Skip to main content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.


The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

False Discovery Rate Estimation for Hybrid Mass Spectral Library Search Identifications in Bottom-up Proteomics



Meghan C. Burke, Zheng Zhang, Yuri A. Mirokhin, Dmitrii V. Tchekhovskoi, Yuxue Liang, Stephen E. Stein


We present a method for FDR estimation of mass spectral library search identifications made by a recently developed method for peptide identification, the hybrid search, based on an extension of the target-decoy approach. In addition to estimating confidence for a given identification, this allows users to compare and integrate identifications from the hybrid mass spectral library search method with other peptide identification methods, such as a sequence database-based method. In addition to a score, each hybrid score is associated with a ‘ΔMass’ value, which is the difference in mass of the search and library peptide, which can correspond to the mass of a modification. We explored the relation between FDR and ΔMass using 100 concatenated random decoy libraries, and discovered that a small number of ΔMass values were especially likely to result from decoy searches. Using these values, FDR values could be adjusted for these specific values, and a reliable FDR generated for any ΔMass value. Finally, using this method, we find and examine common, reliable identifications made by the hybrid search for a range of proteomic studies.
ACS Journal of Proteome Research


Peptide mass spectral library, hybrid mass spectral library search, false discovery rate, target-decoy approach
Created July 31, 2019, Updated February 13, 2020