3.3 Protein Inference panel - PRIDE-Archive/pride-inspector GitHub Wiki

Detailed protein inference information can either be included or not in mzIdentML and mzTab files. In mzIdentML, this information is detailed if ‘Protein Groups’ are reported. The ‘Protein inference panel’ shows the identified proteins and the peptides and PSMs included in a particular protein group. The panel can be used to select the proteins and show the identified peptides and PSMs with the corresponding scores and metadata (e.g. modifications, sequence). The ‘score threshold panel’ enables filtering by PSM score and therefore, to remove evidences below a particular score threshold. The ‘Protein inference panel’ also enables to see the shared peptides and PSMs between the proteins that belong to a particular protein group.

The visualisation is composed of nodes, representing either proteins/accessions (rectangular, green), peptides (orange, rounded corners), PSMs (light blue, rounded corners) or just connecting nodes (blue circles). The color and thickness of the edges as well as whether a shape is filled and the filling color describes the relation to the selected protein.

A selected protein (or protein group) is highlighted by a red border and is fileld in dark green. All proteins, which have regardingto the set PSM score filter exactly the same PSMs (and thus peptides), are also filled in dark green and have a black border. All peptides belonging to the selected protein are filled in vivid orange, the PSMs in vivid light blue, both also with black borders. Proteins, which are sub-proteins (i.e. all PSMs are also contained in the selected protein) are filled in pastal green without border. Super-proteins (which contain every PSM/peptide of the selected) are also in pastel green with dark green border, and “siblings” (having the same super-proteins) are in pastel green with black border. Peptides and PSMs, which are not contained in the selected but in a super-protein, are filled in pastell with a dark border. Proteins, peptides and PSMs, which have no relation to the currently selected, but are not filtered out, have a thick dark border and no filling. If a PSM, peptide or even protein is filtered out due to the score threshold, the corresponding node has no filling and a thin, black border.

The ‘protein inference panel’ has options for node picking and transforming and also zoom in and out functionality are enabled. Different colours and shapes are used for proteins (green rectangle), peptides (orange rectangle), PSMs (blue rectangle) and protein groups (blue circles).