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


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


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



    • Related Articles

    • What's the purpose of SpectroDive™?

      ​ SpectroDive was developed to analyze targeted proteomics experiments. It supports multiple reaction monitoring (MRM), parallel reaction monitoring (PRM), and SureQuant proteomics data. SpectroDive is more intuitive than other software solutions and ...
    • Which mass spectrometric vendors are supported by SpectroDive™?

      SpectroDive for targeted proteomics is a vendor independent software and currently supports the following instruments:   MRM (triple quadrupole -QQQ- and hybrid quadrupole-linear ion trap -QTrap- MS) • Thermo Scientific™ TSQ Series I and II • SCIEX ...
    • How can I get a license for SpectroDive™?

      At Biognosys, we’re sure you’ll love our software solutions and we’re excited about you trying them out. We provide a free 30 day trial license for all of our software packages. Simply contact us here to obtain your license and start your SpectroDive ...
    • What are the minimum system requirements to run SpectroDive™?

      Although SpectroDive is developed to use as little resources as possible, the calculations made by the software are still intensive. We recommend the following settings: ​Minimum Operating System:  Windows 10, x64 CPU: Intel ® Core™ CPU, 2.7 GHz ...
    • What are MRM and PRM?

      Multiple reaction monitoring (MRM), also known as selected reaction monitoring (SRM), and parallel reaction monitoring (PRM) are targeted proteomics technologies aimed at quantifying up to hundreds of proteins in the same experiment. Multiple ...