Scaffold Software Comparison

We can divide Scaffold software tools into two -omics subcategories: proteomics (both DDA and DIA) and small molecule analysis. Two of our programs, Scaffold Elements and Scaffold DIA, are end-to-end tools. That is, they process and search raw mass spectrometry data as well as provide visualization, quantitation and statistical analysis. In contrast to those, we also have programs for the post-processing of popular proteomics search engine data including: Mascot, MaxQuant, Proteome Discoverer and more. Each one of our tools has a free viewer to aid in data sharing and collaboration. A PDF version of this document is also available.

End-to-end Tools

Small Molecule Analysis

  • Scaffold Elements
    • Library searching for metabolites, lipids and other small molecules
    • Quantification (precursor intensity)
    • Statistical Analysis (volcano plot, ANOVA, t-test, etc)

Data Independent Acquisition (DIA) Proteomics

  • Scaffold DIA
    • Library and FASTA searching for DIA proteomics
    • Quantification (fragment intensity)
    • Gene Ontology annotations (GOA)
    • Statistical analysis (volcano plot, ANOVA, t-test, etc)

DDA Proteomics: Scaffold and the Q+ Modules

  • Scaffold
    • Supports popular search engine results and mzIdentML (MZID) files
    • Spectrum counting and precursor intensity quantitative techniques
    • Statistical analysis (volcano plot, ANOVA, t-test, etc)
    • Gene Ontology annotations (GOA)
    • Pathway analysis via Wiki Pathways and Reactome
  • Scaffold Q+
    • Adds support for reporter ion (iTRAQ, TMT) quantitation
    • More complex quantitative analysis including intensity weighting
  • Scaffold Q+S
    • Adds support for precursor ion (SILAC and Dimethyl) labeling
    • More complex quantitative analysis including intensity weighting

DDA Proteomics: Large Scale, and PTM Experiments

  • Scaffold perSPECtives
    • Supports mzIdentML and SFDB exports from Scaffold, and some search engines
    • Spectrum counting and precursor intensity quantitative techniques
    • Statistical analysis (volcano plot, ANOVA, t-test, etc)
    • Heatmap and principal component analysis (PCA)
    • Gene Ontology annotations (GOA)
  • Scaffold PTM
    • Supports mzIdentML exports from Scaffold and some search engines
    • Visualization of post-translational modifications
    • Includes the Ascore algorithm for the determination of modification site localization
    • Supports reporter and precursor ion PTM quantification when data is exported from Scaffold Q+ or Scaffold Q+S

 

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