Import of protein and peptide identifications

Import of search results to the hits report is a two step process. In the first step each peak list file is assigned to a local sample id and optionally a fraction. In the case of 1D gel, each gel slice could represent a fraction. The second step is to import search results, and these are then automatically linked to the right sample and fraction.

1. Registration of peak lists. There are two different ways to register peak lists. In cases were the files are already linked to Proteios samples, that information can be used to speed up the process. To find out if files are linked to samples: In the file list, click on the file name. Then switch to the 'Annotations' view of the file. If there is a table 'Annotated biomaterials' at the bottom it shows the sample link. Likewise an annotation 'fraction' in the 'Annotation' table to the right is the fraction information for the file. Automatic annotation of files can be obtained through the usage of info files which are part of the BILS workflow. In case your files are annotated with file information follow the instruction under (b), otherwise proceed with (a).

a) Select as Local sample id input: 'Select existing or enter new' and click next.

b) Select as Local Sample id input: 'From associated biomaterial for peaklist file' and click next.

2. In this step the output files from Mascot, X!Tandem or OMSSA searches are selected and imported. Once the generated jobs are done, the hits list will be populated. You may then want to continue with the combined hits report to combine searches from multiple search engines, and / or calculate combined FDR values (which are actually q-values), which are used to filter the report at a given FDR.
   As an alternative to the second step it is also possible to use the automatic import option when starting searches in Mascot or X!Tandem. Note that you need to run step 1 of the Hits Impirt first in order for this to work.