SpectroDive™ allows you to generate libraries from the result of various search engines (MaxQuant, Proteome Discoverer™, and Protein Pilot™). Additionally, any search result can be reformatted into BGS Generic Format, which is a plain‑text file where each row represents a PSM. Alternatively, you can import already generated libraries into SpectroDive.
To generate a library in SpectroDive, go to the Library Perspective and click on Generate Spectral Library from… at the bottom left corner (figure 1). When selecting your search engine, you will be prompted to browse your search results and your shotgun raw files. In some cases, you will also have to import the modifications file. See table 1 for more information.
Figure 1. Generating a library from search results in SpectroDive
To import a modifications file, go to the Settings Perspective, Modifications page and click on Import Modifications from… at the bottom left corner (figure 2). Choose your modifications source and you will be asked to browse and select the corresponding file.
As already mentioned, you will have to assign run files to the search results. After choosing your library settings and your protein database, the Load button at the bottom right corner will trigger the generation of the library (figure 1).
Figure 2. Importing peptide modifications files into SpectroDive
If you would like to have additional search engines supported, please contact us here and we can try to get the API and make it compatible in future software releases.
Learn more about libraries in our article here.
Created by SEZ. Last update 2018-03-15 by SEZ