Table 2 Entrapment analysis of FDR control of three DIA analysis tools

From: Assessment of false discovery rate control in tandem mass spectrometry analysis using entrapment

Dataset

DIA-NN

EncyclopeDIA

Spectronaut

Precursor

Protein

Peptide

Protein

Precursor

Protein

Human-astral

0.7–1.3 (?)

1.5–2.1 (X)

–

–

0.8–1.5 (?)

1.6–2.3 (X)

Human-qe

0.7–1.3 (?)

1.5–2.2 (X)

0.7–1.3 (?)

4.7–7.0 (X)

0.7–1.4 (?)

1.3–1.9 (X)

Human-tripletof

0.6–1.1 (?)

1.0–1.5 (X)

0.7–1.3 (?)

3.2–4.8 (X)

0.7-1.4 (?)

1.5–2.8 (X)

Yeast-lumos

0.6–1.0 (✓)

1.2–1.4 (X)

0.4–0.8 (✓)

4.3–5.2 (X)

0.8–1.5 (?)

1.3–1.6 (X)

Mouse-qe

0.7–1.3 (?)

0.8–1.1 (?)

–

–

0.7–1.4 (?)

1.3–1.9 (X)

Human-timstof2

0.6–1.1 (?)

0.8–1.2 (?)

–

–

0.7–1.5 (?)

1.4–2.1 (X)

Human-timstof1

0.7–1.2 (?)

0.8–1.2 (?)

–

–

0.7–1.3 (?)

1.1–1.7 (X)

100cell-eclipse

0.9–1.6 (?)

1.3–1.8 (X)

–

–

0.9–1.7 (?)

1.8–2.9 (X)

1cell-eclipse

2.3–4.7 (X)

2.0–3.5 (X)

–

–

3.8–7.6 (X)

3.0–5.6 (X)

Human-lumos

0.9–1.7 (?)

2.1–2.6 (X)

0.7–1.2 (?)

6.7–9.1 (X)

0.7–1.3 (?)

2.0–3.0 (X)

  1. Each entry in the table lists the lower bound and paired-estimated upper bound on the empirical FDP among the target + entrapment discoveries reported by the DIA search engine at an FDR threshold of 1%. The entrapment procedures used shuffled entrapment sequences with r = 1 and were applied at both the peptide or precursor level and the protein-level. Each entry is followed by an indicator for whether the FDR control for this tool on this dataset is deemed valid (✓), invalid (X) or inconclusive (?). EncyclopeDIA results are provided only for the four datasets with gas phase fractionation data available. Note that the evaluation of each method is based on the full results presented in Fig. 4 and Supplementary Figs. 4–9.
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