False discovery rates in spectral identification

BMC Bioinformatics

Table 1 Details on experiments performed

Search#¹	Spectra²	Database³	Decoy⁴	PMTol⁸	Note¹¹
I-1	ISB-02	ISB	Rev⁵	2.5 Da ⁹
I-2	ISB-02	ISB	Shfl⁶	2.5 Da
I-3	ISB-02	ISB+Yeast	Rev	2.5 Da
I-4	ISB-02	ISB+Yeast	Shfl	2.5 Da
I-5	ISB-02+AB-TC	ISB+Yeast	Rev	2.5 Da
I-6	ISB-02+AB-TC	ISB+Yeast	Shfl	2.5 Da
I-7	ISB-02+AB-TC	ISB+AT	Rev	2.5 Da
I-8	ISB-02+AB-TC	ISB+AT	Shfl	2.5 Da
I-9	ISB-02	ISB	Sep.Rev⁷	2.5 Da
I-10	ISB-02+AB-TC	ISB+Yeast	Sep.Rev	2.5 Da
I-11	ISB-02+AB-TC	ISB+AT	Sep.Rev	2.5 Da
I-12	ISB-02	ISB+Yeast	Rev	2.5 Da	Alt.Formula¹²
I-13	ISB-02+AB-TC	ISB+Yeast	Rev	2.5 Da	Alt.Formula
I-14	ISB-02+AB-TC	ISB	Rev	2.5 Da
I-15	ISB-02+AB-All	ISB+Yeast	Rev	2.5 Da
I-16	ISB-02	ISB	Rev	30 ppm¹⁰
I-17	ISB-02+AB-TC	ISB+Yeast	Rev	30 ppm
I-18	ISB-02+AB-TC	ISB+AT	Rev	30 ppm
I-19	ISB-02	ISB	Rev	2.5 Da	Alt.Score¹³
I-20	ISB-02+AB-TC	ISB+Yeast	Rev	2.5 Da	Alt.Score
I-21	ISB-02+AB-TC	ISB+AT	Rev	2.5 Da	Alt.Score
I-22	ISB-All+AB-TC	ISB+Yeast	Rev	2.5 Da
I-23	ISB-All+AB-TC	ISB	Rev	2.5 Da
Y-1	Y-Small+AB-TC	Yeast+AT	Rev	30 ppm
Y-2	Y-Small+AB-TC	Yeast+AT	Shfl	30 ppm
Y-3	Y-Small+AB-TC	Yeast+AT	Sep.Rev	30 ppm
Y-4	Y-Small+AB-TC	Yeast+AT	Rev	30 ppm	Alt.Formula
Y-5	Y-Small+AB-TC	Yeast	Rev	30 ppm
Y-6	Y-Small+AB-All	Yeast+AT	Rev	30 ppm
Y-7	Y-Small+AB-TC	Yeast+AT	Rev	30 ppm	Alt.Score
Y-8	Y-All+AB-TC	Yeast+AT	Rev	30 ppm
Y-9	Y-All+AB-TC	Yeast	Rev	30 ppm
Y-10	Y-Small+AB-TC	Yeast+AT	Rev	30 ppm	TwoPass(1)¹⁴
Y-11	Y-Small+AB-TC	Yeast+AT	Rev	30 ppm	TwoPass(2)
Y-12	Y-Small+AB-TC	Yeast+AT	Rev	30 ppm	TwoPass(3)
Y-13	Y-Small+AB-TC	Yeast+AT	Rev	30 ppm	TwoPass(4)

For each of the searches I-1 to I-23 (Y-1 to Y-13), we counted the numbers of positive target PSMs (N_target) at factual/empirical FDR 5% (1%) and computed the corresponding factual/empirical FDR of the positive PSMs. The underlined characters represent either dummy spectra, dummy databases, or dummy tolerance. ¹Search identifier; ²MS/MS spectra used; ³Protein database; ⁴Decoy database type; ⁵Reversed decoy database; ⁶Shuffled decoy database; ⁷Separate search against target and reversed decoy database; ⁸Parent mass tolerance; ⁹Dalton; ¹⁰Parts per million; ¹¹Additional note; ¹²Alternative formula was used to calculate FDR (see text); ¹³Alternative score was used to calculate FDR (see text); ¹⁴Two-pass searches (see text and Table 11).

ISSN: 1471-2105