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 — PXD017876

SpeciesOrbicella annularis
TissueCoral skeleton
PRIDE accessionPXD017876
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)
Proteins17
Peptides (q≤0.01)190
PSMs (q≤0.01)541
reprocessed against the CnidoSite reference proteome
15 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 101 36 51.8 517 0.00526316
TRINITY_DN8845_c3_g1 TRINITY_DN8845_c3_g1_i1.p1 74 33 44.7 609 0.00526316
TRINITY_DN27672_c1_g4 TRINITY_DN27672_c1_g4_i1.p1 41 20 28.8 590 0.00526316
TRINITY_DN27673_c0_g1 TRINITY_DN27673_c0_g1_i3.p1 22 9 45.1 275 0.00526316
TRINITY_DN33035_c0_g1 TRINITY_DN33035_c0_g1_i1.p1 5 3 12.7 150 0.00526316
TRINITY_DN34501_c0_g1 TRINITY_DN34501_c0_g1_i1.p1 3 2 20.8 106 0.00526316
TRINITY_DN98637_c0_g1 TRINITY_DN98637_c0_g1_i1.p1 3 2 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 3 1 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
TRINITY_DN3756_c0_g1 TRINITY_DN3756_c0_g1_i1.p1 1 1 0.8 921 0.00526316
TRINITY_DN85116_c0_g1 TRINITY_DN85116_c0_g1_i1.p1 1 1 7.2 335 0.00526316
Total protein records: 17  (+15 contaminants hidden)
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