Proteomic Dataset PXD017816

PXD017816 — Orbicella annularis — Coral skeleton

SpeciesOrbicella annularis

ClassHexacorallia

Tissue / sampleCoral skeleton

Treatment / condition-

InstrumentQ Exactive HF

PRIDE project PXD017816

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; 14 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≤0.01	Peptides at q≤0.01	Gene-linked proteins	Contaminants (excluded)
298	153	18	14

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 PXD017816 # retrieve peak lists from PRIDE python3 2.pipeline/03_build_search_db.py "Orbicella annularis" # proteome + cRAP python3 2.pipeline/04_run_search.py PXD017816 # writes comet.params, runs Comet python3 2.pipeline/05_fdr_percolator.py PXD017816 # Percolator, q ≤ 0.01 python3 2.pipeline/06_map_to_genes.py PXD017816 # peptides -> CnidoSite genes python3 2.pipeline/07_build_tables.py --release 1.1 # load tables + SQL

Most strongly supported proteins in this dataset

Gene	Protein	Unique peptides	PSMs	Coverage (%)	Length	Best q
TRINITY_DN8845_c3_g1	TRINITY_DN8845_c3_g1_i1.p1	24	40	34.8	609	0.00653595
TRINITY_DN27672_c1_g3	TRINITY_DN27672_c1_g3_i1.p1	23	41	40.2	517	0.00653595
TRINITY_DN27672_c1_g4	TRINITY_DN27672_c1_g4_i1.p1	18	31	30.5	590	0.00653595
TRINITY_DN33035_c0_g1	TRINITY_DN33035_c0_g1_i1.p1	11	16	62.7	150	0.00653595
TRINITY_DN27673_c0_g1	TRINITY_DN27673_c0_g1_i3.p1	6	6	22.5	275	0.00653595
TRINITY_DN85116_c0_g1	TRINITY_DN85116_c0_g1_i1.p1	4	5	19.1	335	0.00653595
TRINITY_DN98637_c0_g1	TRINITY_DN98637_c0_g1_i1.p1	2	3	27.8	108	0.00653595
TRINITY_DN88935_c0_g1	TRINITY_DN88935_c0_g1_i1.p1	1	1	6.7	135	0.00653595
TRINITY_DN8567_c1_g2	TRINITY_DN8567_c1_g2_i1.p1	1	1	3.7	513	0.00653595
TRINITY_DN85017_c0_g1	TRINITY_DN85017_c0_g1_i1.p1	1	1	6.1	329	0.00653595
TRINITY_DN77524_c0_g1	TRINITY_DN77524_c0_g1_i1.p1	1	1	4.9	225	0.00653595
TRINITY_DN73582_c0_g1	TRINITY_DN73582_c0_g1_i1.p1	1	1	7.2	167	0.00653595
TRINITY_DN405_c1_g1	TRINITY_DN405_c1_g1_i1.p1	1	1	1	581	0.00653595
TRINITY_DN34501_c0_g1	TRINITY_DN34501_c0_g1_i1.p1	1	1	7.5	106	0.00653595
TRINITY_DN19929_c0_g1	TRINITY_DN19929_c0_g1_i1.p1	1	1	2.6	459	0.00653595

View all 18 proteins »