Proteomic Dataset Details

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PXD017814 — Orbicella annularis — Coral skeleton

SpeciesOrbicella annularis
ClassHexacorallia
Tissue / sampleCoral skeleton
Treatment / condition-
InstrumentQ Exactive HF
PRIDE project PXD017814
Publication –
Raw files1
Search space is a transcriptome assembly, not a reference proteome
Orbicella annularis 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 not stated Comet 2026.01 + Percolator (Crux 4.2)
Sequence database modern O. annularis transcriptome (this study's own assembly) /mnt/sdb/jackie/cnidaria_omics/transcriptome_proteins/Orbicella_annularis.rep.pep
De novo Trinity transcriptome assembly of Orbicella annularis; TransDecoder representative proteins (43,475 sequences), not BUSCO-validated
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; 12 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)
759 223 65 12

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 PXD017814 # retrieve peak lists from PRIDE python3 2.pipeline/03_build_search_db.py "Orbicella annularis" # proteome + cRAP python3 2.pipeline/04_run_search.py PXD017814 # writes comet.params, runs Comet python3 2.pipeline/05_fdr_percolator.py PXD017814 # Percolator, q ≤ 0.01 python3 2.pipeline/06_map_to_genes.py PXD017814 # 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_DN8845_c3_g1 TRINITY_DN8845_c3_g1_i1.p1 32 113 50.7 609 0.0052356
TRINITY_DN27672_c1_g3 TRINITY_DN27672_c1_g3_i1.p1 26 108 44.7 517 0.0052356
TRINITY_DN58504_c0_g1 TRINITY_DN58504_c0_g1_i3.p1 12 66 13.2 1108 0.0052356
TRINITY_DN27673_c0_g1 TRINITY_DN27673_c0_g1_i3.p1 12 35 45.1 275 0.0052356
TRINITY_DN27672_c1_g4 TRINITY_DN27672_c1_g4_i1.p1 9 25 14.7 590 0.0052356
TRINITY_DN25487_c0_g1 TRINITY_DN25487_c0_g1_i4.p1 7 38 26.4 144 0.0052356
TRINITY_DN3716_c0_g1 TRINITY_DN3716_c0_g1_i1.p1 4 9 2.8 1686 0.0052356
TRINITY_DN4958_c0_g1 TRINITY_DN4958_c0_g1_i7.p1 4 6 6.7 684 0.0052356
TRINITY_DN146178_c0_g1 TRINITY_DN146178_c0_g1_i1.p1 3 43 11 264 0.0052356
TRINITY_DN9570_c0_g1 TRINITY_DN9570_c0_g1_i1.p1 3 8 7.5 451 0.0052356
TRINITY_DN325_c0_g3 TRINITY_DN325_c0_g3_i1.p1 3 7 3.4 1137 0.0052356
TRINITY_DN21605_c0_g1 TRINITY_DN21605_c0_g1_i1.p1 3 6 6.5 765 0.0052356
TRINITY_DN78804_c0_g1 TRINITY_DN78804_c0_g1_i1.p1 3 5 8.4 463 0.0052356
TRINITY_DN33035_c0_g1 TRINITY_DN33035_c0_g1_i1.p1 3 5 18 150 0.0052356
TRINITY_DN3831_c0_g4 TRINITY_DN3831_c0_g4_i1.p1 3 3 3.8 1001 0.0052356

View all 65 proteins »

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