Simple, Experiment-Driven Quantitative Analysis for Proteomics

Investigate Large/Complex Experiments

Export data from Scaffold and combine multiple data sets, as well as load data from Mascot, PEAKS via mzIdentML. Standard, repeeated-measures and two-way analyses, and proper support for fractionation,technical, and biological replicates.

Principal Component Analysis (PCA)

Scaffold perSPECtives offers full support for PCA, displaying the Scores Plot, Scree Plot and Loadings Plot for each pair of Principal Components selected in the Overview plot.

Assess Biological Meaning wit Gene Ontology

This version parses accession numbers to allow application of GO Terms even with more complex formats, and two new charts assist in identifying protein associated with specific biological functions.

Compare across samples or biological functions.

Quantitative Visualization Options

Scaffold perSPECtives 3.0 introduces powerful new tools to reveal meaningful biological insights from your data. All the charts and tables are linked, enabling universal protein selection and tagging.

A Volcano Plot facilitates interrogation of interesting proteins and a Scatterplot enables comparison between samples or categories.

New Features and Improvements

Import and configure your experimental design with hierarchical summarization. Import CSV files from your LIMS for metadata definitions.

Compare sequence coverage across samples. Easily publish and share data with collaboration tools. Export customizable publication-quality graphics with ease.