Proteome Software have created the Scaffold application to allow scientists to quickly visualize, and validate complex MS/MS Proteomics Experiments.

Visualize
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 annotation of the proteins aids you in interpreting the biological relevance of your data.

Validate
Identify proteins from MS/MS data by validating Mascot*/Sequest*/X! Tandem*/Phenyx* searches. Scaffold uses proven statistical algorithms (PeptideProphet and ProteinProphet) to calculate the probability that proteins are actually in your biological samples. Detailed results help detect false positives by allowing you to focus on a protein and examine the peptide and spectra evidence supporting the identification.

Collaborate
Organize and share key MS/MS data with colleagues. 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.

Additional features include:
Analyze up to 8 million spectra
Quantitative framework based on spectral counting
Post-translational modification and mass tolerance filtering
Advanced peptide assignment for protein grouping
Improved false discovery rate estimation
Export in ProtXML format

Further Information
See Downloadable Resources for further information.

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