Working With Hits Reports

Much of the work in Proteios SE is centered around protein identification. The Hits report for a project is a table which contain protein identifications for a project. The table can contain both 2D gel-based and gel-free protein and peptide identifications. Importing of data to the report can be performed using the non-gel or gel-based imports. To generate the complete report for a gel-based project follow these instructions. For a description on how to simplify inspection of the Hits table, see Hits Report Table Features.

There are also some special fetures in the Hits table, accessible through the toolbar at the bottom:

Combination of search results

Search results from different search engines can be combined in Proteios SE, either on the peptide level or on the protein level. After running the search results combination plug-in, the Hits report is edited so that it is possible to filter for a specific false discovery rate.

Protein assembly

Using this feature, proteins are assembled from all peptides that pass a certain cutoff. This is useful when evaluating data from peptide-based proteomic experiments.

Exclusion list generation

Based on peptide identifications it is possible to generate exclusion lists for LC-MS, useful when trying to find low-abundance peptides.