Synthace supports the simulation and execution of RoboColumns protocols driven by Design of Experiments (DOE). Whilst the data from these experiments can be analyzed in the usual way in the Chromatography Analysis tool, DOE modeling is not currently supported in Synthace for RoboColumns experiments.
Synthace supports filtering of your chromatography results by the various DOE factors and their levels in the Chromatography Analysis tool.
To analyze your RoboColumns data with DOE modeling, Synthace will help you structure your chromatography data to the DOE design file for export and analysis in third-party statistical software.
In this tutorial you will learn:
How to access the miniaturized purification DOE results - Chromatography visualization
Where to find and interact with DOE factors in the Chromatography visualization
How to extract the data aligned to the DOE design, for DOE analysis externally of Synthace
Other ways of investigating and extracting your DOE data
Get Started
Build and simulate a RoboColumns workflow with a DOE design. You can find guidance on how to do this here or here. Once you have simulated and executed your workflow you should have some data to begin analyzing.
How to launch the chromatography analysis app
After the successful simulation and execution of a RoboColumns workflow, navigate to the execution page by clicking on the navigation button on the simulation details page.
Click the Analyse Chromatography Result button on the execution details page to launch the chromatography analysis tool.
If your miniaturized purification DOE was executed in multiple parts, you can link together the data from multiple parts by clicking Select Purification Data.
Select the executions of interest, then click Load.
You have now opened your miniaturized purification DOE results ready for chromatography analysis!
To learn how to use the Chromatography analysis tool in more detail, click here.
Where to find and interact with DOE factors in the Chromatography analysis tool
Raw Chromatograms
In the Raw Chromatograms tab, Synthace displays a series of pseudo-chromatograms.
In the left-hand data selection panel, DOE factor names and levels used in the experiment can be toggled on and off to filter the pseudo-chromatograms.
Raw Purification Data
In the Raw Purification Data tab, you will find the raw data corresponding to the Source Liquids (liquids that were loaded through the Purification Columns), Analysed Liquids (output liquids that were analyzed in a plate reader), and the Purification Columns.
In the left-hand data selection panel you can choose to include the DOE factors and their levels in the data tables by clicking on the relevant check boxes.
Processed Data
The Plate View section of the Analyse tab displays pseudo-chromatograms of the processed data, as well as the collection plates used in your miniaturized purification DOE.
To visualize the data in tabular format, click on Sample Data. There, you will be able to see the data corresponding to each well in the collection plates.
In the left-hand data selection panel you can choose to include the DOE factors and their levels in the data tables by clicking on the relevant check boxes.
Additionally, you can visualise your data structured by Purification Column, under Cumulative Data. Here, you can choose to aggregate data by summation or averaging, and you can choose which stage of your purification you want to include.
In the left-hand data selection panel you can choose to include the DOE factors and their levels in the data table by clicking on the relevant check boxes.
How to export data aligned to the DOE design
Chromatography analysis data can be structured to the DOE design file for DOE analysis in third-party statistical tools. The context of the RoboColumns experiment can be used to structure specific data to the DOE design that you are interested in, or all raw data can be structured to the DOE design file.
Raw Purification Data
In the Raw Purification Data tab, you can visualize your raw data corresponding to Source Liquids, Analysed Liquids, and Purification Columns. Select the DOE factors and any other data you want to include in your data table by clicking on the relevant check boxes in the left-hand data selection panel.
You can extract the corresponding data, in .csv format, by clicking ‘Download’ underneath the table of interest (see this figure)
Processed Data
In the Analyse tab, in the Sample Data and Cumulative Data sections, you can visualize your processed data alongside the DOE design factors. Select the DOE factors and any other data you want to include in your data table by clicking on the relevant check boxes in the left-hand data selection panel.
In Sample Data, the data is aligned with respect to the wells fractions were collected in. Underneath the table(s) (Measured Plate Data and, if applicable, Unmeasured Collection Plate Data), you can extract the data in the tables, by clicking on the ‘Export’ button. This will download the table in a .csv format file which you can then import into your chosen third-party tool for DOE analysis.
In Cumulative Data, the data is aligned with respect to the Purification Columns. Here, you can choose if you wish for your data to be aggregated by summation or averaging (indicated by the red box in the screenshot below).
Moreover, you can choose which purification stages and fraction dilutions are of interest and you wish to include in the data aggregation, as well as whether the Unmeasured Collection plates data should be included, if applicable (indicated by the purple box in the screenshot below).
Once you have made your desired selections, you can extract the data by clicking on the ‘Export’ button. This will download the table in a .csv format file which you can then import into your chosen third-party tool for DOE analysis.
Other ways of investigating and extracting your DOE data
On the execution details page, click the Structure DOE Data button.
The Prepare Data tool will open. All data will be structured against the DOE design.
Note: in the Prepare Data application the data context is not specific to the RoboColumns context. Therefore, due to multiple fractions being associated with a single DOE run, the table is structured in a wide format and the readings are appended with suffixes (e.g. ‘:1’), to indicate the corresponding fraction number.
Click on the Download Selected button underneath the table to export the data in a .csv format.
Note: We recommend that you use the Analyse Chromatography visualization application in order to extract your miniaturized purification DOE data in a format that accounts for the experimental context, as outlined here.
Well done for making it to the end of this tutorial.