Proteomic Analysis

Peptides and proteins identified by re-processing the raw mass-spectrometry data of every proteomic dataset with a single documented pipeline (Comet 2026.01 against the CnidoSite reference proteome plus cRAP contaminants, with Percolator target-decoy FDR control). Search parameters are dataset-specific and are shown in full for each dataset; peptides were mapped onto CnidoSite gene models, so every row links to its gene page.

Dataset
Contaminants

Dataset provenance & search parameters — PXD017816

SpeciesOrbicella annularis
TissueCoral skeleton
PRIDE accessionPXD017816
Statusreprocessed
Search engineComet 2026.01
Reference proteome/mnt/sdb/jackie/cnidaria_omics/transcriptome_proteins/Orbicella_annularis.rep.pep
Enzymetrypsin
Missed cleavages2
Precursor tolerance10 ppm
Fragment tolerance0.02 Da
Fixed modificationC+57.021464
Variable modificationM+15.9949
Decoy strategyComet internal reversed (1:1)
FDR (PSM)0.01
Quantificationspectral counting (PSMs)
Proteins18
Peptides (q≤0.01)153
PSMs (q≤0.01)298
reprocessed against the CnidoSite reference proteome
14 cRAP contaminant protein s (keratins, trypsin, serum albumin …) were identified in this dataset and are excluded from the table below. Tick “include cRAP contaminants” to display them.
Gene Protein PSMs Unique peptides Coverage (%) Length Best q-value Description
TRINITY_DN8845_c3_g1 TRINITY_DN8845_c3_g1_i1.p1 40 24 34.8 609 0.00653595
TRINITY_DN27672_c1_g3 TRINITY_DN27672_c1_g3_i1.p1 41 23 40.2 517 0.00653595
TRINITY_DN27672_c1_g4 TRINITY_DN27672_c1_g4_i1.p1 31 18 30.5 590 0.00653595
TRINITY_DN33035_c0_g1 TRINITY_DN33035_c0_g1_i1.p1 16 11 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 5 4 19.1 335 0.00653595
TRINITY_DN98637_c0_g1 TRINITY_DN98637_c0_g1_i1.p1 3 2 27.8 108 0.00653595
TRINITY_DN18629_c0_g1 TRINITY_DN18629_c0_g1_i1.p1 1 1 9.4 170 0.00653595
TRINITY_DN18964_c0_g2 TRINITY_DN18964_c0_g2_i1.p1 1 1 11.1 162 0.00653595
TRINITY_DN19315_c0_g1 TRINITY_DN19315_c0_g1_i3.p1 1 1 4.1 268 0.00653595
TRINITY_DN19929_c0_g1 TRINITY_DN19929_c0_g1_i1.p1 1 1 2.6 459 0.00653595
TRINITY_DN34501_c0_g1 TRINITY_DN34501_c0_g1_i1.p1 1 1 7.5 106 0.00653595
TRINITY_DN405_c1_g1 TRINITY_DN405_c1_g1_i1.p1 1 1 1 581 0.00653595
TRINITY_DN73582_c0_g1 TRINITY_DN73582_c0_g1_i1.p1 1 1 7.2 167 0.00653595
TRINITY_DN77524_c0_g1 TRINITY_DN77524_c0_g1_i1.p1 1 1 4.9 225 0.00653595
TRINITY_DN85017_c0_g1 TRINITY_DN85017_c0_g1_i1.p1 1 1 6.1 329 0.00653595
TRINITY_DN8567_c1_g2 TRINITY_DN8567_c1_g2_i1.p1 1 1 3.7 513 0.00653595
TRINITY_DN88935_c0_g1 TRINITY_DN88935_c0_g1_i1.p1 1 1 6.7 135 0.00653595
Total protein records: 18  (+14 contaminants hidden)
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