Table II. Comparison between the DeMix and MaxQuant workflow, with four database searching methods, based on the combined HeLa triplicate dataset.
| Search engine | MaxQuant |
DeMix |
||||||
|---|---|---|---|---|---|---|---|---|
| Andromeda | Mascot | MS-GF+ Percolator | Morpheus-AS | |||||
| Deconvolutiona | - | + | - | + | - | + | - | + |
| Peptide-spectrum matchesb | 115135 | 131597 | 78063 | 80096 | 118715 | 193450 | 122208 | 200292 |
| PSM per MS/MS | 0.714 | 0.816 | 0.484 | 0.497 | 0.736 | 1.199 | 0.758 | 1.242 |
| Unique peptides | 32646 | 38112 | 23133 | 23095 | 35468 | 45022 | 33712 | 41628 |
| PSM per peptide | 3.53 | 3.45 | 3.37 | 3.47 | 3.35 | 4.30 | 3.63 | 4.81 |
| Confetti supportedc | 86.4% | 84.6% | 89.3% | 89.4% | 85.4% | 83.0% | 86.3% | 84.6% |
| Protein groups | 4409 | 4642 | 3800 | 3801 | 4831 | 5443 | 4707 | 5167 |
| Strongly supportedd | 3597 | 3985 | 2865 | 2868 | 3776 | 4446 | 3691 | 4222 |
| Mean coverage | 24.4% | 25.1% | 22.9% | 22.9% | 24.7% | 25.7% | 24.6% | 25.6% |
a Deconvolution: secondary peptides in MaxQuant or spectra cloning in DeMix are allowed (+) or not (-).
b PSM lists were trimmed to E-value < 0.05 for Mascot, or to FDR < 0.01 for Andromeda, MS-GF+ Percolator and Morpheus-AS.
c Proportion of unique peptide sequences found in the Confetti database (34).
d Protein groups supported by two or more unique peptides are considered to be strongly supported; and mean coverage was calculated for these strongly supported proteins.