TABLE 1.
Comparison of the main output characteristics of the proteomic tools run of mouse liver protein extracts
| Tool | DDASSQ | PD | MQ |
|---|---|---|---|
| Quantified proteins | 3083 | 1422 | 1427 |
| Total peptides selected for quantification | 21287 | 9789 | 10392 |
| Peptide number (mean) | 6.90 | 6.88 | 7.29 |
| Peptide number (median) | 4.00 | 5.00 | 5.00 |
| Peptides/protein (max) | 106 | 80 | 83 |
| LFQ zero values (shared proteins, fraction F2) | 1025 | 186 | 1123 |
| LFQ zero values (shared proteins, fraction F1) | 20 | 1 | 38 |
Statistics are representative of proteins quantified based on at least n = 2 unique peptides. OpenMS
Abbreviations: DDASSQ, de novo, database assisted, spectral search and quantification; PD, Proteome Discoverer; MQ, MaxQuant.