Exporting spectrum libraries

Proteios SE supports export of libraries from protein identification (hits) reports in a project. The spectrum libraries can be used for spectral search engines like X!hunter or for generation of targeted SRM methods in for example Skyline.

To create a spectrum library for usage in Skyline, the following workflow should be followed:

1. Upload peak lists (MGF /mzData) to Proteios SE and perform searches in one or more search engines.
2. Perform non-gel hits import (Registration of peak lists and import of search results).
3. Create a peptide level combined hits report.
4. At the bottom of the Hits table, press the "Spectrum library export" button. If this button does not exist: ask your server administrator to install the 'Spectrum Library Export' extension that can be found in the contrib directory of Proteios.
5. Select a false discovery rate (FDR) cutoff. Spectra from all peptide identifications in the project that are passing the FDR limit will be exported. The export format should be .msp.
6. Download the generated .msp file to your compputer.
7. In Skyline select Settings->Peptide settings->library->edit list->Add. Invent a name that your library will be known as in Skyline and select your .msp file.
8. Check the checkbox in front of the library in the library list to activate it.