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 — PXD022770

SpeciesCeratonova shasta
TissueDevelopmental stages (in Ascites fluid)
PRIDE accessionPXD022770
Statusreprocessed
Search engineComet 2026.01
Reference proteome/mnt/sdb/jackie/cnidaria_omics/transcriptome_proteins/Ceratonova_shasta.rep.pep
Enzymetrypsin/P
Missed cleavages2
Precursor tolerance10 ppm
Fragment tolerance0.02 Da
Fixed modificationC+57.021464
Variable modificationM+15.9949,n+42.010565
Decoy strategyComet internal reversed (1:1)
FDR (PSM)0.01
Quantificationspectral counting (PSMs)
Proteins2239
Peptides (q≤0.01)12107
PSMs (q≤0.01)103880
reprocessed against the CnidoSite reference proteome
41 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_DN4961_c0_g1 TRINITY_DN4961_c0_g1_i2.p1 65 10 62.5 248 0.000124719
TRINITY_DN13386_c1_g1 TRINITY_DN13386_c1_g1_i1.p1 64 10 64 114 0.000124719
TRINITY_DN23373_c0_g1 TRINITY_DN23373_c0_g1_i19.p1 64 10 63.1 111 0.000124719
TRINITY_DN10795_c0_g1 TRINITY_DN10795_c0_g1_i1.p1 63 10 47.7 149 0.000124719
TRINITY_DN40510_c1_g1 TRINITY_DN40510_c1_g1_i1.p1 62 10 52.4 105 0.000124719
TRINITY_DN7721_c0_g1 TRINITY_DN7721_c0_g1_i1.p1 62 10 36.1 216 0.000124719
TRINITY_DN16679_c0_g1 TRINITY_DN16679_c0_g1_i13.p2 58 10 40.3 154 0.000124719
TRINITY_DN24150_c0_g1 TRINITY_DN24150_c0_g1_i1.p1 58 10 35.6 160 0.000124719
TRINITY_DN11818_c0_g1 TRINITY_DN11818_c0_g1_i1.p1 57 10 30.5 213 0.000124719
TRINITY_DN5334_c0_g1 TRINITY_DN5334_c0_g1_i3.p1 54 10 60.1 163 0.000124719
TRINITY_DN9931_c0_g2 TRINITY_DN9931_c0_g2_i2.p1 54 10 40.3 186 0.000124719
TRINITY_DN17102_c0_g3 TRINITY_DN17102_c0_g3_i3.p1 53 10 54.1 233 0.000124719
TRINITY_DN974_c0_g1 TRINITY_DN974_c0_g1_i10.p1 53 10 86.8 106 0.000124719
TRINITY_DN15017_c0_g1 TRINITY_DN15017_c0_g1_i19.p1 52 10 63.9 155 0.000124719
TRINITY_DN434_c0_g3 TRINITY_DN434_c0_g3_i1.p1 51 10 63.2 182 0.000124719
TRINITY_DN6561_c0_g1 TRINITY_DN6561_c0_g1_i3.p1 49 10 55.6 142 0.000124719
TRINITY_DN7018_c0_g1 TRINITY_DN7018_c0_g1_i13.p1 47 10 59.8 174 0.000124719
TRINITY_DN391_c0_g1 TRINITY_DN391_c0_g1_i33.p1 44 10 31.7 265 0.000124719
TRINITY_DN2659_c0_g1 TRINITY_DN2659_c0_g1_i1.p1 42 10 66 147 0.000124719
TRINITY_DN3948_c0_g3 TRINITY_DN3948_c0_g3_i1.p1 41 10 54.2 131 0.000124719
TRINITY_DN20507_c0_g1 TRINITY_DN20507_c0_g1_i1.p1 37 10 61.4 210 0.000124719
TRINITY_DN12432_c0_g2 TRINITY_DN12432_c0_g2_i10.p1 593 9 55.4 130 0.000124719
TRINITY_DN8164_c0_g1 TRINITY_DN8164_c0_g1_i4.p1 158 9 38.3 120 0.000124719
TRINITY_DN2225_c0_g1 TRINITY_DN2225_c0_g1_i1.p2 137 9 62.3 114 0.000124719
TRINITY_DN5693_c0_g5 TRINITY_DN5693_c0_g5_i1.p1 126 9 31.3 150 0.000124719
Total protein records: 2239  (+41 contaminants hidden)
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