Table 10 Comparison between peptide-level factual FDR and PSM-level FDR

From: False discovery rates in spectral identification

				EmpiricalFDR fixed
Search#	Spectra	Database	PMTol	N _target	# peptides¹	FactPepFDR(%)²	p-value(%)
I-5	ISB-02+AB-TC	ISB+Yeast	2.5 Da	1490/569	600/262	12.0/11.8	0.0/0.1
I-22	ISB-All+AB-TC	ISB+Yeast	2.5 Da	13441/5086	1375/538	38.6/38.1	0.0/0.0
I-14	ISB-02+AB-TC	ISB	2.5 Da	2262/984	815/361	13.1/10.5	0.0/0.1
I-23	ISB-All+AB-TC	ISB	2.5 Da	19501/8497	1628/556	42.8/39.6	0.0/0.0
Y-1	Y-Small+AB-TC	Yeast+AT	30 ppm	2574/1988	2355/1841	1.1/1.4	37.8/15.8
Y-8	Y-All+AB-TC	Yeast+AT	30 ppm	9005/6269	3567/2640	2.4/2.0	0.0/0.0
Y-5	Y-Small+AB-TC	Yeast	30 ppm	3340/2734	3033/2515	1.2/1.0	19.1/54.5
Y-9	Y-All+AB-TC	Yeast	30 ppm	11151/8969	4341/3582	2.3/2.3	0.0/0.0

Score thresholds were determined using PSM-level FDR thresholds and used to calculate factual peptide-level FDRs. The results illustrate that PSM-level empirical FDR underestimates peptide-level FDR significantly (e.g., the searches I-22 and I-23).
¹Number of distinct peptides; ²Factual peptide-level empirical FDR.

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