Monday, June 3, 2013

Stop Guessing, Start Knowing - Score threshold and FDR control in PEAKS

In an MCP guideline published in 2004, "a significant but undefined number of proteins being reported as identified in proteomics articles are likely to be false positives".

To tackle this problem and control the "quality" of the identification results, over the past decade, false discovery rate (FDR) becomes the most accepted result validation method.

Although many search engines have the FDR estimation integrated into their package, in order to get the result under a particular FDR, e.g. 1%, the researchers usually have to do several round of "trial and error" on the score threshold used for filtering the result. Even worse, this process may have to be performed on every results.

PEAKS introduced a score selection tool to make this process very simple. Normally, it only takes three mouse clicks. Here is how to do it. On the top of the result summary pane, there is a FDR button.

Simply click that button will give you the score selection dialog. In this dialog, you can quickly select the commonly used FDR values on the right by a single click of the corresponding button. Or you can hover the mouse cursor on the chart to find the desired FDR value. When the value is found, right-click and then select "copy score threshold", the score to be used for the desired FDR will be filled into the score filter automatically. Click the "Apply Filters" button, you will get the result under the desired FDR.


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