How to generate targeted panel in SpectroDive™?

How to generate targeted panel in SpectroDive™?

In SpectroDive you can generate new targeted panels directly from a library. To do that you first need to have your library loaded into the Library Perspective in SpectroDive. We recommend generating your library with Pulsar, Biognosys' search engine, integrated in SpectroDive. However, you can also generate a library from third party search results or import it from the available repositories.

Once you have a spectral library to work with, click on “Generate New Panel…” in the Prepare Perspective of SpectroDive to start the panel generation wizard (Figure 1). 

 

Figure 1. Generating new targeted panel in the Prepare Perspective of SpectroDive

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The wizard will guide you through the process step by step. First you will be asked to select the library for the generation of the new targeted panel. Secondly you can select specific proteins from the library to include them in a panel (Figure 2, 1). In the next step you can select chosen precursors for each preselected protein. Conveniently, you can use filters to select precursors fulfilling specific criteria for your experiment (Figure 2, 2). In the next step of panel generation, you can select the fragment ions that will be monitored and used for quantification of each of the precursors. Again, a set of convenient filters will help you to choose fragments with a specified characteristic, e.g., specific ion type and charge (Figure 2, 3). Finally, you will be able to apply a labeling to your panel. This option allows you, for example, to generate a panel for both unlabeled and isotopically labeled peptides, using a library generated only from unlabeled sample data (Figure 2, 4).

 

Figure 2. Panel generation wizard

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In the last step of panel generation, a proper panel type must be selected. You can generate MRM or PRM panel (Figure 3). For the SureQuant application, a PRM panel should be chosen.


 

Figure 3. Saving targeted panel as PRM or MRM panel



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