Table 2.
Data-independent tandem mass spectrometry gives fewer identifications than standard top-10 data dependent acquisition. Of the four DIA strategies, the best method used ten 10-Thompson windows, shifting to higher m/z later in the elution. DIA with shifting 10-Th windows outperforms DDA by 12% at the protein level and 20% at the peptide level when we limit attention to DDA precursors of m/z 500 – 600. The identification numbers shown are the mean, minimum, and maximum over 4 replicates. The reproducibility percentage is the mean percent of peptides re-identified over all 12 ordered pairs of replicates.
| Type of Data Acquisition | Proteins Mean (Min, Max) | Peptides Mean (Min, Max) | Reproducibility Mean between pairs |
|---|---|---|---|
| DIA, 5-Th windows | 131.75 (127, 137) | 310.5 (295, 327) | 85.0% |
| DIA, 10-Th windows, no DeMux | 170.25 (166, 172) | 335.0 (297, 356) | 82.5% |
| DIA, 10-Th windows | 204.0 (197, 212) | 412.0 (393, 454) | 84.4% |
| DIA, 10-Th windows, shifting | 227.25 (220, 235) | 370.5 (347, 386) | 82.0% |
| DDA, all m/z | 542.25 (476, 640) | 1280.25 (1175, 1423) | 65.4% |
| DDA, m/z 500 - 600 | 201.75 (183, 216) | 316.75 (264, 361) | 66.8% |