression levels with multiple metrics including:
  • Spectral counting, Precursor Intensity (AUC), TIC
  • View protein and peptide changes in time-course experiments
  • View category differences through Venn diagrams
  • Evaluate significance through parametric statistics
  • Assess advanced quantitation in Scaffold Q+ and Scaffold Q+S:
  • Non-parametric statistics and permutation testing
  • Bonferroni Correction
  • Intensity weighting and error estimation
  • Easily describe experimental methods
  • Automatically capture search engine and analysis parameters
  • Export figures and graphics needed for publication
  • Export to PRIDE through standard mzIdentML format
  • Share data with the free viewer
  • Set password-protected settings

Try Scaffold now with a 14-day free evaluation.