Proteomic Dataset Details

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PXD022770 — Ceratonova shasta — Developmental stages (in Ascites fluid)

SpeciesCeratonova shasta
ClassMyxozoa
Tissue / sampleDevelopmental stages (in Ascites fluid)
Treatment / conditionInfection in Rainbow Trout
InstrumentQ Exactive Plus
PRIDE project PXD022770
Publication PMID Link
Raw files8
Search space is a transcriptome assembly, not a reference proteome
Ceratonova shasta has no genome annotation, so no CnidoSite reference proteome exists for it. The search database is the representative protein set predicted from a Trinity de novo assembly of this species' own public RNA-seq. Peptides therefore map to transcript contigs and not to CnidoSite gene pages; no gene ID is displayed for this dataset.

Original study vs CnidoSite re-processing

Parameter As reported by the original study As applied by CnidoSite
Search engine MaxQuant 1.5.2.8 (Andromeda) Comet 2026.01 + Percolator (Crux 4.2)
Sequence database O. mykiss UniProt + C. shasta transcriptome ORFs (TransDecoder) /mnt/sdb/jackie/cnidaria_omics/transcriptome_proteins/Ceratonova_shasta.rep.pep
De novo Trinity transcriptome assembly of Ceratonova shasta; TransDecoder representative proteins (5,145 sequences), not BUSCO-validated
Enzyme – (not restated) trypsin/P (fully enzymatic, 2 termini)  ·  up to 2 missed cleavages
Precursor tolerance not stated 10 ppm
Fragment tolerance not stated 0.02 Da
Fixed modification – C+57.021464 (carbamidomethyl cysteine)
Variable modification – M+15.9949,n+42.010565 (methionine oxidation)
Decoy strategy – Comet internal reversed (1:1)
False discovery rate 1% q ≤ 0.01 at the PSM level (Percolator q-values, target-decoy); protein level q ≤ 0.01
Quantification – spectral counting (PSMs)
Contaminants – cRAP appended and flagged; 41 contaminant proteins identified and excluded from the reported protein list
Gene mapping – Peptides are reported against transcript sequences. This species has no CnidoSite gene models, so no protein links to a gene page.

Outcome of re-processing

Re-processed successfully. reprocessed against the CnidoSite reference proteome
PSMs at q≤0.01Peptides at q≤0.01 Gene-linked proteinsContaminants (excluded)
103,880 12,107 2,239 41

Pipeline version cnidosite-proteomics 1.0 · CnidoSite release 1.1 · incorporated 2026-09-21

Reproducing this dataset

Every stage is a single command; the parameter file written by stage 2 is the one shown in the table above.

python3 2.pipeline/02_fetch_pride.py PXD022770 # retrieve peak lists from PRIDE python3 2.pipeline/03_build_search_db.py "Ceratonova shasta" # proteome + cRAP python3 2.pipeline/04_run_search.py PXD022770 # writes comet.params, runs Comet python3 2.pipeline/05_fdr_percolator.py PXD022770 # Percolator, q ≤ 0.01 python3 2.pipeline/06_map_to_genes.py PXD022770 # peptides -> CnidoSite genes python3 2.pipeline/07_build_tables.py --release 1.1 # load tables + SQL

Most strongly supported proteins in this dataset

GeneProtein Unique peptidesPSMsCoverage (%) LengthBest qDescription
TRINITY_DN1241_c0_g4 TRINITY_DN1241_c0_g4_i5.p1 60 743 64.7 453 0.000124719
TRINITY_DN23861_c0_g2 TRINITY_DN23861_c0_g2_i9.p1 42 666 78.8 325 0.000124719
TRINITY_DN4080_c0_g1 TRINITY_DN4080_c0_g1_i7.p1 38 490 72.1 312 0.000124719
TRINITY_DN2907_c0_g1 TRINITY_DN2907_c0_g1_i10.p1 38 443 76.2 286 0.000124719
TRINITY_DN2968_c0_g2 TRINITY_DN2968_c0_g2_i3.p1 36 423 90.9 351 0.000124719
TRINITY_DN46125_c0_g2 TRINITY_DN46125_c0_g2_i1.p1 36 336 58.5 398 0.000124719
TRINITY_DN2260_c0_g2 TRINITY_DN2260_c0_g2_i2.p1 35 2216 75.4 268 0.000124719
TRINITY_DN32671_c0_g1 TRINITY_DN32671_c0_g1_i9.p1 34 614 75.7 276 0.000124719
TRINITY_DN1303_c7_g1 TRINITY_DN1303_c7_g1_i1.p1 34 533 85.3 177 0.000124719
TRINITY_DN546_c0_g2 TRINITY_DN546_c0_g2_i5.p1 32 654 87.5 184 0.000124719
TRINITY_DN1467_c1_g1 TRINITY_DN1467_c1_g1_i18.p1 32 555 91.8 196 0.000124719
TRINITY_DN41537_c0_g1 TRINITY_DN41537_c0_g1_i1.p1 32 354 55.3 318 0.000124719
TRINITY_DN679_c0_g2 TRINITY_DN679_c0_g2_i2.p1 30 338 71.8 330 0.000124719
TRINITY_DN11234_c0_g1 TRINITY_DN11234_c0_g1_i10.p1 29 408 72.1 323 0.000124719
TRINITY_DN17855_c0_g1 TRINITY_DN17855_c0_g1_i2.p1 29 232 74.5 231 0.000124719

View all 2,239 proteins »

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