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Hartl"],"technology_type":["Data-dependent acquisition","Affinity purification coupled with mass spectrometry proteomics","Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Human","Embryonic kidney","Lc-msms","Flpin-t-rex 293 cells","Lamtor baits","Turboid"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD080046"],"tissue":["Cell Culture"],"sample_protocol":["Proximity labelling was carried out as follows: Cells were incubated with 500 μM biotin (in DMSO) full medium for 15 min at 37°C, 5% CO2. The reaction was stopped by transferring plates on ice and medium was decanted. Cells were immediately spin-washed three times with cold PBS and subsequently lysed in RIPA buffer supplemented with cOmpleteTM, Mini, EDTA-free protease-inhibitor cocktail (40694200; Roche) on ice. Cell lysates were transferred to low-binding microcentrifuge tubes (022431081; Eppendorf) and 1 mg protein in 1 ml total volume was incubated with 200 μl prewashed Streptavidin magnetic beads (88817; Pierce) at 4 °C overnight on a rotating wheel. The beads were washed three times with RIPA buffer and five times with detergent-free washing buffer (50 mM Tris-HCl, 50 mM NaCl, pH 7.4). Beads were kept on ice until further processing. Sample preparation for mass spectrometry analysis: Beads were resuspended in 50 μL 1 M urea, 50 mM ammonium bicarbonate. Disulfide bonds were reduced with 2 μL of 250 mM dithiothreitol (DTT) for 30 min at room temperature before adding 2 μL of 500 mM iodoacetamide and incubating for 30 min at room temperature in the dark. Remaining iodoacetamide was quenched with 1 μL of 250 mM DTT for 10 min. Proteins were digested adding 300 ng trypsin (Trypsin Gold, Promega) followed by incubation at 37°C overnight. The digest was stopped by addition of trifluoroacetic acid (TFA) to a final concentration of 0.5 % and the supernatant was transferred to a fresh tube. The peptides were cleaned up according to the SP2 protocol by Waas et al. Peptides were separated on an Ultimate 3000 RSLC nano-flow chromatography system (Thermo-Fisher Scientific), using a pre-column for sample loading (Acclaim PepMap C18 5mm × 300 µm, 5 μm, Thermo-Fisher Scientific), and a C18 analytical column (Acclaim PepMap C18, 50 cm × 75 µm, 2 μm, Thermo-Fisher Scientific), applying a segmented linear gradient from 2% to 35% over 120 min and finally 80% solvent B (80 % acetonitrile, 0.08 % formic acid; solvent A 0.1 % formic acid) at a flow rate of 230 nL/min. The nano-LC was interfaced online via a nano-spray ion-source to a Q Exactive HF-X Orbitrap mass spectrometer (Thermo-Fisher Scientific). The mass spectrometer was operated in a data-dependent acquisition mode (DDA). Survey scans were obtained in a mass range of 375-1500 m/z, at a resolution of 120k at 200 m/z and an AGC target value of 3E6. The 8 most intense ions were selected with an isolation width of 1.6 m/z, at a target value of 1E5 with a max. IT of 250 ms, and fragmented in the HCD cell with 28% normalized collision energy. The spectra were recorded at a resolution of 30k. Peptides with a charge of +2 to +6 were included for fragmentation, the peptide match and the exclude isotopes features were enabled. Selected precursors were dynamically excluded from repeated sampling for 30 seconds."],"repository":["Pride"],"quantification_method":["Not available"],"modification":[""],"data_protocol":["MS raw data were analyzed using the MaxQuant software package (version 1.6.0.16) searching the Uniprot Homo sapiens reference proteome (www.uniprot.org), the sequences of the protein constructs as well as a database of common contaminants. The search was performed with full trypsin specificity and a maximum of two missed cleavages at a protein and peptide spectrum match false discovery rate of 1%. Carbamidomethylation of cysteine residues was set as fixed, oxidation of methionine and acetylation of the protein Nterminus as variable modifications. For label-free quantification the “match between runs” feature and the LFQ function were activated - all other parameters were left at default.  The output from MaxQuant was analysed using Amica (https://github.com/tbaccata/amica). Proteins from reverse database identifications, potential contaminant proteins and proteins only identified by a modified peptide were removed. Proteins with at least 2 Razor + unique peptides, at least 3 MS/MS counts, and valid values in 3 replicates in at least one group were considered quantified. LFQ intensities of quantified proteins were log2-transformed and quantile normalized. Intensities with missing values were imputed from a normal distribution downshifted 1.8 standard deviations from the mean with a width of 0.3 standard deviations. Differential expression analysis was performed with DeqMS (version 1.10.0)."],"omics_type":["Proteomics"],"labhead":["Prof. Manuela Baccarini"],"instrument_platform":[""],"submission_type":["PARTIAL"],"labhead_affiliation":["Max-Perutz Labs/ Mechanistic Cell and Developmental Biology/University of Vienna, Dr.-Bohr-Gasse 9, 1030 Vienna, Austria"],"species":["Homo Sapiens (human)"],"publication":["Not available"],"submitter_mail":["proteomics@maxperutzlabs.ac.at"],"submitter_affiliation":["Max Perutz Labs, Mass Spectrometry Facility, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, Vienna, Austria"],"submitter_country":["Austria"],"additional_accession":[]},"is_claimable":false,"name":"Proximity-dependent TurboID labeling screen on the LAMTOR complex","description":"This proximity-dependent labeling screen was set up to investigate the “proxisome” (i.e. the sum of proteins in the labeling diameter around a bait protein) of the LAMTOR complex. Furthermore, we aimed at understanding the recruitment dynamics of known and unknown proteins to and from the LAMTOR complex upon changing environmental conditions. Therefore, cells were exposed to three different conditions: Full medium (FM), amino acid and growth factor starvation (EBSS) and replenishment of amino acid and growth factors after starvation (HF). To achieve that, we generated stable cell lines expressing the biotin ligase TurboID fused to two LAMTOR subunits (LAMTOR3 and LAMTOR5) as well as to a lysosomal (TMEM192) and cytosolic (nuclear exclusion sequence NES) control. After induction of the biotin-ligase reaction in living cells, biotinylated proteins were extracted from cell lysates via streptavidin beads and further processed for mass spectrometry analysis.","dates":{"publication":"2026-07-10","submission":"2026-06-23"},"accession":"PXD080046","cross_references":{"TAXONOMY":["NEWT:330879","NEWT:377960","NEWT:2042546","NEWT:259447","NEWT:295546","NCBITaxon:2719036","NCBITaxon:1280","NEWT:112503","NEWT:1129","NEWT:309807","NEWT:59753","NEWT:89184","NEWT:309800","NEWT:281395","NEWT:1211601","NEWT:876138","NEWT:44271","NEWT:193516","NEWT:1073882","NEWT:475174","NEWT:111205","NEWT:1117","NEWT:498257","NEWT:10036","NEWT:1590","NEWT:10034","NEWT:661410","NEWT:638632","NEWT:224326","NEWT:376619","NCBITaxon:79857","NEWT:1096976","NEWT:1589","NEWT:135622","NEWT:67352","NEWT:35786","NEWT:1580","NEWT:399784","NEWT:96731","NEWT:656064","NEWT:383379","NEWT:418106","NEWT:10029","NEWT:913645","NEWT:641809","NEWT:38815","NEWT:317447","NEWT:4688","NEWT:111225","NEWT:7719","NEWT:868565","NEWT:135674","NEWT:79329","NEWT:30069","NEWT:12637","NEWT:59729","NEWT:2164133","NEWT:295105","NEWT:108061","NEWT:60711","NEWT:224308","NEWT:3347","NEWT:160621","NEWT:212790","NEWT:110368","NEWT:1310161","NEWT:77133","NEWT:145481","NEWT:1310165","NEWT:29058","NCBITaxon:79824","NEWT:1912919","NEWT:44688","NEWT:44689","NEWT:498211","NEWT:347256","NEWT:5518","NEWT:398007","NEWT:1527468","NEWT:498217","NEWT:498216","NEWT:11320","NEWT:246196","NEWT:246197","NEWT:145458","NEWT:44685","NEWT:161934","NEWT:1148","NEWT:5508","NEWT:3329","NEWT:419481","NEWT:5507","NEWT:410661","NEWT:1140","NCBITaxon:2157","NEWT:1143","NEWT:1287689","NEWT:1094343","NEWT:1462472","NEWT:1336795","NEWT:644042","NEWT:1182590","NEWT:3712","NEWT:3711","NEWT:270643","NEWT:2065263","NEWT:177437","NEWT:10418","NEWT:118698","NEWT:1616117","NEWT:118696","NEWT:34865","NEWT:52283","NEWT:284812","NEWT:8175","NEWT:43330","NEWT:980415","NEWT:1603293","NEWT:44664","NEWT:43346","NEWT:3702","NEWT:1245466","NEWT:244366","NEWT:1246791","NEWT:118694","NEWT:2850","NEWT:118691","NEWT:34871","NEWT:33548","NEWT:52299","NEWT:8165","NEWT:96794","NEWT:3708","NEWT:332648","NEWT:44670","NEWT:536231","NEWT:376219","NEWT:219813","NEWT:1510","NEWT:460519","NEWT:1515","NEWT:572307","NEWT:1432138","NEWT:1424507","NEWT:1194599","NEWT:272844","NEWT:1348799","NEWT:1303443","NEWT:9483","NEWT:485","NEWT:56636","NEWT:2709072","NEWT:2853422","NEWT:1679718","NEWT:480","NEWT:67767","NEWT:46835","NEWT:109757","NEWT:582580","NEWT:1185650","NEWT:216778","NEWT:294607","NEWT:1502","NEWT:128017","NEWT:376686","NEWT:95486","NEWT:1883446","NEWT:1233435","NEWT:109760","NEWT:29031","NEWT:317047","NEWT:460523","NEWT:235443","NEWT:1757312","NEWT:85694","NEWT:108458","NEWT:5936","NEWT:320637","NEWT:1078283","NEWT:3750","NEWT:983964","NEWT:11706","NEWT:32644","NEWT:527796","NEWT:499175","NEWT:109779","NEWT:3745","NEWT:1715989","NCBITaxon:4751","NEWT:3747","NEWT:1116234","NEWT:1255228","NEWT:410289","NEWT:373153","NEWT:472","NEWT:940825","NEWT:529507","NEWT:1071661","NEWT:470","NEWT:5911","NCBITaxon:50557","NEWT:39251","NEWT:29491","NEWT:101841","NEWT:446","NEWT:153481","NEWT:2014887","NEWT:33952","NEWT:445","NEWT:153009","NEWT:261756","NEWT:166313","NEWT:63366","NEWT:63367","NEWT:215402","NEWT:1547","NEWT:906914","NEWT:9031","NEWT:27292","NEWT:1050722","NEWT:108931","NEWT:1293497","NEWT:1055524","NEWT:150475","NEWT:267872","NEWT:381666","NEWT:172269","NEWT:9534","NEWT:5180","NEWT:256737","NEWT:9541","NEWT:8694","NEWT:33936","NEWT:8692","NEWT:2903","NEWT:185579","NEWT:13076","NEWT:1006581","NEWT:8673","NEWT:33940","NEWT:550","NEWT:554","NEWT:451516","NEWT:552","NEWT:1325291","NEWT:36185","NEWT:1054211","NEWT:1225786","NEWT:51338","NEWT:575412","NEWT:28112","NEWT:6493","NEWT:6494","NEWT:6491","NEWT:507601","NEWT:520","NEWT:186441","NEWT:643680","NEWT:214092","NCBITaxon:6157","NEWT:13095","NEWT:162425","NEWT:104105","NEWT:216257","NEWT:9986","NEWT:8654","NEWT:8658","NEWT:1268063","NEWT:8657","NEWT:9983","NEWT:8655","NEWT:5147","NEWT:28108","NEWT:28104","NEWT:407821","NEWT:568703","NCBITaxon:2","NEWT:568708","NEWT:986","NEWT:52641","NEWT:28532","NEWT:353152","NEWT:298176","NEWT:227377","NEWT:40674","NEWT:1194669","NEWT:51329","NEWT:443906","NEWT:519","NEWT:2510939","NEWT:7394","NEWT:6063","NEWT:1328388","NEWT:1548728","NEWT:667127","NEWT:9557","NEWT:377586","NEWT:300641","NEWT:39655","NEWT:9554","NEWT:38323","NEWT:475932","NEWT:256318","NEWT:206411","NCBITaxon:6191","NEWT:229533","NEWT:2925","NEWT:214053","NEWT:80863","NEWT:90675","NEWT:52638","NEWT:57075","NEWT:1666905","NEWT:8697","NEWT:8695","NEWT:884204","NEWT:1123869","NEWT:9544","NEWT:9545","NEWT:979","NEWT:7370","NEWT:83906","NEWT:99488","NEWT:1134506","NEWT:255470","NEWT:38783","NEWT:6426","NEWT:33090","NEWT:9935","NEWT:287889","NEWT:305959","NEWT:13489","NEWT:29829","NEWT:92867","NEWT:92866","NCBITaxon:3055","NEWT:51750","NEWT:202950","NEWT:295027","NCBITaxon:11320","NEWT:632957","NEWT:9925","NCBITaxon:9606","NEWT:90690","NEWT:1436183","NEWT:300273","NEWT:4232","NEWT:416348","NEWT:11298","NEWT:4236","NEWT:7742","NEWT:196627","NEWT:200308","NEWT:242507","NEWT:200302","NEWT:870435","NEWT:9913","NEWT:9915","NEWT:105841"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