Table 1 Comparison between label free quantification in MS data acquisition with or without dynamic exclusion by LFQ (XIC) and label-free (MS/MS) algorithms through using yeast tryptic digest (three technical replicates).
| Â | LFQ (XIC) | Label-free (MS/MS) | ||||||
|---|---|---|---|---|---|---|---|---|
DE | Without DE | DE | Without DE | |||||
Protein | Peptide | Protein | Peptide | Protein | Peptide | Protein | Peptide | |
Count | 696 | 4181 | 513 | 2563 | 1112 | 5036 | 1177 | 5447 |
Median ratio | 0.997 | 1.012 | 0.992 | 0.987 | 1.029 | 0.978 | 1.016 | 1.010 |
S.D. of ratios | 0.114 | 0.360 | 0.105 | 0.394 | 0.361 | 0.533 | 0.180 | 0.313 |
Percentage of ratios in the range 0.5–2 | 100% | 97.3% | 100% | 96.8% | 98.4% | 93.3% | 99.9% | 98.4% |
