Which assay panels can I use with SpectroDive™?

SpectroDive™ is quite flexible regarding the use of panels. Panels can be either generated or imported into SpectroDive in a variety of formats. You can do both, generate and import, in the Prepare Perspective of SpectroDive™ (figure 1 and figure 4).

 

Figure 1. Generating a panel in SpectroDive. Panels are generated using a spectral library as a background

 

Generating a panel

Panels can be generated in SpectroDive from imported or generated spectral libraries. Thus, to generate a panel, you need to first have your library loaded into the Library Perspective (figure 1). If you don’t know how to get your library into the Library Perspective, read our article about it here.

To generate your panel, go to the Prepare Perspective and click on Generate New Panel in the bottom left corner (figure 1). The Generate Panel wizard will open and guide you through the process.

Briefly:

  1. Select the background library from which you would like to generate your panel.
  2. Choose the precursors you want to include. You can also look for precursors by sequence using the search field (figure 2).

 

Figure 2. Selecting the precursors for your panel. You can see whether the precursor is proteotypic or not indicated by the color coding of the precursor in the right window

 

  1. Select the fragments you want to use for each precursor. SpectroDive will suggest the theoretically best fragments from the library according to the settings applied.
  2. Specify the workflow and, if applicable, the labels of your heavy‑labeled standards. A typical experiment is a spike in workflow for which you would have to specify your labels (figure 3).
  3. Finally, specify a name for the panel and select the type of acquisition method, MRM or PRM.

 

Figure 3. Specifying the quantitation workflow of the targeted approach, and the labels, if applicable

 

Importing a panel

SpectroDive allows importing panels in different formats. To do this, go to the Prepare Perspective and click on Import New Panel in the bottom left corner (figure 4). You can import panels either in Biognosys' .kit format or in a compatible spreadsheet plain text format such as .tsv or .csv. If you import a text format file, SpectroDive will try to detect the columns values using the headers. Finally, you will have to specify whether the panel is an MRM or a PRM panel.

 

Figure 4. Importing a panel in SpectroDive

 

Biognosys also provides ready to use assay panels for absolute peptide quantification of several cancer, cardiovascular and metabolic disease biomarkers. To know more about our assay panel kits, please read our article here.

 

To learn more about our software for targeted proteomics, SpectroDive, please, keep on reading here. If you would like to request a trial license for SpectroDive, please do it through our web shop here.

 

 

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