« All proteomic datasets | Browse the 4572 identified proteins »
| Parameter | As reported by the original study | As applied by CnidoSite |
|---|---|---|
| Search engine | SEQUEST HT (Proteome Discoverer 2.4) | Comet 2026.01 + Percolator (Crux 4.2) |
| Sequence database | custom multi-cnidarian database | /mnt/sdb/jackie/cnidaria_omics/transcriptome_proteins/Actinia_tenebrosa.rep.pep Surrogate: transcriptome-derived proteome of the congener Actinia tenebrosa (22,231 representative proteins). No proteome of Actinia fragacea is available. |
| 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 | 1% (Scaffold, >=1 unique peptide) | 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; 15 contaminant proteins identified and excluded from the reported protein list |
| Gene mapping | – | Peptides are reported against transcript sequences. This species has no CnidoSite gene models, so no protein links to a gene page. |
| PSMs at q≤0.01 | Peptides at q≤0.01 | Gene-linked proteins | Contaminants (excluded) |
|---|---|---|---|
| 130,483 | 24,717 | 4,572 | 15 |
Pipeline version cnidosite-proteomics 1.0 · CnidoSite release 1.1 · incorporated 2026-09-21
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 |
|---|---|---|---|---|---|---|---|
| TRINITY_DN14886_c0_g1 | TRINITY_DN14886_c0_g1_i1.p1 | 303 | 5226 | 58.9 | 2835 | 0.0000713063 | |
| TRINITY_DN4034_c0_g1 | TRINITY_DN4034_c0_g1_i1.p1 | 223 | 2224 | 69.6 | 2414 | 0.0000713063 | |
| TRINITY_DN2432_c0_g2 | TRINITY_DN2432_c0_g2_i1.p1 | 196 | 686 | 27.1 | 8589 | 0.0000713063 | |
| TRINITY_DN3916_c0_g1 | TRINITY_DN3916_c0_g1_i6.p1 | 168 | 2164 | 63.8 | 2923 | 0.0000713063 | |
| TRINITY_DN10490_c0_g1 | TRINITY_DN10490_c0_g1_i1.p1 | 156 | 2203 | 56.8 | 1948 | 0.0000713063 | |
| TRINITY_DN50101_c0_g1 | TRINITY_DN50101_c0_g1_i1.p1 | 149 | 633 | 39.2 | 3603 | 0.0000713063 | |
| TRINITY_DN10266_c0_g1 | TRINITY_DN10266_c0_g1_i2.p1 | 145 | 1268 | 51.5 | 2363 | 0.0000713063 | |
| TRINITY_DN1849_c0_g1 | TRINITY_DN1849_c0_g1_i2.p1 | 137 | 528 | 52.1 | 2093 | 0.0000713063 | |
| TRINITY_DN6838_c0_g1 | TRINITY_DN6838_c0_g1_i2.p1 | 135 | 1087 | 53.4 | 1961 | 0.0000713063 | |
| TRINITY_DN47509_c0_g1 | TRINITY_DN47509_c0_g1_i1.p1 | 133 | 582 | 42 | 2463 | 0.0000713063 | |
| TRINITY_DN8301_c0_g1 | TRINITY_DN8301_c0_g1_i1.p1 | 124 | 305 | 21.1 | 7058 | 0.0000713063 | |
| TRINITY_DN2379_c3_g2 | TRINITY_DN2379_c3_g2_i1.p1 | 112 | 529 | 37.4 | 2698 | 0.0000713063 | |
| TRINITY_DN1832_c0_g2 | TRINITY_DN1832_c0_g2_i1.p1 | 107 | 256 | 27.7 | 4667 | 0.0000713063 | |
| TRINITY_DN9050_c0_g1 | TRINITY_DN9050_c0_g1_i1.p1 | 91 | 681 | 47.5 | 2562 | 0.0000713063 | |
| TRINITY_DN57403_c0_g1 | TRINITY_DN57403_c0_g1_i1.p1 | 78 | 402 | 27.7 | 3141 | 0.0000713063 |
