Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry

Joshua E Elias & Steven P Gygi

Supplementary Fig. 1 (pdf 416 KB)
False positive identifications can be estimated by doubling decoy hits from a search against a concatenated target/decoy database.

Supplementary Fig. 2 (pdf 22 KB)
The distributions of potential peptide matches is consistent between target and decoy databases.

Supplementary Fig. 3 (pdf 47 KB)
Example supporting the necessity for target/decoy competition.

Supplementary Fig. 4 (pdf 41 KB)
Relative scores shift to smaller values for less than half of peptide hits when searched against composite target-decoy databases as opposed to separate databases.

Supplementary Fig. 5 (pdf 160 KB)
Using decoy hits to guide selection of appropriate selection criteria.

Supplementary Table 1 (pdf 14 KB)
Slopes of best-fit lines for precision values shown in Figure 5b.

Supplementary Methods (doc 43 KB)

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