Table 1.
Alternative Integration Strategies for Differently Used Transcripts and Peptides Detected by SWATH Mass Spectrometry
| Transcript Set (DTU All No.) | Peptide Set (No.) | Initial Overlap | After Assignment | Correlation Coefficient (ρ) | Agreement (%) | |
|---|---|---|---|---|---|---|
| DTU All Transcripts and Uniquely Mapping Peptides | ||||||
| transcript | 30 | 30 | ρ 0.487 | Y, 21 (70) | ||
| transcripts (452) | peptides (2,974) | peptides | 65 | 65 | p value 0.01688 | N, 9 (30) |
| genes (388) | genes (859) | genes | 30 | 30 | ||
| DTU All Transcripts and All Peptides | ||||||
| transcript | 158 | 118 | ρ 0.274 | Y, 68 (57.63) | ||
| transcripts (452) | peptides (14,695) | peptides | 700 | 530 | p value 0.00378 | N, 50 (42.37) |
| genes (388) | genes (2,805) | genes | 128 | 116 | ||
| DTU Major Transcripts and Uniquely Mapping Peptides | ||||||
| transcript | 27 | 27 | ρ 0.498 | Y, 20 (74.07) | ||
| transcripts (291) | peptides (2,974) | peptides | 61 | 61 | p value 0.01672 | N, 7 (25.93) |
| genes (263) | genes (859) | genes | 27 | 27 | ||
| DTU Major Transcripts and All Peptides | ||||||
| transcript | 97 | 77 | ρ 0.486 | Y, 56 (72.73) | ||
| transcripts (291) | peptides (14,695) | peptides | 481 | 419 | p value 1.97E−05 | N, 21 (27.27) |
| genes (263) | genes (2,805) | genes | 84 | 75 | ||