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Exploring Protein Expression Profiles

Posted by ludesi in How to's in REDFIN

Often it is of specific interest to find proteins that follow a certain expression pattern. This can be as simple as determining proteins that are being up- or downregulated relative to a control sample, or more complex such as when an expression profile is studied over time.

The expression profile filter in the Ludesi REDFIN software allows you to do just that and can be used for both simple queries as well as complex multi-group queries.

Scenario 1: Looking for up-regulated proteins

Step1: Open any project and push the “Set profile filter” button.

click here to set the profile filter in the Ludesi REDFIN software

Step 2: Check the box to activate the filter and move the sliders to filter for proteins that have a higher volume in Group 2 relative to Group 1. Click “OK”.

Adjust the sliders accordingly

Step 3: Now, all proteins shown in the list are up-regulated in Group 2 relative to Group 1.

Only up-regulated proteins showing

Scenario 2: Exploring a time-course experiment

Step 1: Open your time-course experiment and push the “Set profile filter” button.

Step2: This time, we will look for proteins that steadily increase in expression over time. Adjust the sliders so that spot volumes have to increase with each group.

Expression profile example for a time-course experiment

 Step 3: Click “OK”. All proteins in the list now show the desired expression profile.

BEFORE filter

AFTER filter

Double-click on any item in the list to see the spot in detail.

Example of a protein after filtering for the expression profile

Don’t forget that you can get get more information about how to use REDFIN at our online user-guides , as well as access instructional videos on our tutorials page!