A procedure for controlling the false discovery rate of de novo peptide sequencing

De novo sequencing is a powerful method for identifying peptides from mass spectrometry proteomics experiments without the use of a protein database. However, applications of de novo sequencing are currently severely limited by the lack of a reliable procedure for controlling the false discovery rate (FDR). Here, we introduce an FDR control procedure for the de novo setting which is at least as powerful as database search, give empirical evidence that it is statistically valid, and demonstrate its utility on a set of common de novo applications.