Proteomic Dataset PXD017876

PXD017876 — Orbicella annularis — Coral skeleton

SpeciesOrbicella annularis

ClassHexacorallia

Tissue / sampleCoral skeleton

Treatment / condition-

InstrumentQ Exactive HF

PRIDE project PXD017876

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; 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.

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)
541	190	17	15

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 PXD017876 # retrieve peak lists from PRIDE python3 2.pipeline/03_build_search_db.py "Orbicella annularis" # proteome + cRAP python3 2.pipeline/04_run_search.py PXD017876 # writes comet.params, runs Comet python3 2.pipeline/05_fdr_percolator.py PXD017876 # Percolator, q ≤ 0.01 python3 2.pipeline/06_map_to_genes.py PXD017876 # 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_DN27672_c1_g3	TRINITY_DN27672_c1_g3_i1.p1	36	101	51.8	517	0.00526316
TRINITY_DN8845_c3_g1	TRINITY_DN8845_c3_g1_i1.p1	33	74	44.7	609	0.00526316
TRINITY_DN27672_c1_g4	TRINITY_DN27672_c1_g4_i1.p1	20	41	28.8	590	0.00526316
TRINITY_DN27673_c0_g1	TRINITY_DN27673_c0_g1_i3.p1	9	22	45.1	275	0.00526316
TRINITY_DN33035_c0_g1	TRINITY_DN33035_c0_g1_i1.p1	3	5	12.7	150	0.00526316
TRINITY_DN34501_c0_g1	TRINITY_DN34501_c0_g1_i1.p1	2	3	20.8	106	0.00526316
TRINITY_DN98637_c0_g1	TRINITY_DN98637_c0_g1_i1.p1	2	3	27.8	108	0.00526316
TRINITY_DN19315_c0_g1	TRINITY_DN19315_c0_g1_i3.p1	2	2	7.8	268	0.00526316
TRINITY_DN149261_c0_g1	TRINITY_DN149261_c0_g1_i1.p2	1	3	12.2	147	0.00526316
TRINITY_DN148326_c0_g1	TRINITY_DN148326_c0_g1_i1.p1	1	1	8.2	110	0.00526316
TRINITY_DN18964_c0_g2	TRINITY_DN18964_c0_g2_i1.p1	1	1	11.1	162	0.00526316
TRINITY_DN19927_c0_g3	TRINITY_DN19927_c0_g3_i1.p1	1	1	2.4	462	0.00526316
TRINITY_DN22097_c0_g1	TRINITY_DN22097_c0_g1_i1.p1	1	1	0.6	1612	0.00526316
TRINITY_DN25578_c0_g1	TRINITY_DN25578_c0_g1_i1.p1	1	1	1.6	370	0.00526316
TRINITY_DN3736_c0_g1	TRINITY_DN3736_c0_g1_i9.p1	1	1	12.2	123	0.00526316

View all 17 proteins »