{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/SamplesTable.xlsx"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/QEAJS220609_17.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/QEAJS220609_03.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/QEAJS220609_09.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/QEAJS220609_11.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/QEAJS220609_05.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/QEAJS220609_15.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/QEAJS220609_13.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/QEAJS220609_07.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/F122107.dat","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/F122111.dat","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/F122105.dat","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/F122108.dat","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/F122109.dat","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/F122110.dat","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/F122112.dat","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/02/PXD065512/F122106.dat"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["odile.schiltz@ipbs.fr"],"submitter":["Alexandre STELLA"],"technology_type":["Data-dependent acquisition","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Raggtpase","Muscle cells/myotube","Lamtors","Mtorc1","Phosphonositides","Mtm1"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD065512"],"tissue":["Cell Culture"],"sample_protocol":["Lyso-Tag (3XHA-TMEME-192) lentivirus infection, homogenization and purification using immunoprecipitation (HA beads), proteomics analysis.  Each sample dried protein extracts were solubilized with 50µl of 5% SDS. Proteins were submitted to reduction and alkylation of cysteine residues by addition of TCEP and chloroacetamide to a final concentration respectively of 10mM and 40mM. Protein samples were then processed for trypsin digestion on S-trap Micro devices (Protifi) according to manufacturer’s protocol, with the following modifications: precipitation was performed using 491µl S-Trap buffer; 1µg Trypsin was added per sample for digestion, in 25µl ammonium bicarbonate 50mM pH7. Tryptic peptides were resuspended in 17µl of 2% acetonitrile and 0.05% trifluoroacetic acid and analyzed by nano-liquid chromatography (LC) coupled to tandem MS, using an UltiMate 3000 system (NCS-3500RS Nano/Cap System; Thermo Fisher Scientific) coupled to an Orbitrap QExactive Plus mass spectrometer (Thermo Fisher Scientific). Around 5µl of each sample was loaded on a C18 precolumn (300µm inner diameter × 5 mm, Thermo Fisher Scientific) in a solvent made of 2% acetonitrile and 0.05% trifluoroacetic acid, at a flow rate of 20 µl/min. After 5 min of desalting, the precolumn was switched online with the analytical C18 column (75 μm inner diameter × 50 cm; in-house packed with Reprosil C18) equilibrated in 95% solvent A (5% acetonitrile, 0.2% formic acid) and 5% solvent B (80% acetonitrile, 0.2% formic acid). Peptides were eluted using a 5%-50% gradient of solvent B over 105 min at a flow rate of 300 nl/min. The mass spectrometer was operated in data-dependent acquisition mode with the Xcalibur software. MS survey scans were acquired with a resolution of 70,000 and an AGC target of 3e6. The 10 most intense ions were selected for fragmentation by high-energy collision induced dissociation, and the resulting fragments were analyzed at a resolution of 17500, using an AGC target of 1e5 and a maximum fill time of 50ms. Dynamic exclusion was used within 30 s to prevent repetitive selection of the same peptide"],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Raw MS files were processed with the Mascot software (version 2.7.0) for database search and Proline (Bouyssie et al, Bioinformatics 2020) for label-free quantitative analysis (version 2.1.2). Data were searched against Mus musculus entries of the UniProtKB protein database (release SwissProt 20201022, 17060 entries). Carbamidomethylation of cysteines was set as a fixed modification, whereas oxidation of methionine was set as variable modifications. Specificity of trypsin/P digestion was set for cleavage after K or R, and two missed trypsin cleavage sites were allowed. The mass tolerance was set to 10 ppm for the precursor and to 20 mmu in tandem MS mode. Minimum peptide length was set to 7 amino acids, and identification results were further validated in Proline by the target decoy approach using a reverse database at both a PSM and protein false-discovery rate of 1%. For label-free relative quantification of the proteins across biological replicates and conditions, cross-assignment of peptide ions peaks was enabled inside group with a match time window of 1 min, after alignment of the runs with a tolerance of +/- 600s"],"omics_type":["Proteomics"],"labhead":["Odile Schiltz"],"instrument_platform":[""],"labhead_affiliation":["Institut de Pharmacologie et de Biologie Structurale Équipe \"Protéomique et Spectrométrie de Masse de Biomolécules\" ProteoToul Toulouse 205, route de Narbonne - BP 64182 - 31077 Toulouse Cedex - France"],"submission_type":["PARTIAL"],"species":["Mus Musculus (mouse)"],"submitter_mail":["alexandre.stella@ipbs.fr"],"publication":["41851531 Picot M, Hifdi N, Vaucourt M, Mansat M, Li P, Singer I, Chicanne G, Stella A, Kuang S, Miceli C, Henneman NF, Payrastre B, Vandromme M, Schiltz O, Nemazanyy I, de Araujo MEG, Panasyuk G, Viaud J, Lämmerhofer M, Hnia K. Lysosomal phosphoinositide turnover acts upstream of RagGTPase-mTORC1 and controls muscle growth. Nat Metab. 2026 8(3):624-645 10.1038/s42255-026-01484-1"],"submitter_affiliation":["CNRS"],"submitter_country":["France"],"pubmed_abstract":["Lysosomes act as metabolic signalling hubs that integrate nutrient availability to coordinate anabolic and catabolic programmes. Mechanistic target of rapamycin complex 1 (mTORC1) is activated at the lysosomal surface by amino acids through RagGTPases recruited by the lysosomal adaptor and MAPK and mTOR activator complex, yet the contribution of lysosomal lipid composition to this pathway remains unclear. Here we identify lysosomal phosphoinositides, PI3P and PI(3,5)P2, as key regulators of lysosomal adaptor and MAPK and mTOR activator complex stability and dynamics at the lysosome. These lipid pools are controlled by the phosphoinositide 3-phosphatase MTM1, mutated in myotubular myopathy, via endoplasmic reticulum-lysosome membrane contact sites. Under endoplasmic reticulum stress, MTM1-dependent phosphoinositide remodelling suppresses RagGTPase-mTORC1 signalling, thereby regulating anabolic-catabolic balance during myogenic differentiation. Restoring mTORC1 activity or lysosomal phosphoinositide homeostasis rescues Rag-dependent signalling and muscle growth in cellular and mouse models of myopathy, uncovering a lysosome-centred metabolic checkpoint with direct disease relevance."],"pubmed_title":["Lysosomal phosphoinositide turnover acts upstream of RagGTPase-mTORC1 and controls muscle growth."],"pubmed_authors":["Picot Melanie M, Hifdi Nesrine N, Vaucourt Mathilde M, Mansat Melanie M, Li Peng P, Singer Isabel I, Chicanne Gaëtan G, Stella Alexandre A, Kuang Shen S, Miceli Caterina C, Henneman Nathaniel F NF, Payrastre Bernard B, Vandromme Marie M, Schiltz Odile O, Nemazanyy Ivan I, de Araujo Mariana E G MEG, Panasyuk Ganna G, Viaud Julien J, Lämmerhofer Michael M, Hnia Karim K"],"additional_accession":[]},"is_claimable":false,"name":"Lysosome proteomics from muscle cell in CTRL and X-linked centronuclear myopathy models","description":"Lyso-Tag (3XHA-TMEME-192) isolation and purification followed by proteomic analysis in C2C12 vs MTM1-KO  myotubes (4 replicates for each 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