{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/KEY.xlsx"],"Tabular":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/Mouse_2025.pr_matrix.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/Mouse_2025.pg_matrix.tsv","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/Sotiropoulos_40629_2TR.unique_genes_matrix.tsv"],"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20207_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20205_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20196_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20198_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20206_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20199_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20204_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20197_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20207_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20205_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20196_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20198_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20204_2.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20199_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20206_1.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD073466/20197_2.raw"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["ioannis@bio.demokritos.gr"],"submitter":["Martina Samiotaki"],"technology_type":["Mass Spectrometry","Bottom-up proteomics","Data-independent acquisition"],"software":[""],"submitter_keywords":["Mus musculus","Mapt knockout","Tau knockout","Quantitave proteomics","Dia","Hippocampus"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD073466"],"tissue":["Hippocampus"],"sample_protocol":["Lysed protein samples were processed using the Single-Pot Solid-Phase-enhanced Sample Preparation (SP3) method. Eluates were alkylated with 200 mM iodoacetamide. For protein capture, 20 μg of a 1:1 mixture of hydrophilic and hydrophobic paramagnetic beads was added to each sample, adjusted to a final concentration of 50% ethanol to induce binding. Using a magnetic rack, the supernatant was discarded, and the bead-bound proteins were washed three times with 80% ethanol. Digestion was performed on-bead overnight at 37°C using a Trypsin/LysC enzyme mix in 100 mM TEAB. Following digestion, peptides were purified from the supernatant using the modified for peptides SP3 protocol. Finally, the peptide samples were vacuum-dried, reconstituted in 0.1% formic acid, and analyzed via liquid chromatography-tandem mass spectrometry (LC-MS/MS). Peptide separation and analysis were performed using a Dionex Ultimate 3000 RSLC system coupled online to a Q Exactive HF-X Hybrid Quadrupole-Orbitrap mass spectrometer (Thermo Fisher Scientific). Samples were directly injected onto a PepSep C18 analytical column (25 cm, 75 μm Inner Diameter and, 1.9 μm particle size, Bruker). Separation was achieved using a 60-minute gradient with Buffer B (80% acetonitrile, 0.1% formic acid) at a controlled flow rate. The gradient started from 7% to 35% Buffer B over 40 minutes, increased to 45% over 5 minutes, and ramped to 99% in 0.5 minutes, where it was maintained for 14.5 minutes. Mass spectrometry data were acquired in profile mode using a Data Independent Acquisition (DIA) method. Full MS scans were acquired in the range of 375–1400 m/z with a resolution of 120,000, an Automatic Gain Control (AGC) target of 3x106, and a maximum injection time of 60 ms. This was followed by DIA scans using a loop count of 39 with 8Th isolation windows. MS/MS scans were acquired at a resolution of 15,000 with an AGC target of 3x105 and a maximum injection time of 22 ms, and a normalized collision energy (NCE) of 26."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Orbitrap raw data was analysed in DIA-NN 2.3.0 (Data-Independent Acquisition by Neural Networks) through searching against the reference Mus musculus Uniprot databases supplemented with the common contaminant database (21912 proteins/ downloaded September 2025). The search was performed using the library-free mode of the software, allowing up to two tryptic missed cleavages. A spectral library was created by the DIA runs and used to reanalyze them. DIA-NN default settings have been used with oxidation of methionine residues, deamidation of N and Q and acetylation of the protein N-termini set as variable modifications and carbamidomethylation of cysteine residues as fixed modification. N-terminal methionine excision was also enabled. The match between runs (MBR) feature was used for all analyses and the output (precursor) was filtered at 1% FDR and finally the protein inference was performed on the level of genes using only proteotypic (unique) peptides. The cross-run normalization feature was also activated."],"omics_type":["Proteomics"],"labhead":["Ioannis Sotiropoulos"],"instrument_platform":[""],"labhead_affiliation":["ExoBrain - Laboratory of Brain Exosomes & Pathology Institute of Biosciences & Applications NCSR \"Demokritos\" T. Patriarchou Grigoriou & Neapoleos 15341 Athens, Greece"],"submission_type":["PARTIAL"],"species":["Mus Musculus (mouse)"],"submitter_mail":["samiotaki@fleming.gr"],"publication":["Not available"],"submitter_affiliation":["Protein Analysis Laboratory\nB.S.R.C. \"Alexander Fleming\",\nAlexander Fleming Street 34\n16672, Vari,\nGreece"],"submitter_country":["Greece"],"additional_accession":[]},"is_claimable":false,"name":"Comparative Proteomic Profiling of Tau-Knockout and Wild-Type Mouse Hippocampus","description":"Mitochondria fuse, divide, and interact with other organelles to adjust cellular fitness while they provide energy to sustain neuronal activity and health. In contrast to plethora of evidence reporting that accumulation of pathological Tau damages mitochondria function promoting neurodegeneration, there is limited knowledge about the physiological role of Tau on the maintenance of mitochondrial homeostasis. Our mice and C. elegans studies provide multiscale evidence that loss of Tau or its nematode homolog, PTL-1, enhances mitochondrial function and mitochondria quality control promoting a profusion state via mitofusins, that leads to reduced vulnerability to mitochondria stress. Overall, our findings provide solid evidence about the fine-tuning role of Tau protein on mitochondrial function and dynamics in neurons based on two different organisms.","dates":{"publication":"2026-06-15","submission":"2026-01-23"},"accession":"PXD073466","cross_references":{"TAXONOMY":["NEWT:6945","NEWT:184922","NEWT:3555","NEWT:2","NEWT:157546","NEWT:35554","NEWT:38942","NEWT:307972","NEWT:32046","NEWT:544496","NEWT:2042546","NEWT:45351","NEWT:43179","NEWT:4513","NEWT:5722","NEWT:55153","NCBITaxon:10407","NEWT:1736309","NEWT:309800","NEWT:1211601","NEWT:876138","NEWT:3654","NEWT:237561","NEWT:5833","NEWT:6928","NEWT:10036","NEWT:36745","NEWT:1351","NEWT:1438992","NEWT:2649997","NEWT:272563","NEWT:224326","NCBITaxon:79857","NEWT:1096976","NEWT:95648","NEWT:3885","NEWT:3888","NEWT:1589","NEWT:135622","NCBITaxon:4896","NEWT:6915","NEWT:3649","NEWT:101510","NEWT:3880","NEWT:272559","NEWT:3641","NEWT:383379","NEWT:466585","NEWT:10029","NEWT:913645","NEWT:1000589","NEWT:85963","NEWT:85962","NEWT:317447","NEWT:7955","NEWT:7959","NEWT:2261","NEWT:31156","NEWT:398580","NEWT:4565","NEWT:1264690","NEWT:515619","NEWT:192875","NEWT:34305","NEWT:59729","NCBITaxon:183674","NEWT:224308","NEWT:84645","NEWT:626528","NEWT:139927","NEWT:4558","NEWT:209285","NEWT:5888","NEWT:1283","NEWT:931281","NEWT:4550","NEWT:1000561","NEWT:197","NEWT:1390363","NEWT:288705","NCBITaxon:79824","NEWT:4787","NCBITaxon:4563","NEWT:5755","NEWT:44689","NEWT:3218","NEWT:5759","NEWT:1736231","NEWT:1270","NEWT:374990","NEWT:2242","NEWT:4784","NEWT:11320","NEWT:360106","NEWT:286","NEWT:391619","NEWT:287","NEWT:10117","NEWT:10239","NEWT:10116","NEWT:1280","NEWT:1735272","NEWT:83334","NEWT:83332","NEWT:44685","NEWT:317513","NEWT:1148","NEWT:580240","NEWT:294128","NEWT:11676","NEWT:55571","NEWT:100226","NEWT:4530","NEWT:4896","NEWT:75058","NEWT:13616","NEWT:1390","NEWT:1094343","NEWT:296543","NEWT:1773","NEWT:1895","NEWT:1182590","NEWT:3712","NEWT:105023","NEWT:935293","NEWT:64152","NEWT:4924","NEWT:749200","NEWT:375146","NEWT:990346","NEWT:145953","NEWT:257309","NEWT:100816","NEWT:263","NEWT:230741","NEWT:52283","NEWT:284812","NCBITaxon:1313","NEWT:43330","NEWT:1603293","NEWT:408169","NEWT:44544","NEWT:4911","NEWT:645463","NEWT:3702","NEWT:129249","NEWT:243277","NEWT:990119","NEWT:408172","NEWT:408170","NEWT:493760","NEWT:260710","NEWT:257313","NEWT:400772","NEWT:3708","NEWT:128161","NEWT:332648","NEWT:106592","NEWT:536231","NEWT:460519","NEWT:1187947","NEWT:1432138","NEWT:10312","NEWT:1424507","NCBITaxon:1773","NEWT:9598","NEWT:8030","NEWT:1639","NEWT:188229","NEWT:3818","NEWT:480","NEWT:4909","NEWT:67767","NEWT:432359","NEWT:46835","NEWT:1182263","NEWT:2711","NEWT:376686","NEWT:95486","NEWT:9103","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:3635","NEWT:5811","NEWT:235443","NEWT:272623","NEWT:272624","NEWT:411483","NEWT:884019","NEWT:198215","NEWT:411490","NEWT:983964","NEWT:169963","NEWT:32644","NEWT:225117","NEWT:499175","NEWT:109779","NEWT:476272","NEWT:3747","NEWT:195051","NEWT:367830","NEWT:1255228","NEWT:178616","NEWT:410289","NEWT:373153","NEWT:352472","NEWT:357","NEWT:360094","NEWT:470","NEWT:1313","NEWT:411469","NEWT:84023","NEWT:559292","NEWT:39491","NCBITaxon:5811","NEWT:411464","NEWT:411460","NEWT:2014887","NEWT:2762","NEWT:1174673","NEWT:562","NEWT:411470","NEWT:33952","NEWT:2094720","NCBITaxon:2697049","NEWT:571256","NEWT:28038","NEWT:1663","NEWT:1423","NEWT:4932","NEWT:3603","NEWT:2759","NEWT:3847","NEWT:327159","NEWT:178876","NEWT:327160","NEWT:573","NEWT:9031","NEWT:7091","NEWT:108931","NEWT:241368","NEWT:42528","NEWT:190802","NEWT:9778","NEWT:150475","NEWT:303","NEWT:9417","NEWT:7111","NEWT:347515","NEWT:1216979","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:115104","NEWT:1121114","NEWT:663","NEWT:1081927","NEWT:1238993","NEWT:67825","NEWT:185579","NEWT:941442","NEWT:220668","NEWT:13076","NEWT:1249668","NEWT:7108","NEWT:317","NEWT:7227","NEWT:7469","NEWT:885318","NEWT:9402","NEWT:415540","NEWT:550","NEWT:675060","NEWT:4081","NEWT:334542","NEWT:554","NEWT:98334","NEWT:426428","NEWT:7574","NEWT:1715256","NEWT:7215","NEWT:575412","NEWT:29204","NEWT:2172103","NEWT:507601","NEWT:643680","NCBITaxon:6157","NEWT:746360","NEWT:6239","NEWT:470150","NEWT:216257","NEWT:102169","NEWT:9986","NEWT:4054","NEWT:73239","NEWT:226186","NEWT:1268063","NEWT:8782","NEWT:1263854","NEWT:435590","NEWT:1902","NEWT:160488","NEWT:28104","NEWT:1908","NEWT:13164","NEWT:216129","NCBITaxon:2","NEWT:985076","NEWT:1215323","NEWT:52641","NEWT:7038","NEWT:6192","NEWT:28532","NCBITaxon:38727","NEWT:353152","NEWT:2829","NEWT:366581","NEWT:216599","NEWT:216595","NEWT:1194669","NEWT:51329","NEWT:243230","NEWT:8355","NEWT:9685","NEWT:7029","NEWT:1080772","NEWT:8479","NEWT:1283300","NEWT:6183","NEWT:6063","NEWT:630","NEWT:334747","NEWT:61235","NEWT:15368","NEWT:6289","NEWT:436486","NEWT:6287","NEWT:300641","NEWT:727","NEWT:9796","NEWT:725","NEWT:170187","NEWT:469008","NEWT:260707","NEWT:256318","NCBITaxon:6191","NEWT:1836","NEWT:185431","NEWT:29760","NEWT:260704","NEWT:703612","NEWT:260705","NEWT:80863","NEWT:2697049","NEWT:105231","NEWT:1216981","NEWT:4097","NCBITaxon:6073","NEWT:884204","NEWT:6279","NEWT:1123869","NEWT:9544","NEWT:7370","NEWT:83906","NEWT:607699","NEWT:6282","NEWT:208964","NEWT:1134506","NEWT:575584","NEWT:38783","NEWT:8727","NEWT:4006","NEWT:8726","NEWT:6426","NEWT:6669","NEWT:10090","NEWT:4120","NEWT:51515","NEWT:5693","NEWT:8724","NEWT:51511","NEWT:92867","NEWT:8723","NEWT:5334","NEWT:37334","NEWT:382352","NCBITaxon:10359","NEWT:242619","NEWT:632957","NEWT:34073","NEWT:373995","NEWT:5689","NEWT:544404","NEWT:9925","NEWT:8839","NEWT:4232","NEWT:2758385","NEWT:37349","NEWT:4113","NEWT:837","NEWT:11298","NEWT:171101","NEWT:714","NEWT:36015","NEWT:421932","NEWT:196627","NEWT:5691","NEWT:48479","NEWT:627025","NEWT:1097677","NEWT:61674","NEWT:1117957","NEWT:9913","NEWT:8709","NEWT:4100","NEWT:1076","NEWT:6763","NEWT:803","NEWT:29722","NEWT:380394","NEWT:1692259","NEWT:180066","NEWT:817","NEWT:135588","NEWT:1843183","NEWT:58002","NEWT:326423","NEWT:36111","NEWT:4577","NEWT:1416333","NEWT:5664","NEWT:2157","NEWT:1678078","NEWT:749906","NEWT:418985","NEWT:146479","NEWT:749907","NEWT:1911079","NEWT:69373","NEWT:264203","NEWT:1480154","NEWT:1274414","NEWT:27606","NEWT:59202","NEWT:9975","NEWT:9612","NEWT:38865","NEWT:51953","NEWT:3197","NEWT:9615","NEWT:10299","NEWT:860688","NEWT:112273","NEWT:36329","NEWT:1147787","NCBITaxon:3044782","NEWT:1440772","NEWT:72407","NEWT:1355477","NEWT:349741","NEWT:9605","NEWT:9606","NEWT:90371","NEWT:157295","NEWT:641501","NEWT:7668","NEWT:915099","NEWT:74940","NEWT:9721","NEWT:137221","NEWT:9600","NEWT:1450511","NEWT:1143193","NEWT:411901","NEWT:9838","NEWT:105884","NCBITaxon:9615","NEWT:9839","NEWT:58334","NEWT:1193501","NEWT:3055","NEWT:58331","NEWT:6326","NEWT:6689","NEWT:5476","NEWT:299767","NEWT:1274432","NEWT:1274426","NEWT:70448","NEWT:9825","NEWT:1274423","NEWT:393765","NEWT:698936","NEWT:39946","NEWT:9823","NEWT:9940","NEWT:95602","NEWT:8732","NEWT:521001","NEWT:39947","NEWT:224911","NEWT:1274420","NEWT:578458"],"ORCID":["0000-0001-9952-0636"]}}