The Biognosys Factory Settings or default settings are suitable for most of the experimental setups. However, sometimes non‑default settings are necessary. The process described below is applicable to any Biognosys software, although the screenshots shown here are taken from Spectronaut.

You can change the default settings in three ways:

1. Creating and saving your own settings schema.

Open the software and go to the Settings Perspective (see figure 1). You will find several tabs, each corresponding to the various elements you can change the settings for. For example, if you are carrying out a data independent acquisition (DIA) workflow in Spectronaut, go to the DIA analysis page and select one of the schemas, e.g. the BGS Factory Settings (default) schema. On the 2nd level, you can see the different aspects of the analysis. On the 3rd level, you can finally see and edit the settings. If you hover over each, a brief explanation pops up. Some settings will be shown only if the higher-class check-box is checked, like with Generate Decoys on figure 1.


Figure 1. Exploring the Settings Perspective


Once you have edited the schema with your ideal settings, save it by clicking on Save As on the left bottom corner, give it a name, and click OK (see figure 2). Now you will see your custom schema listed under Schemas. Unlike the BGS Factory Settings (default) schema, created schemas can be removed and edited.


Figure 2. Saving and naming the new schema


2. Changing the settings on the go.

When you start an analysis on the Review Perspective (Monitor in QuiC), you can change the default settings on the Experiment Setup window (see figure 3). At the bottom half of the window, you can see the Analysis Settings. For each aspect of the analysis, you can choose your preferred settings. Click start or OK when the experiment has been configured. In this case, the changes will only apply to the ongoing analysis and won’t be saved for future setups.


Figure 3. Changing the analysis settings in the Experiment Setup window


3. Recalculating an already analyzed dataset (not applicable to QuiC).

On the Review Perspective, right click on the experiment tab and choose Settings (figure 4). Now, at the bottom half of the window, you can see the Analysis Settings (figure 5). Similarly to point number 2, for each aspect of the analysis, you can choose your preferred settings. Click OK to start recalculating.


Figure 4. Changing the settings to an already analyzed dataset


Figure 5. Choosing your preferred settings to recalculate the analysis


To know how to find out which settings are best for your analysis, visit this article here.



Related content:

Which are the best analysis settings for my Spectronaut™ experiment?

How does DIA differ from classic shotgun proteomics (DDA)?




Created by SEZ. Last update 2018-02-12 by SEZ