An implementation of the Search All, Asses Subset strategy for FDR estimation in shotgun proteomics.

The search-all-assess-subset FDR procedure has been published in Sticker et al. Nature Methods 14, 643–644 (2017) doi:10.1038/nmeth.4338

Mass spectrometrists should search for all peptides, but assess only the ones they care about
(Adriaan Sticker, Lennart Martens, Lieven Clement)

Please include this reference if you use search-all-assess-subset FDR procedure as part of a publication.

A user-friendly GUI version of saas is hosted here.

More information on the FDR estimation procedure for subsets and the usage of the SAAS package can be found in the vignette


You first need to install the devtools package.


Then install saas using the install_github function in the devtools package.


Running the saas GUI

When saas is installed, you can easily launch the GUI from R. By default, you can see the GUI by visiting


Or if you want to run saas immediately from the terminal.

 R -e "library(saas);saas_gui()"