Scaffold Software Comparison

We can divide Scaffold Software tools into two -omics subcategories: proteomics (both DDA and DIA) and small molecule analysis. Scaffold Elements identifies potential metabolites in raw mass spectrometry data as well as provides visualization, quantitation and statistical analysis. Scaffold DIA works in a similar manner but allows for identification and quantification of proteins from DIA experiments. We also have programs for the post-processing of popular proteomics search engines, including: Mascot, MaxQuant and Proteome Discoverer. With the release of Scaffold 5, raw data can be loaded into Scaffold thanks to an integration with MSFragger. Each one of our tools has a free viewer to aid in data sharing and collaboration.

Small Molecule -omics

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

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 Scaffold Q+S

  • 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+S
    • Includes all features found in Scaffold
    • Adds support for precursor ion (SILAC and Dimethyl) and reporter ion (iTRAQ, TMT) quantitation
    • More complex quantitative analysis including intensity weighting and error estimation

DDA Proteomics: Large Scale, and PTM Experiments

  • Scaffold LFQ
    • 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+S


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