PMC

The TPP provides tools for format conversion, spectrum identification, search result validation, protein assignment and quantification. It allows for the use of multiple algorithms at any step where they exist (e.g., Comet, X!Tandem, Mascot or SpectraST for database search). Currently each of these steps is run directly by the user using either the TPP Petunia graphical user interface or via command-line interface scripts.

A partial screenshot showing a self-organizing map shown as a heatmap. On the X-axis are the 13 experiments ordered by clustering results. Plotted across the Y-axis is the union of all proteins in these samples, also ordered by clustering results. The view is zoomed such that many more proteins are out of view on this screen shot. The colors of the boxes range from blue for low abundance to red for high abundance, in this case based on label-free spectral counting quantification. Gray boxes represent missing data.

A partial screenshot depicting proteins organized by Gene Ontology (GO) category with an example dataset. The size of each rectangle is relative to the abundance (spectral counts in this case) of each protein (inner rectangles) and GO annotation (outer rectangles). The colors are autogenerated. GO categories that have many proteins in them are shown as rectangles with many other rectangles inside. Rectangles with one or few inner rectangles represent GO categories with few associated proteins. The rectangles are ordered in order of relative abundance associated with each GO category. More information for each rectangle can be viewed via mouse over, with hyperlinks out to UniProtKB. The word “stress” is typed in the search term filter box, thereby shading yellow all GO terms that have the substring “stress” in them.