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_DN10830_c0_g1 TRINITY_DN10830_c0_g1_i1.p1 11 2 19.5 128 0.00233645
TRINITY_DN6596_c0_g1 TRINITY_DN6596_c0_g1_i1.p1 10 2 11 145 0.00233645
TRINITY_DN786_c1_g1 TRINITY_DN786_c1_g1_i1.p1 10 2 1.5 1419 0.00233645
TRINITY_DN808_c0_g1 TRINITY_DN808_c0_g1_i1.p1 8 2 11.3 151 0.00233645
TRINITY_DN8992_c1_g1 TRINITY_DN8992_c1_g1_i1.p1 8 2 7.2 400 0.00233645
TRINITY_DN11725_c0_g1 TRINITY_DN11725_c0_g1_i1.p1 6 2 6.8 355 0.00233645
TRINITY_DN21494_c0_g1 TRINITY_DN21494_c0_g1_i1.p1 6 2 9.9 372 0.00233645
TRINITY_DN408_c1_g1 TRINITY_DN408_c1_g1_i2.p1 6 2 6 284 0.00233645
TRINITY_DN970_c0_g1 TRINITY_DN970_c0_g1_i1.p1 6 2 10.3 156 0.00233645
TRINITY_DN18130_c0_g1 TRINITY_DN18130_c0_g1_i1.p1 5 2 2.3 768 0.00233645
TRINITY_DN23005_c0_g1 TRINITY_DN23005_c0_g1_i1.p1 4 2 5.5 452 0.00233645
TRINITY_DN1771_c0_g1 TRINITY_DN1771_c0_g1_i1.p2 3 2 13.6 177 0.00233645
TRINITY_DN22587_c0_g1 TRINITY_DN22587_c0_g1_i1.p1 3 2 7.4 419 0.00233645
TRINITY_DN17900_c0_g1 TRINITY_DN17900_c0_g1_i1.p1 2 2 4.5 311 0.00606061
TRINITY_DN5690_c0_g1 TRINITY_DN5690_c0_g1_i1.p1 2 2 7.1 254 0.00769231
TRINITY_DN11605_c0_g1 TRINITY_DN11605_c0_g1_i1.p1 11 1 3.7 187 0.00769231
TRINITY_DN353_c0_g1 TRINITY_DN353_c0_g1_i1.p1 9 1 1.6 501 0.00233645
TRINITY_DN13961_c0_g1 TRINITY_DN13961_c0_g1_i1.p1 8 1 4.7 211 0.00233645
TRINITY_DN5697_c0_g3 TRINITY_DN5697_c0_g3_i1.p1 7 1 2.3 428 0.00233645
TRINITY_DN15167_c0_g1 TRINITY_DN15167_c0_g1_i1.p1 6 1 0.9 1269 0.00606061
TRINITY_DN6978_c0_g1 TRINITY_DN6978_c0_g1_i6.p1 6 1 5 140 0.00233645
TRINITY_DN3274_c0_g1 TRINITY_DN3274_c0_g1_i21.p1 5 1 1.1 741 0.00233645
TRINITY_DN539_c0_g1 TRINITY_DN539_c0_g1_i1.p1 5 1 1 704 0.00436681
TRINITY_DN2101_c0_g1 TRINITY_DN2101_c0_g1_i1.p1 4 1 3.7 188 0.00436681
TRINITY_DN715_c1_g1 TRINITY_DN715_c1_g1_i1.p1 4 1 0.9 1113 0.00233645
Total protein records: 108  (+9 contaminants hidden)
Show: proteins per page
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