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This guide is intended for proteomics bioinformaticians. If you are a mass spectrometry data analyst or operator, you can jump directly to QSample Website Operation.
- The charts below provide a visual summary of the complete software pipeline used for installing and operating QSample. The charts are categorized for Thermo Fisher instruments and other instruments.
- Each red bullet point with a number corresponds to the detailed steps outlined in the right panel of this page.
- The flow of the software pipeline follows the steps numbered 1 to 5, but the installation sequence should proceed as follows:
- First, install the QSample
atlaspipeline (Point 4) and the server (Point 5). - Then proceed with the installation and configuration instructions in Point 0, Points 1 and 2, and Point 3.
- First, install the QSample
QSample currently supports processing folders with the .d extension, which is the proprietary data format used by Bruker instruments. To ensure correct functionality, follow the instructions below:
-
Copying the
.dFolders:
The data folder with the.dextension should be manually copied or moved using an automated script to the designatedincoming_folder. Once placed in this location, QSample will automatically detect and process the data. -
DDA Workflows Only:
Currently, QSample only supports Data-Dependent Acquisition (DDA) workflows for Bruker instruments. Ensure that the experiments adhere to this workflow before processing. -
Automated Processing:
Once the folders are copied to theincoming_folderand the pipeline is configured, QSample will handle the data processing automatically without any further manual intervention.
Tip: You can set up an automated script to streamline the data transfer process from the instrument to the
incoming_folder, minimizing manual work and potential errors.
