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 — PXD017880

SpeciesOrbicella annularis
TissueCoral skeleton
PRIDE accessionPXD017880
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)529
reprocessed against the CnidoSite reference proteome
5 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_DN22679_c0_g1 TRINITY_DN22679_c0_g1_i2.p1 26 10 38 276 0.00813008
TRINITY_DN19315_c0_g1 TRINITY_DN19315_c0_g1_i3.p1 31 7 37.7 268 0.00813008
TRINITY_DN27672_c1_g3 TRINITY_DN27672_c1_g3_i1.p1 13 7 17 517 0.00813008
TRINITY_DN149261_c0_g1 TRINITY_DN149261_c0_g1_i1.p2 22 4 29.3 147 0.00813008
TRINITY_DN8021_c0_g2 TRINITY_DN8021_c0_g2_i1.p1 9 4 46.4 112 0.00813008
TRINITY_DN22503_c0_g1 TRINITY_DN22503_c0_g1_i2.p1 6 3 13.7 102 0.00813008
TRINITY_DN8845_c3_g1 TRINITY_DN8845_c3_g1_i1.p1 4 3 8.2 609 0.00813008
TRINITY_DN1685_c1_g3 TRINITY_DN1685_c1_g3_i1.p1 3 2 9 445 0.00813008
TRINITY_DN146334_c0_g1 TRINITY_DN146334_c0_g1_i1.p1 3 1 1.5 678 0.00813008
TRINITY_DN672_c1_g1 TRINITY_DN672_c1_g1_i3.p1 3 1 0.5 2190 0.00813008
TRINITY_DN14945_c0_g2 TRINITY_DN14945_c0_g2_i1.p1 1 1 4.9 142 0.00813008
TRINITY_DN17004_c1_g1 TRINITY_DN17004_c1_g1_i1.p1 1 1 9.2 360 0.00813008
TRINITY_DN2778_c1_g1 TRINITY_DN2778_c1_g1_i3.p1 1 1 2.1 660 0.00813008
TRINITY_DN2923_c0_g1 TRINITY_DN2923_c0_g1_i30.p1 1 1 7.8 154 0.00813008
TRINITY_DN4504_c0_g2 TRINITY_DN4504_c0_g2_i1.p1 1 1 3.6 772 0.00813008
TRINITY_DN5468_c0_g1 TRINITY_DN5468_c0_g1_i1.p1 1 1 15 147 0.00813008
TRINITY_DN6195_c0_g3 TRINITY_DN6195_c0_g3_i2.p2 1 1 8 314 0.00813008
TRINITY_DN76343_c0_g1 TRINITY_DN76343_c0_g1_i1.p1 1 1 5.3 152 0.00813008
TRINITY_DN86792_c0_g1 TRINITY_DN86792_c0_g1_i1.p1 1 1 6.9 173 0.00813008
TRINITY_DN933_c0_g1 TRINITY_DN933_c0_g1_i2.p1 1 1 5.9 152 0.00813008
TRINITY_DN97821_c0_g1 TRINITY_DN97821_c0_g1_i1.p1 1 1 4.2 259 0.00813008
Total protein records: 21  (+5 contaminants hidden)
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