{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD028485/PXD028485_community_annotated.sdrf.tsv"],"Msf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD028485/PR563_PL_RS_TMT6_129_131_Tube_2_Rep1_Rep3_Cassio_ProtCnid_Low.msf"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD028485/PR563_PL_RS_TMT6_129_131_Tube_2_Rep3.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD028485/PR563_PL_RS_TMT6_129_131_Tube_2_Rep2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD028485/PR563_PL_RS_TMT6_129_131_Tube_2_Rep1.raw"],"Mgf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD028485/PR563_PL_RS_TMT6_129_131_Tube_2_Rep1_Rep3_Low.mgf"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["paul.long@kcl.ac.uk"],"submitter":["Steven Lynham"],"technology_type":["Mass Spectrometry","Shotgun proteomics"],"software":[""],"submitter_keywords":["Cassiopea andromeda","Toxin","Tmt6plex","Venom","Lc-ms/ms","Antioxidant defense"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD028485"],"tissue":["Nematocyst"],"sample_protocol":["Lyophilised nematocyst samples were resuspended in triethylammonium bicarbonate (TEAB; 100mM)/lysis buffer (7.5M urea, 2M thiourea, 0.1% SDS; all Merck) and incubated for 2 hours on ice. Each sample was vortexed well and centrifuged at 12,000 x g for 5 min at 4oC to form a silt pellet from which the supernatant was removed and assayed using Bradford reagent (Biorad). A normalised protein amount (40 mg) was calculated for each sample prior to mixing with Laemmli buffer (4x) and loaded into a BisTris 1D PAGE gel for minimal resolution (80v constant, 10 min) to stack the entire protein complement into a small section and remove the urea/detergent mix prior to enzymatic digestion. Gels were briefly stained with Imperial stain (Thermo Fisher Scientific) to visualise the resolved protein front. Gel sections were excised, and proteins reduced with dithiothreitol (10 mM) for 1 hour at 56oC then reduced with iodoacetamide (55 mM) at room temperature in the dark for 30 min. Trypsin (bovine; Merck) digestion was performed overnight at 37oC in a ratio of 1:40 enzyme/substrate in 50 mM TEAB. Following digestion, each sample was labelled with a Tandem Mass Tag reagent (TMT6plex, Lot# TA259519; Thermo Fisher Scientific). A volume of 41 ml of each reporter ion label was added as follows: Cassiopea Itarema (TMT129), Cassiopea Key Largo (TMT130) and Cassiopea Alagoas (TMT131) and incubated for 1 hour at room temperature. The reaction was quenched by adding 5% hydroxylamine prior to combining the TMT-labelled samples and lyophilisation."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Mass spectrometry raw data files were processed for database spectral matching using Proteome Discoverer (PD) version 2.2 (Thermo Fisher Scientific). The triplicate sample injections were processed together as one TMT experiment and searched using the Sequest algorithm embedded in PD (Eng et al., 1994). The algorithm specified trypsin as the digestion enzyme with at least two missed cleavages and allowing for cysteine carbamidomethylation as a fixed modification and oxidized methionine, TMT6plex (N-term) and TMT6plex (K) as variable modifications. A precursor ion mass tolerance of 10 ppm and a fragment ion mass tolerance of 0.6 Da were set. Fragmentation spectra were searched against the annotated draft genome of C. andromeda assembled in this study. The search was at low stringency 5% FDR. Grouped protein identifications with their corresponding normalised TMT reporter ion data was exported into Perseus [v1.6.2.1; Tyanova et al., 2016) for calculation of abundance changes between the samples. The log2 value of the TMT reporter ion signals (absolute area under the peak) was used to measure the abundance for each peptide to determine the abundance for each detected peptide across the TMT3plex. The value for each peptide of an identified protein was summed into a single measurement for a protein to calculate the fold-change and determine up- or down-regulation of the identified proteins."],"omics_type":["Proteomics"],"labhead":["Paul F Long"],"instrument_platform":[""],"labhead_affiliation":["Professor of Marine Biotechnology & Therapeutics, Institute of Pharmaceutical Science, King's College London."],"submission_type":["PARTIAL"],"species":["Cassiopea Andromeda"],"publication":["Not available"],"submitter_mail":["steven.lynham@kcl.ac.uk"],"submitter_affiliation":["King's College London"],"submitter_country":["United Kingdom"],"additional_accession":[]},"is_claimable":false,"name":"Quantitative TMT6plex LC-MS/MS of Cassiopea andromeda","description":"Cassiopea andromeda is an ideal species for examining antioxidant stress response by non-calcifying zooxanthellate cnidarians because unlike its sister species Cassiopea xamachana, which is geographically restricted to Florida and the West Indies, C. andromeda typically occurs in tropical and subtropical waters worldwide. However, the molecular and cellular basis of antioxidant defences in Cassiopea species have largely been ignored but are fundamental to understanding the survival and distribution of these cnidarians, especially given that Cassiopea spp. themselves maybe useful indicators of marine ecosystem health in the face of increasing anthropogenic pollution and global climate change. Here we produced a high-quality draft genome sequence of C. andromeda that improves that will provide a foundational resource for advancing Cassiopea as a model research system for early diverging metazoans.","dates":{"publication":"2026-08-19","submission":"2021-09-15"},"accession":"PXD028485","cross_references":{"TAXONOMY":["NEWT:3555","NEWT:71647","NEWT:330879","NEWT:35554","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:32049","NEWT:1392696","NEWT:259447","NEWT:295546","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:180454","NEWT:5722","NCBITaxon:1280","NEWT:1129","NEWT:309807","NEWT:55153","NEWT:10244","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:10036","NEWT:1590","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:1147161","NEWT:638632","NEWT:263737","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:5702","NEWT:95648","NEWT:1589","NEWT:135622","NEWT:1349","NEWT:96731","NEWT:383379","NEWT:10029","NEWT:913645","NEWT:44491","NEWT:556484","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:3112","NEWT:4442","NEWT:31155","NEWT:192875","NEWT:1214915","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:108061","NEWT:1316931","NEWT:224308","NEWT:3347","NEWT:511145","NEWT:931281","NEWT:4432","NEWT:658457","NEWT:1310161","NEWT:77133","NEWT:295358","NEWT:145481","NCBITaxon:79824","NEWT:2246","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:44447","NEWT:752555","NEWT:498211","NEWT:5759","NEWT:1736231","NEWT:5518","NEWT:398007","NEWT:1392","NEWT:498217","NEWT:498216","NEWT:2242","NEWT:11320","NEWT:286","NEWT:391619","NEWT:246196","NEWT:287","NEWT:246197","NEWT:633149","NEWT:10239","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:5507","NEWT:410661","NEWT:55571","NEWT:35500","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:4896","NEWT:1287689","NEWT:1390","NEWT:11557","NEWT:1094343","NEWT:1336795","NEWT:644042","NEWT:294","NEWT:1773","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:3711","NEWT:935293","NEWT:375146","NEWT:2065263","NEWT:118698","NEWT:1616117","NEWT:263","NEWT:118696","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:408169","NEWT:44664","NEWT:47946","NEWT:3702","NEWT:243277","NEWT:7067","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:33548","NEWT:274","NEWT:408172","NEWT:408170","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:1436733","NEWT:460519","NEWT:1247411","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:9483","NEWT:333760","NEWT:1513458","NEWT:1233681","NCBITaxon:40559","NEWT:506599","NEWT:84588","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:508771","NEWT:1883446","NEWT:253","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:93062","NCBITaxon:4932","NEWT:644223","NEWT:235443","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:320637","NEWT:2719099","NEWT:983964","NEWT:118499","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:3988","NEWT:1255228","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:3983","NEWT:352472","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:2014887","NEWT:33952","NEWT:261756","NEWT:571256","NEWT:40483","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:272634","NEWT:9031","NEWT:1872122","NEWT:7091","NEWT:141262","NEWT:108931","NEWT:1055524","NEWT:4087","NEWT:9778","NEWT:306","NEWT:150475","NEWT:303","NEWT:267872","NEWT:7111","NEWT:347515","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:4090","NEWT:4092","NEWT:9541","NEWT:8694","NEWT:4093","NEWT:4096","NEWT:8692","NEWT:185579","NEWT:941442","NEWT:13076","NEWT:1226408","NEWT:7108","NEWT:40479","NEWT:43989","NEWT:4076","NEWT:317","NEWT:1006581","NEWT:885318","NEWT:39488","NEWT:550","NEWT:4081","NEWT:273068","NEWT:554","NEWT:98334","NEWT:451516","NEWT:4084","NEWT:63577","NEWT:36185","NEWT:1225786","NEWT:7574","NEWT:1715256","NEWT:30640","NEWT:575412","NEWT:929793","NEWT:29204","NEWT:28112","NEWT:114155","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:6239","NEWT:162425","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8655","NEWT:1263854","NEWT:118503","NEWT:2059687","NEWT:160488","NEWT:28104","NEWT:207559","NEWT:407821","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:986","NEWT:52641","NEWT:7159","NEWT:28532","NEWT:198618","NEWT:353152","NEWT:8496","NEWT:27448","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:243230","NEWT:1080772","NEWT:519","NEWT:8479","NEWT:8485","NEWT:6063","NEWT:49240","NEWT:104395","NEWT:6289","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:469008","NEWT:256318","NEWT:9321","NEWT:206411","NCBITaxon:6191","NEWT:596153","NEWT:229533","NEWT:1836","NEWT:2925","NEWT:214053","NEWT:80863","NEWT:105231","NEWT:52638","NEWT:57075","NEWT:4097","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:9785","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","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