Scaffold PTM

What’s new in Scaffold PTM 3.0

  • Label Free Quantitation
    It is now possible to load precursor intensity ratios exported from Scaffold Q+/Q+S into Scaffold PTM .
  • Modification Site Quantitation Normalized by Protein Expression with Scatter Plot
    Normalize differences in PTM expression by corresponding differences in protein expression. Samples must be analyzed in parallel for protein and PTM expression using Scaffold Q+/Q+S.
  • Statistical Analysis of PTM Site Quantitation Ratios with Volcano Plot
    This feature provides a confidence assessment that the expression levels are significantly different at any level of summarization, with or without protein expression normalization.
  • Motif Analysis of Selected Peptides
    This new extension of the Scaffold PTM motif search allows users to define a set of PTM peptides to be searched against a custom-defined background, and includes the option to use the remaining peptides as the background.
  • Publish View
    This view provides information about the data loaded into Scaffold PTM and the analyses performed.
  • Gene Ontology Annotations
    GO terms may now be added to the PTM List table.
  • Modification Filtering
    Select which modification types should be displayed and export filtered reports.