Proteomic Dataset Details

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PXD020332 — Corallium rubrum — Coral skeleton

SpeciesCorallium rubrum
ClassOctocorallia
Tissue / sampleCoral skeleton
Treatment / condition-
InstrumentQ Exactive HF
PRIDE project PXD020332
Publication PMID 33514311
Raw files4
Search space is a transcriptome assembly, not a reference proteome
Corallium rubrum has no genome annotation, so no CnidoSite reference proteome exists for it. The search database is the representative protein set predicted from a Trinity de novo assembly of this species' own public RNA-seq. Peptides therefore map to transcript contigs and not to CnidoSite gene pages; no gene ID is displayed for this dataset.

Original study vs CnidoSite re-processing

Parameter As reported by the original study As applied by CnidoSite
Search engine Mascot 2.3 Comet 2026.01 + Percolator (Crux 4.2)
Sequence database red coral transcriptome trinity_v141 /mnt/sdb/jackie/cnidaria_omics/transcriptome_proteins/Corallium_rubrum.rep.pep
De novo Trinity transcriptome assembly of Corallium rubrum; TransDecoder representative proteins (11,590 sequences), not BUSCO-validated
Enzyme – (not restated) trypsin (fully enzymatic, 2 termini)  ·  up to 2 missed cleavages
Precursor tolerance 20 ppm 20 ppm
Fragment tolerance 0.5 Da 0.5 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 95%/99% (Scaffold Prophet) 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; 9 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.

Outcome of re-processing

Re-processed successfully. reprocessed against the CnidoSite reference proteome
PSMs at q≤0.01Peptides at q≤0.01 Gene-linked proteinsContaminants (excluded)
3,703 523 108 9

Pipeline version cnidosite-proteomics 1.0 · CnidoSite release 1.1 · incorporated 2026-09-21

Reproducing this dataset

Every stage is a single command; the parameter file written by stage 2 is the one shown in the table above.

python3 2.pipeline/02_fetch_pride.py PXD020332 # retrieve peak lists from PRIDE python3 2.pipeline/03_build_search_db.py "Corallium rubrum" # proteome + cRAP python3 2.pipeline/04_run_search.py PXD020332 # writes comet.params, runs Comet python3 2.pipeline/05_fdr_percolator.py PXD020332 # Percolator, q ≤ 0.01 python3 2.pipeline/06_map_to_genes.py PXD020332 # peptides -> CnidoSite genes python3 2.pipeline/07_build_tables.py --release 1.1 # load tables + SQL

Most strongly supported proteins in this dataset

GeneProtein Unique peptidesPSMsCoverage (%) LengthBest qDescription
TRINITY_DN3513_c0_g1 TRINITY_DN3513_c0_g1_i1.p2 27 255 54.3 687 0.00233645
TRINITY_DN2206_c1_g1 TRINITY_DN2206_c1_g1_i1.p1 19 116 26 807 0.00233645
TRINITY_DN10552_c0_g1 TRINITY_DN10552_c0_g1_i1.p1 15 57 14.1 1160 0.00233645
TRINITY_DN9967_c0_g1 TRINITY_DN9967_c0_g1_i1.p1 13 96 20.5 606 0.00233645
TRINITY_DN5671_c0_g1 TRINITY_DN5671_c0_g1_i1.p1 12 78 8.7 1628 0.00233645
TRINITY_DN13180_c0_g1 TRINITY_DN13180_c0_g1_i1.p1 11 162 30.2 374 0.00233645
TRINITY_DN144_c1_g1 TRINITY_DN144_c1_g1_i1.p1 11 67 33.7 291 0.00233645
TRINITY_DN376_c16_g1 TRINITY_DN376_c16_g1_i1.p1 11 62 35.9 326 0.00233645
TRINITY_DN7853_c0_g1 TRINITY_DN7853_c0_g1_i1.p1 11 28 11.1 890 0.00233645
TRINITY_DN18473_c0_g2 TRINITY_DN18473_c0_g2_i1.p1 10 224 49.8 235 0.00233645
TRINITY_DN4800_c0_g1 TRINITY_DN4800_c0_g1_i1.p1 10 76 24.5 383 0.00233645
TRINITY_DN21045_c0_g1 TRINITY_DN21045_c0_g1_i2.p1 10 26 4.3 2378 0.00233645
TRINITY_DN18475_c0_g1 TRINITY_DN18475_c0_g1_i1.p1 9 157 39.5 223 0.00233645
TRINITY_DN9089_c0_g1 TRINITY_DN9089_c0_g1_i1.p1 8 69 39 341 0.00233645
TRINITY_DN20444_c0_g1 TRINITY_DN20444_c0_g1_i1.p1 7 53 36.3 284 0.00233645

View all 108 proteins »

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