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. The non-gel import is described here 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 updated so that it is possible to filter for a specific false discovery rate (FDR). Note that the column with the combined FDR may be hidden by default, see Hits Report Table Features. The updated report will have one protein or peptide in the combination updated with the calculated FDR. This is then the 'primary in combination' hit. If you click on the combined false discovery rate in the table, the other search results will also turn up. For example, the primary hit could be the Mascot search result for protein IPIxyz, and when you click on the false discovery rate, also the X!tandem result (if there was one) which resulted in IPIxyz will be shown.

----- Note on file formats ------

For search combination of peptide identifications to work properly, it is imperative that the MS/MS spectrum ids can be retrieved in the results files. This is only the case for mzML, mzData and MGF files. Searches of MS/MS data should therefore be performed with files in one of these formats. MGF files need to have unique Title for each spectrum.

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. If the generate protein hits option is checked, the inferred proteins will be added to the Hits report with a 'Proteios Protein' score.

Isobaric labels

For quantitative experiments where ITRAQ or TMT have been used, the quantitative information is retrieved by Proteios SE when the protein assembly is performed. Just make sure to select the right label and m/z tolerance for matching the reporter ions.

Exclusion list generation

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

Exporting hits data to a PRIDE XML file

Hits data related to peak list files in mzData format may be exported to PRIDE XML. Each export session exports data for a selected gel external id or local sample id. One PRIDE XML file is created for each mzData file. For a description on how to export Hits table data to PRIDE XML, see PRIDE 2.1 XML Export.

Last modified 11 years ago Last modified on Oct 14, 2011, 8:51:22 AM