Perseus plugin in R for dual matrix quality filtering.
This tool was made specifically for filtering SILAC data on the Ratio counts and the Ratio variability, allowing a borderline scenario where low counts are tolerated if the variability is low enough.
-value1 is the minimum ratio count
-value2 is the maximum variability
Copy the file to a destination on your computer and use it from Perseus through the button External > R.
Example for changing the parameters to higher stringency using the additional arguments box:
-value1 3 -value2 20