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 — PXD017878

SpeciesOrbicella annularis
TissueCoral skeleton
PRIDE accessionPXD017878
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)
Proteins21
Peptides (q≤0.01)123
PSMs (q≤0.01)377
reprocessed against the CnidoSite reference proteome
6 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_DN27672_c1_g3 TRINITY_DN27672_c1_g3_i1.p1 70 20 36 517 0.00813008
TRINITY_DN8845_c3_g1 TRINITY_DN8845_c3_g1_i1.p1 51 20 31 609 0.00813008
TRINITY_DN27673_c0_g1 TRINITY_DN27673_c0_g1_i3.p1 11 5 28 275 0.00813008
TRINITY_DN27672_c1_g4 TRINITY_DN27672_c1_g4_i1.p1 11 4 7.3 590 0.00813008
TRINITY_DN19315_c0_g1 TRINITY_DN19315_c0_g1_i3.p1 9 2 10.1 268 0.00813008
TRINITY_DN22679_c0_g1 TRINITY_DN22679_c0_g1_i2.p1 2 2 10.9 276 0.00813008
TRINITY_DN149261_c0_g1 TRINITY_DN149261_c0_g1_i1.p2 5 1 12.2 147 0.00813008
TRINITY_DN33035_c0_g1 TRINITY_DN33035_c0_g1_i1.p1 3 1 6 150 0.00813008
TRINITY_DN19927_c0_g3 TRINITY_DN19927_c0_g3_i1.p1 2 1 2.4 462 0.00813008
TRINITY_DN15617_c1_g1 TRINITY_DN15617_c1_g1_i4.p1 1 1 1 902 0.00813008
TRINITY_DN1685_c1_g3 TRINITY_DN1685_c1_g3_i1.p1 1 1 2.7 445 0.00813008
TRINITY_DN20952_c1_g1 TRINITY_DN20952_c1_g1_i1.p1 1 1 10.1 267 0.00813008
TRINITY_DN22169_c0_g2 TRINITY_DN22169_c0_g2_i2.p1 1 1 6.8 308 0.00813008
TRINITY_DN22503_c0_g1 TRINITY_DN22503_c0_g1_i2.p1 1 1 10.8 102 0.00813008
TRINITY_DN405_c1_g1 TRINITY_DN405_c1_g1_i1.p1 1 1 1 581 0.00813008
TRINITY_DN6195_c0_g3 TRINITY_DN6195_c0_g3_i2.p2 1 1 8 314 0.00813008
TRINITY_DN672_c1_g1 TRINITY_DN672_c1_g1_i3.p1 1 1 0.5 2190 0.00813008
TRINITY_DN71887_c0_g1 TRINITY_DN71887_c0_g1_i1.p1 1 1 2.9 273 0.00813008
TRINITY_DN7902_c0_g1 TRINITY_DN7902_c0_g1_i4.p1 1 1 23.3 103 0.00813008
TRINITY_DN87992_c0_g1 TRINITY_DN87992_c0_g1_i1.p1 1 1 5.4 371 0.00813008
TRINITY_DN97786_c0_g1 TRINITY_DN97786_c0_g1_i1.p1 1 1 1.1 972 0.00813008
Total protein records: 21  (+6 contaminants hidden)
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