Table 1.
Summary of T. pallidum proteins identified based on the detection of one or more peptides.
| Number of T. pallidum proteins detected in each of the 12 biological replicate samples | |||
|---|---|---|---|
| In vivo sample | Number of proteins detected | 1 peptide for protein ID | 2 or more peptides for protein ID |
| 1* | 88 | 14 | 74 |
| 2* | 107 | 8 | 99 |
| 3* | 103 | 16 | 87 |
| 4* | 80 | 20 | 60 |
| 5* | 102 | 14 | 88 |
| 6* | 104 | 12 | 92 |
| 7* | 75 | 41 | 34 |
| 8* | 4 | 3 | 1 |
| 9* | 308 | 54 | 254 |
| 10** | 730 (74.3% proteome coverage) | 105 (10.7% proteome coverage) | 625 (63.6% proteome coverage) |
| 11** | 562 (57.2% proteome coverage) | 110 (11.2% proteome coverage) | 452 (46.0% proteome coverage) |
| 12** | 557 (56.7% proteome coverage) | 103 (10.5% proteome coverage) | 454 (46.2% proteome coverage) |
| Total coverage of the T. pallidum proteome | |||
|---|---|---|---|
| In vivo samples | Number of proteins detected | 1 peptide for protein ID | 2 or more peptides for protein ID |
| 1–12 combined |
758 (77.2% proteome coverage) (596 detected in ≥ 2 biological replicates) (520 detected in ≥ 3 biological replicates) |
105 (10.7% proteome coverage) |
653 (66.5% proteome coverage) (570 detected in ≥ 2 biological replicates) (510 detected in ≥ 3 biological replicates) |
| Proteome coverage of T. pallidum: this study and previous studies24, 25 | |||
|---|---|---|---|
| In vivo samples | Number of proteins detected | 1 peptide for protein ID | 2 or more peptides for protein ID*** |
| 1–12 combined and previous studies24, 25 |
847 (86.25% proteome coverage) (264 proteins identified only in the present study) |
62 (6.31% proteome coverage) |
785 (79.94% proteome coverage) (202 proteins identified only in the present study) |
| Detection of T. pallidum Miniproteins of unknown function | |||
|---|---|---|---|
| In vivo samples | Number of miniproteins detected | 1 peptide for protein ID | 2 or more peptides for protein ID |
| 1–12 combined |
28 (41.2% miniprotein coverage) (19 miniproteins identified only in the present study) |
8 (11.8% miniprotein coverage) |
20 (29.4% miniprotein coverage) (13 miniproteins identified only in the present study) |
| Detection of hypothetical proteins and proteins of unknown function | |||
|---|---|---|---|
| In vivo samples | Number of proteins detected | 1 peptide for protein ID | 2 or more peptides for protein ID |
| 1–12 combined |
175/264 total proteins detected (66.3% coverage) 98/162 “hypothetical proteins” (60.5% coverage) 17/35 DUF domain proteins (48.6% coverage) 60/67 “poorly annotated proteins” (89.6% coverage) |
29 (11.0% coverage) 14 (8.6% coverage) 5 (14.3% coverage) 10 (14.93% coverage) |
146 (55.3% coverage) 84 (51.9% coverage) 12 (34.3% coverage) 50 (74.63% coverage) |
| Detection of known or predicted OMPs | |||
|---|---|---|---|
| In vivo samples | Number of proteins detected | 1 peptide for protein ID | 2 or more peptides for protein ID |
| 1–12 combined |
27 (79.4% known/predicted OMP coverage) (11 OMPs identified only in the present study) |
9 (26.5% known/predicted OMP coverage) |
18 (52.9% known/predicted OMP coverage) (5 OMPs identified only in the present study) |
| Detection of putative pathogenesis-related proteins (PRPs) | |||
|---|---|---|---|
| In vivo samples | Number of proteins detected | 1 peptide for protein ID | 2 or more peptides for protein ID |
| 1–12 combined |
28 (82.4% coverage) (7 PRPs identified only in the present study) |
4 (11.8% coverage) |
24 (70.6% coverage) (6 PRPs identified only in the present study) |
*Method development samples; **optimized method samples; ***protein identifications based on two or more peptides in the present study.