False discovery rates in spectral identification

BMC Bioinformatics

Table 8 Comparison between searches with strict and loose parent mass tolerance.

Search#	Spectra	Database	PMTol	EmpiricalFDR fixed			FactFDR fixed
				N _target	FactFDR(%)	p-value(%)	N _target	EmpiricalFDR(%)
I-1	ISB-02	ISB	2.5 Da	2329/1009	5.8/4.4	10.9/30.9	2279/1024	3.9/5.7
I-16	ISB-02	ISB	30 ppm	2128/1009	N/A¹	N/A	N/A	N/A
I-5	ISB-02+AB-TC	ISB+Yeast	2.5 Da	1490/569	5.0/5.8	50.2/31.2	1480/553	4.5/4.3
I-17	ISB-02+AB-TC	ISB+Yeast	30 ppm	1638/569	6.4/5.3	3.1/45.2	1570/565	3.9/4.8
I-7	ISB-02+AB-TC	ISB+AT	2.5 Da	1320/441	4.6/4.1	36.6/38.0	1342/464	5.8/7.3
I-18	ISB-02+AB-TC	ISB+AT	30 ppm	1358/463	3.2/5.1	2.0/50.3	1425/463	6.5/4.3

As expected, when using strict parent mass tolerance more PSMs were identified (at the same factual FDR threshold) in most cases.
¹ For the search I-16, the factual FDR is not available because no dummy element is used.

ISSN: 1471-2105