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 — PXD020332

SpeciesCorallium rubrum
TissueCoral skeleton
PRIDE accessionPXD020332
Statusreprocessed
Search engineComet 2026.01
Reference proteome/mnt/sdb/jackie/cnidaria_omics/transcriptome_proteins/Corallium_rubrum.rep.pep
Enzymetrypsin
Missed cleavages2
Precursor tolerance20 ppm
Fragment tolerance0.5 Da
Fixed modificationC+57.021464
Variable modificationM+15.9949
Decoy strategyComet internal reversed (1:1)
FDR (PSM)0.01
Quantificationspectral counting (PSMs)
Proteins108
Peptides (q≤0.01)523
PSMs (q≤0.01)3703
reprocessed against the CnidoSite reference proteome
9 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_DN3513_c0_g1 TRINITY_DN3513_c0_g1_i1.p2 255 27 54.3 687 0.00233645
TRINITY_DN2206_c1_g1 TRINITY_DN2206_c1_g1_i1.p1 116 19 26 807 0.00233645
TRINITY_DN10552_c0_g1 TRINITY_DN10552_c0_g1_i1.p1 57 15 14.1 1160 0.00233645
TRINITY_DN9967_c0_g1 TRINITY_DN9967_c0_g1_i1.p1 96 13 20.5 606 0.00233645
TRINITY_DN5671_c0_g1 TRINITY_DN5671_c0_g1_i1.p1 78 12 8.7 1628 0.00233645
TRINITY_DN13180_c0_g1 TRINITY_DN13180_c0_g1_i1.p1 162 11 30.2 374 0.00233645
TRINITY_DN144_c1_g1 TRINITY_DN144_c1_g1_i1.p1 67 11 33.7 291 0.00233645
TRINITY_DN376_c16_g1 TRINITY_DN376_c16_g1_i1.p1 62 11 35.9 326 0.00233645
TRINITY_DN7853_c0_g1 TRINITY_DN7853_c0_g1_i1.p1 28 11 11.1 890 0.00233645
TRINITY_DN18473_c0_g2 TRINITY_DN18473_c0_g2_i1.p1 224 10 49.8 235 0.00233645
TRINITY_DN4800_c0_g1 TRINITY_DN4800_c0_g1_i1.p1 76 10 24.5 383 0.00233645
TRINITY_DN21045_c0_g1 TRINITY_DN21045_c0_g1_i2.p1 26 10 4.3 2378 0.00233645
TRINITY_DN18475_c0_g1 TRINITY_DN18475_c0_g1_i1.p1 157 9 39.5 223 0.00233645
TRINITY_DN9089_c0_g1 TRINITY_DN9089_c0_g1_i1.p1 69 8 39 341 0.00233645
TRINITY_DN20444_c0_g1 TRINITY_DN20444_c0_g1_i1.p1 53 7 36.3 284 0.00233645
TRINITY_DN969_c0_g1 TRINITY_DN969_c0_g1_i1.p1 48 7 32.3 229 0.00233645
TRINITY_DN13028_c0_g1 TRINITY_DN13028_c0_g1_i1.p1 44 7 13.6 477 0.00233645
TRINITY_DN2592_c0_g1 TRINITY_DN2592_c0_g1_i1.p1 33 7 16.3 515 0.00233645
TRINITY_DN11477_c0_g1 TRINITY_DN11477_c0_g1_i1.p1 51 6 44.6 112 0.00233645
TRINITY_DN160_c0_g1 TRINITY_DN160_c0_g1_i10.p1 39 6 13.8 509 0.00233645
TRINITY_DN13701_c0_g1 TRINITY_DN13701_c0_g1_i1.p1 21 6 8 950 0.00233645
TRINITY_DN18904_c0_g1 TRINITY_DN18904_c0_g1_i1.p1 19 6 50.9 167 0.00233645
TRINITY_DN17150_c0_g1 TRINITY_DN17150_c0_g1_i1.p1 39 5 14.7 407 0.00233645
TRINITY_DN3917_c0_g1 TRINITY_DN3917_c0_g1_i1.p1 37 5 8.8 399 0.00233645
TRINITY_DN1568_c0_g1 TRINITY_DN1568_c0_g1_i1.p1 34 5 25.8 267 0.00233645
Total protein records: 108  (+9 contaminants hidden)
Show: proteins per page
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