False discovery rate estimation using candidate peptides for each spectrum.

ABSTRACT:

Background

False discovery rate (FDR) estimation is very important in proteomics. The target-decoy strategy (TDS), which is often used for FDR estimation, estimates the FDR under the assumption that when spectra are identified incorrectly, the probabilities of the spectra matching the target or decoy peptides are identical. However, no spectra matching target or decoy peptide probabilities are identical. We propose cTDS (target-decoy strategy with candidate peptides) for accurate estimation of the FDR using the probability that the spectrum is identified incorrectly as a target or decoy peptide.

Results

Most spectrum cases result in a probability of having the spectrum identified incorrectly as a target or decoy peptide of close to 0.5, but only about 1.14-4.85% of the total

SUBMITTER: Lee S 

PROVIDER: S-EPMC9623924 | biostudies-literature | 2022 Nov

REPOSITORIES: biostudies-literature