False discovery rates in spectral identification

BMC Bioinformatics

Table 2 2 × 2 tables for Fisher's exact test.

	Estimator	# positives	# estimated false positives
a	FactFDR¹	N _target	N_dummy + N_false
	EmpiricalFDR²	N _target	N _decoy
b	FactFDR	N_target + N_dummy + N_false	2 · N_dummy + N_false
	EmpiricalFDR	N_target + N_decoy	2 · N_decoy
c	FactPepFDR³	N _{target peptides}	N_{dummy peptides} + N_{false peptides}
	EmpiricalFDR	N _target	N _decoy
d	FactPepFDR	N _{target peptides}	N_{dummy peptides} + N_{false peptides}
	EmpiricalPepFDR⁴	N _{target peptides}	N _{decoy peptides}

When the p-value of the Fisher's exact test (the Fisher's p-value) for a specific experiment was smaller than 5%, we regarded the empirical FDR for the experiment as inaccurate. For most searches the definitions in (a) were used. The definitions in (b) were used only for the searches I-12, I-13, and Y-4 (i.e., searches using the alternative formula - see Table 5 and text). The definitions in (c) were used for experiments in Table 10 (empirical PSM-level FDR vs. factual peptide-level FDR), and the definitions in (d) were for experiments in Table 11 (empirical peptide-level FDR vs. factual peptide-level FDR). ¹factual FDR; ²empirical FDR; ³factual peptide-level FDR; ⁴empirical peptide-level FDR; N_target: the number of positive target PSMs; N_dummy: the number of positive dummy PSMs; N_false: the estimated number of false positive putative PSMs; N_decoy: the number of positive decoy PSMs; N_{target peptides}: the number of positive target peptides; N_{dummy peptides}: the number of positive dummy peptides; N_{false peptides}: the estimated number of false positive putative peptides; N_{decoy peptides}: the number of positive decoy peptides.

ISSN: 1471-2105