« All proteomic datasets | Browse the 3675 identified proteins »
| Parameter | As reported by the original study | As applied by CnidoSite |
|---|---|---|
| Search engine | PEAKS Studio 8.5 | Comet 2026.01 + Percolator (Crux 4.2) |
| Sequence database | in-house zoantharian contig database | /mnt/sdb/jackie/cnidaria_omics/transcriptome_proteins/Zoanthus_sociatus.rep.pep Surrogate: transcriptome-derived proteome of the congener Zoanthus sociatus (88,116 representative proteins). No proteome of Zoanthus natalensis is available. |
| Enzyme | – (not restated) | trypsin (fully enzymatic, 2 termini) · up to 2 missed cleavages |
| Precursor tolerance | 10 ppm | 10 ppm |
| Fragment tolerance | 0.05 Da | 0.02 Da |
| Fixed modification | – | C+57.021464 (carbamidomethyl cysteine) |
| Variable modification | – | M+15.9949,n+42.010565,NQ+0.984016 (methionine oxidation) |
| Decoy strategy | – | Comet internal reversed (1:1) |
| False discovery rate | 1% peptide and protein | 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; 10 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) |
|---|---|---|---|
| 50,724 | 13,401 | 3,675 | 10 |
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_DN26230_c0_g1 | TRINITY_DN26230_c0_g1_i4.p1 | 99 | 358 | 30.8 | 4242 | 0.000100503 | |
| TRINITY_DN22100_c0_g1 | TRINITY_DN22100_c0_g1_i4.p1 | 88 | 594 | 34.1 | 3198 | 0.000100503 | |
| TRINITY_DN34694_c0_g1 | TRINITY_DN34694_c0_g1_i1.p1 | 88 | 266 | 13.3 | 9356 | 0.000100503 | |
| TRINITY_DN58800_c0_g1 | TRINITY_DN58800_c0_g1_i1.p1 | 75 | 419 | 34 | 2417 | 0.000100503 | |
| TRINITY_DN712_c0_g2 | TRINITY_DN712_c0_g2_i3.p1 | 74 | 549 | 25.5 | 1956 | 0.000100503 | |
| TRINITY_DN68000_c0_g1 | TRINITY_DN68000_c0_g1_i1.p1 | 72 | 563 | 29.5 | 1972 | 0.000100503 | |
| TRINITY_DN92509_c0_g1 | TRINITY_DN92509_c0_g1_i1.p1 | 69 | 334 | 49.6 | 1681 | 0.000100503 | |
| TRINITY_DN24130_c0_g5 | TRINITY_DN24130_c0_g5_i1.p1 | 68 | 353 | 32.6 | 2361 | 0.000100503 | |
| TRINITY_DN24081_c0_g1 | TRINITY_DN24081_c0_g1_i1.p1 | 64 | 327 | 19.7 | 2820 | 0.000100503 | |
| TRINITY_DN116_c0_g1 | TRINITY_DN116_c0_g1_i1.p1 | 55 | 286 | 29.1 | 2569 | 0.000100503 | |
| TRINITY_DN103_c0_g1 | TRINITY_DN103_c0_g1_i4.p1 | 36 | 253 | 26.2 | 887 | 0.000100503 | |
| TRINITY_DN517_c0_g2 | TRINITY_DN517_c0_g2_i1.p1 | 36 | 133 | 23.4 | 1617 | 0.000100503 | |
| TRINITY_DN21694_c0_g4 | TRINITY_DN21694_c0_g4_i1.p1 | 35 | 248 | 41.5 | 884 | 0.000100503 | |
| TRINITY_DN169007_c0_g1 | TRINITY_DN169007_c0_g1_i1.p1 | 33 | 256 | 64.7 | 538 | 0.000100503 | |
| TRINITY_DN2075_c0_g3 | TRINITY_DN2075_c0_g3_i1.p2 | 33 | 172 | 56 | 806 | 0.000100503 |
