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 — PXD060643

SpeciesActinia fragacea
Tissuenematocysts, various tissues
PRIDE accessionPXD060643
Statusreprocessed
Search engineComet 2026.01
Reference proteome/mnt/sdb/jackie/cnidaria_omics/transcriptome_proteins/Actinia_tenebrosa.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)
Proteins4572
Peptides (q≤0.01)24717
PSMs (q≤0.01)130483
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_DN6350_c0_g1 TRINITY_DN6350_c0_g1_i4.p1 38 17 35.9 468 0.0000713063
TRINITY_DN910_c1_g1 TRINITY_DN910_c1_g1_i1.p1 36 17 6.6 3040 0.0000713063
TRINITY_DN1030_c1_g1 TRINITY_DN1030_c1_g1_i3.p1 34 17 12.7 1179 0.0000713063
TRINITY_DN6665_c2_g1 TRINITY_DN6665_c2_g1_i1.p1 386 16 72.4 134 0.0000713063
TRINITY_DN107_c2_g4 TRINITY_DN107_c2_g4_i1.p1 258 16 49.5 295 0.0000713063
TRINITY_DN6100_c0_g1 TRINITY_DN6100_c0_g1_i1.p1 159 16 14.9 831 0.0000713063
TRINITY_DN41406_c0_g1 TRINITY_DN41406_c0_g1_i1.p1 148 16 62.7 236 0.0000713063
TRINITY_DN29747_c0_g1 TRINITY_DN29747_c0_g1_i1.p1 131 16 28.4 550 0.0000713063
TRINITY_DN152_c0_g1 TRINITY_DN152_c0_g1_i10.p1 129 16 37.1 334 0.0000713063
TRINITY_DN41326_c0_g1 TRINITY_DN41326_c0_g1_i1.p1 125 16 43.6 312 0.0000713063
TRINITY_DN395_c4_g1 TRINITY_DN395_c4_g1_i2.p1 116 16 35.2 571 0.0000713063
TRINITY_DN625_c0_g1 TRINITY_DN625_c0_g1_i26.p1 113 16 31 654 0.0000713063
TRINITY_DN10932_c0_g1 TRINITY_DN10932_c0_g1_i1.p1 112 16 46.8 406 0.0000713063
TRINITY_DN3884_c0_g5 TRINITY_DN3884_c0_g5_i1.p1 108 16 36.9 498 0.0000713063
TRINITY_DN79_c5_g2 TRINITY_DN79_c5_g2_i3.p1 104 16 23.3 776 0.0000713063
TRINITY_DN953_c7_g1 TRINITY_DN953_c7_g1_i1.p1 89 16 24.6 784 0.0000713063
TRINITY_DN15050_c1_g1 TRINITY_DN15050_c1_g1_i1.p1 86 16 35.8 358 0.0000713063
TRINITY_DN5921_c0_g1 TRINITY_DN5921_c0_g1_i3.p1 83 16 40 430 0.0000713063
TRINITY_DN92_c3_g2 TRINITY_DN92_c3_g2_i2.p1 83 16 28.2 659 0.0000713063
TRINITY_DN15802_c0_g1 TRINITY_DN15802_c0_g1_i7.p1 80 16 41.2 515 0.0000713063
TRINITY_DN35261_c0_g1 TRINITY_DN35261_c0_g1_i1.p1 79 16 49 367 0.0000713063
TRINITY_DN1640_c1_g2 TRINITY_DN1640_c1_g2_i1.p1 77 16 25 641 0.0000713063
TRINITY_DN42600_c0_g1 TRINITY_DN42600_c0_g1_i1.p1 77 16 38.9 414 0.0000713063
TRINITY_DN2015_c0_g1 TRINITY_DN2015_c0_g1_i4.p1 68 16 42.2 386 0.0000713063
TRINITY_DN8248_c0_g1 TRINITY_DN8248_c0_g1_i1.p1 67 16 24.2 665 0.0000713063
Total protein records: 4572  (+15 contaminants hidden)
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