{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073209/md5sum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073209/WT_3_6.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073209/P2_1_7.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073209/WT_2_5.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073209/P2_2_8.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073209/WT_1_4.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073209/P2_3_9.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073209/132830_sp_MJ20241224098_PP20250206010.sne"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["tanhuanj@163.com"],"submitter":["Huanjiao Tan"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["pseudomonas plecoglossicida","Larimichthys crocea","mitochondria","Larimichthys crocea; pseudomonas plecoglossicida; pptse6; mitochondria;","pptse6"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD073209"],"tissue":["Hepatocyte","Liver"],"sample_protocol":["1. Experimental Fish Approximately 50 g large yellow croakers (Larimichthys crocea) from Ningde, China, were acclimated for one week at 18°C in a recirculating system without feeding. 2. Experimental Infection and Sampling A total of 300 fish (in triplicate trials of 100 fish each) were randomly divided into five groups (n=20 per group). WT groups received 10³ and 10⁴ CFU/fish, while Δpptse6 groups received 10⁵ and 5×10⁶ CFU/fish, respectively; a PBS group served as control. Mortality was recorded daily for 10 days. Moribund fish showing severe symptoms were sampled from the pptse6 and WT groups. Liver tissues (≥3 biological replicates per group) were collected, snap-frozen in liquid nitrogen, and stored at −80°C. 3. Protein Extraction and Proteomic Analysis After adding protein lysis buffer, samples were homogenized three times, followed by 30 min of low-temperature sonication. Supernatants were collected by centrifugation,with protein concentration determined by BCA assay and analyzed via SDS-PAGE electrophoresis. A total of 100 µg protein was reacted with 100 mM TEAB and 10 mM TCEP, followed by 40 min reaction with 40 mM iodoacetamide. Acetone-precipitated samples were centrifuged, dissolved, and digested. Peptides were vacuum concentrated.Samples were redissolved in 0.1% TFA, desalted via HLB cartridges, vacuum concentrated,and finally quantified using a NanoDrop One UV spectrophotometer (Thermo, Waltham,MA, USA) .Peptides were separated by Vanquish Neo LC system and analyzed on Orbitrap Astral MS, with data acquired using Thermo Xcalibur 4.7. DIA mode (100–1700 m/z) was used. Raw data were processed with Spectronaut™ 19 (large yellow croaker database) for bioinformatic analysis. GO and KEGG pathway analyses were performed for functional clustering of differentially expressed proteins, and R language t-test was used to calculate the significance (p value) and fold change between groups."],"repository":["Pride"],"modification":[""],"quantification_method":[""],"data_protocol":["Data Processing and Bioinformatics Analysis Raw mass spectrometry data files (.raw) were processed using Spectronaut™.Searches were performed against a customized protein sequence database of Larimichthys crocea.Quantification was performed using the DIA (Data-Independent Acquisition) workflow with default settings in Spectronaut."],"omics_type":["Proteomics"],"labhead":["Huanjiao Tan"],"instrument_platform":[""],"labhead_affiliation":["Master's student,Laboratory of Aquatic Animal Disease,Fisheries college of Jimei University"],"submission_type":["PARTIAL"],"species":["Larimichthys Crocea (large Yellow Croaker) (pseudosciaena Crocea)"],"submitter_mail":["tanhuanj@163.com"],"publication":["10.1016/J.FSI.2026.111356"],"submitter_affiliation":["Fisheries College of JiMei University"],"submitter_country":["China"],"additional_accession":[]},"is_claimable":false,"name":"Liver proteomics data of Larimichthys crocea infected with the Pseudomonas plecoglossicida pptse6 mutant strain and wild-type strain","description":"The large yellow croaker (Larimichthys crocea) is a vital mariculture fish species in China. Its industry is severely constrained by visceral white-nodules disease caused by Pseudomonas plecoglossicida, yet the key virulence factors and pathogenic mechanisms of this bacterium remain incompletely understood. This study investigated the role of the pptse6 gene during infection by constructing a pptse6 gene deletion mutant (Δpptse6) of P. plecoglossicida. Results demonstrated that compared to the wild-type strain (NZBD9), the Δpptse6 strain exhibited significantly attenuated virulence. Infection with the mutant resulted in higher survival rates and alleviated hepatic mitochondrial damage and metabolic disturbances (such as triglyceride accumulation and glycogen depletion) in large yellow croakers.","dates":{"publication":"2026-06-28","submission":"2026-01-19"},"accession":"PXD073209","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:6703","NEWT:3555","NEWT:71647","NEWT:2","NEWT:157546","NEWT:474186","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:1496","NEWT:544496","NEWT:2102","NEWT:2042546","NEWT:259447","NEWT:45351","NEWT:445974","NEWT:43179","NEWT:4513","NEWT:180454","NEWT:5722","NEWT:1247","NEWT:6938","NEWT:1129","NEWT:376741","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:281395","NEWT:10360","NEWT:1211601","NEWT:876138","NEWT:47664","NEWT:317548","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:498019","NEWT:1351","NEWT:1438992","NEWT:1352","NEWT:2649997","NEWT:272563","NEWT:1147161","NEWT:224326","NEWT:1333499","NCBITaxon:79857","NEWT:1096976","NEWT:82688","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:5821","NEWT:1589","NEWT:44139","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:28903","NEWT:3880","NEWT:272559","NEWT:28909","NEWT:515849","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:143361","NEWT:317447","NEWT:4688","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4442","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NEWT:2164133","NCBITaxon:183674","NEWT:1316931","NEWT:224308","NEWT:167387","NEWT:84645","NEWT:44586","NEWT:626528","NEWT:3347","NEWT:511145","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:211586","NEWT:747078","NEWT:1282","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:2133","NEWT:294381","NEWT:197","NEWT:1390363","NEWT:77133","NEWT:288705","NEWT:29176","NEWT:145481","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:556182","NEWT:1270","NEWT:374990","NEWT:1392","NEWT:498217","NEWT:156471","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:156476","NEWT:286","NEWT:391619","NEWT:360104","NEWT:246196","NEWT:287","NEWT:246197","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:161934","NEWT:1148","NEWT:580240","NEWT:5508","NEWT:294128","NEWT:5507","NEWT:11676","NEWT:55571","NEWT:35500","NEWT:1140","NEWT:100226","NEWT:4530","NEWT:1143","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:1336795","NEWT:644042","NEWT:296543","NEWT:316435","NEWT:42157","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:82380","NEWT:1034304","NEWT:105023","NEWT:866628","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:9378","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NEWT:8175","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:47946","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:1077286","NEWT:243277","NEWT:990119","NEWT:7067","NEWT:2850","NEWT:1111708","NEWT:408172","NEWT:227321","NEWT:408170","NEWT:493760","NEWT:106590","NEWT:260710","NEWT:257313","NEWT:3827","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:930945","NEWT:106592","NEWT:536231","NEWT:46704","NEWT:1436733","NEWT:460519","NEWT:1187947","NEWT:572307","NEWT:1432138","NEWT:269796","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:1194599","NEWT:272844","NEWT:54571","NEWT:9598","NEWT:8030","NEWT:9483","NEWT:1513458","NCBITaxon:40559","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:759272","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:109757","NEWT:943146","NEWT:2711","NEWT:300852","NEWT:1502","NEWT:376686","NEWT:95486","NEWT:9103","NEWT:508771","NEWT:1883446","NEWT:29159","NEWT:253","NEWT:10306","NCBITaxon:2759","NEWT:1233435","NEWT:93061","NEWT:8022","NEWT:145943","NCBITaxon:4932","NEWT:595536","NEWT:240906","NEWT:593117","NEWT:89920","NEWT:29158","NEWT:3635","NEWT:5811","NEWT:235443","NEWT:180923","NEWT:108458","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:118499","NEWT:169963","NEWT:32644","NEWT:527796","NEWT:225117","NEWT:746128","NEWT:499175","NEWT:109779","NEWT:43665","NEWT:1266464","NEWT:1715989","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:649908","NEWT:410289","NEWT:373153","NEWT:375451","NEWT:352472","NEWT:357","NEWT:1071661","NEWT:360094","NEWT:470","NEWT:41364","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:1679","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:29491","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:1328426","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NCBITaxon:138","NEWT:40483","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:38293","NEWT:1428","NEWT:327159","NEWT:178876","NEWT:1660","NEWT:327160","NEWT:573","NEWT: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