Import a Search Result

There are two possibilities to import Search Results:

- import multiple Search Results in “All Imported” and put them later in different datasets.

- import directly a Search Result in a dataset.

To import in “All Imported”:

- right click on “All Imported” to show the popup

- click on the menu “Add Search Result…”

In the Import Search Results Dialog :

- select the file(s) you want to import thanks to the file button (the Parser will be automatically selected according to the type of file selected)

- select the different parameters (see description below)

- click on OK button

Note 1 : You can only browse the files accessible from the server according to the configuration done by your IT Administrator. Ask him if your files are not reachable. ( look for Setting up Mount-points paragraph in setupguide page )

Note 2 : The “Save Spectrum Matches” option does no longer exists. The Spectrum matches can be generated on demand when the Search Result is imported.

Note 3 : Proline is able to import OMSSA files compressed with BZip2.

Parameters description :

• Software Engine: the software which generated your interrogation file
• Instrument: mass-spectrometer used for sample analysis
• Peaklist Software: the software used for the peaklist creation

• Decoy Strategy: The type of decoy search which was performed.
  • “No Decoy Database”: if the search was performed against a target database only.
  • “Concatenated Decoy Database”: if target and decoy sequences were merged into a single database.
  • “Software Decoy”: if the “Decoy” sequences were generated on-the-fly by your search engine.
  • Protein Match Decoy Rule: for concatenated searches only. Select the rule to apply for the discrimination of target and decoy protein matches.

• Parser Parameters: according to your Software Engine, this will display some extra-parameters.
  • Mascot:
    • Ion Score Cutoff: peptide matches with a score lower than this value won't be imported
    • Subset Threshold: the percentage of score between a given protein match and the master protein match (superset). Protein matches with a relative score lower than

      Master_protein_score * (1-subset threshold)

      won't be imported.

    • Mascot Server URL : URL of the local Mascot server from where some information would be retrieve.
  • Omssa:
    • User mod file: TODO
    • PTM Composition File: TODO

Importing a Search Result can take some time. While the import is not finished, the “All Imported” is shown grayed with an hour glass and you can follow the imports in the Tasks Log Window ( Menu Window > Tasks Log to show it).

To show all the Search Results imported, double click on “All Imported”, or right click to popup the contextual menu and select “Display List”

From the All Imported window, you can drag and drop one or multiple Search Result to an existing dataset.

It is possible to import a Search Result directly in a Dataset. In this case, the Search Result is available in “All Imported” too.

To import a Search Result in a Dataset, right click on a dataset and then click on “Import Search Result…” menu.