An intuitive software for visualizing & validating MS/MS protein identification data from any mass spectrometer.



Scaffold displays a complete, experiment-wide view of the proteins identified in a tandem mass spectrometry experiment. The side-by-side display of all the samples allows you to understand which proteins are differentially expressed. Protein identification results are displayed as probability scores, allowing you to balance the number of proteins and the confidence level of each identification. Automatic protein annotation aids in interpreting the biological relevance of data.

Identify proteins from MS/MS data by validating search engine results. Scaffold uses proven statistical algorithms of the Trans Proteomic pipeline (PeptideProphet and ProteinProphet) to calculate the probability that proteins are actually in your biological samples. Detailed results help detect false positives by focusing on a protein of interest, examining the peptide & spectra evidence supporting the identification.

With its free viewer, Scaffold makes it easy to share experimental results with colleagues. Scaffold also helps you prepare for publication, by capturing the information proteomics journals require in a paper’s methods section.

Features include:

  • Compareing samples to identify biological relevance.
  • Identifying regulated isoforms and protein PTMs.
  • Ability to drill down into spectrum details and counts.
  • Identifying proteins intuitively and confidently.
  • Creating comprehensive lists of target proteins.
  • Classifying proteins by molecular function or organelle.
  • Harnessing high through-put batch processing.

Data formats supported include :-
Data formats for SEQUEST® = *.dta and *.out, *.ms2 and *.sqt, and *.srf; Mascot® = *.dat; X! Tandem® = *.xml; Phenyx = *.scaffold-pidres.xml; OMSS = *.omx; Waters® IdentityE = *.xml (Note: These files must be created from our plugin in the new version of Waters PLGS); Proteome Discoverer = *.msf

Further Information

See Downloadable Resources for further technical information.

FREE Evaluation

To register for a free 14 day trial of Scaffold or to learn more, please visit the Proteome Software web site – Free Trial.