Table 1.
Comparison of the proteome coverage between CHO global spectral library, 1D library and the latest proteomic studies on CHO-DG44 and CHO-S cells.
| DDA files # | Protein #a | Protein #a (≥2 peptides) | Peptide #a,b | Confidence cutoff | Data processing pipeline | |
|---|---|---|---|---|---|---|
| CHO global spectral library | 63 | 10,974 | 9,549 | 199,102b |
99% peptides confidence & 1% protein FDR |
ProteinPilot & OneOmics |
| CHO-K1 1D library | 3 | 3,134 | 2,810 | 20,249b | 99% peptides confidence & 1% protein FDR |
ProteinPilot & OneOmics |
| CHO-DG44 exponential13 | 48 | N.A | 5,950 | 58,128 | 1% FDR | Proteome Discoverer |
| CHO-DG44 stationary13 | 48 | N.A | 5,593 | 50,194 | 1% FDR | Proteome Discoverer |
| CHO-S exponential13 | 48 | N.A | 6,089 | 53,958 | 1% FDR | Proteome Discoverer |
| CHO-S stationary13 | 48 | N.A | 5,538 | 48,205 | 1% FDR | Proteome Discoverer |
| Combined CHO-DG44 and CHO-S13 | 192 | N.A | 9,359 | N.A | 1% FDR | Proteome Discoverer |
aThe iRT, reverse sequences, and the proteins containing only non-CAM modified peptides were excluded.
bThe modified peptides except for carbamidomethylation on cysteine residue were excluded.