« All proteomic datasets | Browse the 1386 identified proteins »
| Parameter | As reported by the original study | As applied by CnidoSite |
|---|---|---|
| Search engine | not stated | Comet 2026.01 + Percolator (Crux 4.2) |
| Sequence database | CCPRD custom database / study-specific | /mnt/sda/jackie/cnidaria/2.anno/Myxobolus_honghuensis.pep; /mnt/sda/jackie/cnidaria/2.anno/Thelohanellus_kitauei.pep Combined search space of Myxobolus honghuensis (reference), Thelohanellus kitauei (reference) |
| Enzyme | – (not restated) | trypsin (fully enzymatic, 2 termini) · up to 2 missed cleavages |
| Precursor tolerance | not stated | 10 ppm |
| Fragment tolerance | not stated | 0.02 Da |
| Fixed modification | – | C+57.021464 (carbamidomethyl cysteine) |
| Variable modification | – | M+15.9949 (methionine oxidation) |
| Decoy strategy | – | Comet internal reversed (1:1) |
| False discovery rate | not stated | q ≤ 0.01 at the PSM level (Percolator q-values, target-decoy); protein level q ≤ 0.01 |
| Quantification | – | spectral counting (PSMs) |
| Contaminants | – | cRAP appended and flagged; 30 contaminant proteins identified and excluded from the reported protein list |
| Gene mapping | – | Combined search space: peptides are mapped to gene models of whichever species in the deposit they match, and each protein links to that gene page. |
| PSMs at q≤0.01 | Peptides at q≤0.01 | Gene-linked proteins | Contaminants (excluded) |
|---|---|---|---|
| 6,643 | 4,672 | 1,386 | 30 |
Pipeline version cnidosite-proteomics 1.0 · CnidoSite release 1.1 · incorporated 2026-09-18
Every stage is a single command; the parameter file written by stage 2 is the one shown in the table above.
| Gene | Protein | Unique peptides | PSMs | Coverage (%) | Length | Best q | Description |
|---|---|---|---|---|---|---|---|
| EVM0007958.1 | MHONG_EVM0007958.1 | 63 | 198 | 38.5 | 1507 | 0.000289436 | gene=EVM0007958 |
| EVM0013745.1 | MHONG_EVM0013745.1 | 44 | 57 | 30 | 1575 | 0.000289436 | gene=EVM0013745 |
| KII74575.1 | TKITA_KII74575.1 | 33 | 36 | 21.7 | 1592 | 0.000289436 | hypothetical protein RF11_16185 [Thelohanellus kitauei] |
| EVM0008257.1 | MHONG_EVM0008257.1 | 31 | 49 | 22.1 | 1820 | 0.000289436 | gene=EVM0008257 |
| KII71942.1 | TKITA_KII71942.1 | 25 | 31 | 25 | 1089 | 0.000289436 | GTP-binding protein 1 [Thelohanellus kitauei] |
| EVM0003529.1 | MHONG_EVM0003529.1 | 24 | 33 | 65.4 | 488 | 0.000289436 | gene=EVM0003529 |
| EVM0011333.1 | MHONG_EVM0011333.1 | 23 | 47 | 39.6 | 697 | 0.000289436 | gene=EVM0011333 |
| KII73242.1 | TKITA_KII73242.1 | 22 | 117 | 35.2 | 517 | 0.000289436 | Serum response factor [Thelohanellus kitauei] |
| KII64277.1 | TKITA_KII64277.1 | 22 | 32 | 21.1 | 1141 | 0.000289436 | hypothetical protein RF11_10945 [Thelohanellus kitauei] |
| EVM0014152.1 | MHONG_EVM0014152.1 | 21 | 59 | 60.6 | 391 | 0.000289436 | gene=EVM0014152 |
| KII73715.1 | TKITA_KII73715.1 | 20 | 32 | 41.7 | 636 | 0.000289436 | hypothetical protein RF11_11013 [Thelohanellus kitauei] |
| EVM0001225.1 | MHONG_EVM0001225.1 | 20 | 26 | 57.6 | 368 | 0.000289436 | gene=EVM0001225 |
| EVM0011848.1 | MHONG_EVM0011848.1 | 20 | 23 | 13.6 | 1692 | 0.000289436 | gene=EVM0011848 |
| EVM0012092.1 | MHONG_EVM0012092.1 | 19 | 23 | 22.8 | 1021 | 0.000289436 | gene=EVM0012092 |
| EVM0002233.1 | MHONG_EVM0002233.1 | 18 | 19 | 40.9 | 367 | 0.000289436 | gene=EVM0002233 |
