Spectronaut™ allows you to generate libraries in several different ways. The most intuitive and seamless manner is using Pulsar, the search engine developed at Biognosys, integrated in Spectronaut.
Library generation with Pulsar
Pulsar allows library generation not only from data dependent acquisition (DDA) runs but also from data independent acquisition (DIA) and parallel reaction monitoring (PRM) data, including MS1 scans. To generate a library with Pulsar, go to the Prepare Perspective in Spectronaut and click on Generate Library from Pulsar at the bottom left corner (figure 1). A wizard will open to guide you through the process. Briefly, you will be prompted to 1) upload your run files, 2) choose a protein database to perform the search on, 3) configure the search settings and 4) select the library generation settings. To know more details about how to generate a library with Pulsar, please refer to the Spectronaut manual here.
Figure 1. Generating a library from run files on Spectronaut using Pulsar
Library generation with external search results
Additionally, external search engines such as MaxQuant, Proteome Discoverer™, Protein Pilot™ and Mascot™ are supported for library generation. Furthermore, any search result can be reformatted into BGS Generic Format, which is a plain‑text file where each row represents a PSM. To know more about this format, please refer to the Spectronaut manual here.
To generate a library from searches done outside Spectronaut, open the Prepare Perspective in and click on Generate Spectral Library from… at the bottom left corner (figure 2). When selecting your search engine, you will be prompted to browse to 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 2. Generating a library from search results done outside Spectronaut
To import a modifications file, go to the Databases Perspective, Modifications page and click on Import Modifications from… at the bottom left corner (figure 3). Choose your modifications source and you will be asked to browse and select the corresponding file.
Figure 3. Importing peptide modifications files into Spectronaut
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 2).
If you would like to have your favorite search engine supported, please contact us here and together we can try to get the API and make it compatible with future software releases.
Learn more about libraries in our article here.
Created by SEZ. Last update 2018-03-15 by SEZ