{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Xlsx":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD066668/Rawfile_experiment_list_ATG9_CoIP.xlsx"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD066668/20250224_Eclipse_NEO1_Romanov_Martens_MPL_UniWien_MPLID25043_ATG9_R_45p.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD066668/20210219_QExHFX1_RSLC1_Bernklau_Martens_MFPL_onbead_Atg9_50p.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD066668/20250224_Eclipse_NEO1_Romanov_Martens_MPL_UniWien_MPLID25043_WTmock_R_45p.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD066668/20210219_QExHFX1_RSLC1_Bernklau_Martens_MFPL_onbead_WT_50p.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD066668/MaxQuant_results_Rep1.zip","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/08/PXD066668/FragPipe_results_Rep2.zip"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["sascha.martens@univie.ac.at"],"submitter":["Markus Hartl"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":[""],"submitter_keywords":["Human","Hap1 cells","Atg9a vesicles"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD066668"],"sample_protocol":["Cells (110-120×106) were collected by trypsinization and centrifugation. After washing with PBS, cell pellets were flash-frozen and stored at 80°C until use. For vesicle isolation, cell pellets were thawed on ice and resuspended in 1665 µl of Vesicle Isolation Buffer (VIB; 20 mM HEPES pH 7.5, 150 mM NaCl, 250 mM sucrose, 1x cOmplete EDTA-free protease inhibitors (Roche), 20 mM β-Glycerophosphate, 1 mM Sodium Orthovanadate, 1 mM NaF, and 1 mM EDTA pH 8.0). The cell suspension was transferred to a 2 ml microcentrifuge tube and lysed by passing the suspension through a 26G needle 30 times, chilling on ice for 10 min, followed by another 30 passes. After centrifugation at 2000g for 6 min at 4°C, the supernatant was collected and 70 µl of pre-equilibrated FLAG beads were added and incubated overnight at 4°C on a roller. Next day, beads were pelleted at 2000g for 3 min at 4°C, and the supernatant was removed. Beads were resuspended in 1 ml of VIB, transferred to a fresh 2 ml microcentrifuge tube containing 665 µl of VIB. In the second washing step, the beads were resuspended with 1 ml VIB and subsequently 600 µl of Elution Buffer (EB; 20 mM HEPES pH 7.5, 150 mM NaCl, 1x cOmplete EDTA-free protease inhibitors, 20 mM β-Glycerophosphate, 1 mM Sodium Orthovanadate, and 1 mM NaF) were added slowly. After the 3rd wash, the beads were resuspended in 665 µl EB and transferred to a 1.5 ml Eppendorf tube. ATG9A-vesicles were eluted from the beads adding 16.65 µl of 4 mg/ml FLAG peptide (Sigma, F32920-4MG) and incubating for 3 h at 4°C while rolling. The beads were pelleted at 2000g for 3 min and the supernatant incubated overnight with 20 µl of magnetic GFP-TRAP beads (ChromoTek), which were acetylated according to the protocol: https://dx.doi.org/10.17504/protocols.io.kxygxzexkv8j/v3. The beads were then washed 3 times with 100 µl of EB, resuspended with 50 µl of EB and directly submitted for MS analysis. Beads were resuspended in 50 µl of 1 M urea in 50 mM ammonium bicarbonate. Proteins were reduced with dithiothreitol (DTT, 10 mM final conc.) for 30 min at RT and incubated with 25 mM iodoacetamide for 30 min at RT in the dark. The remaining iodoacetamide was quenched by adding 5 mM DTT and the proteins were digested with 150 ng LysC (FUJIFILM Wako chemicals) at 25°C overnight. Supernatant was transferred and incubated with 150 ng trypsin (Trypsin Gold, Promega) at 37°C for 5 h. The digest was stopped by adding trifluoroacetic acid (TFA) to a final conc. of 0.5 %. Peptides were desalted using C18 Stagetips. Rep1: LC-MS analysis was performed on an UltiMate 3000 RSLCnano LC system coupled to an Orbitrap Exploris HF-X mass spectrometer equipped with a Nanospray Flex ion source (all Thermo Scientific) using coated emitter tips (PepSep, MSWil). Peptides were loaded onto a trap column (Acclaim PepMap C18 5µm 300µmx5mm) with 0.1% TFA as mobile phase, separated on an analytical column (Acclaim PepMap 100 C18 column, 2 μm, 75 µm× 50 cm, both Thermo Scientific), applying a linear 2h gradient from 2% solvent B (80% acetonitrile, 0.08% FA) to 35% solvent B (solvent A: 0.1% FA) at a flow rate of 230 nl/min. The analytical column was heated to 30°C. The mass spectrometer was operated in data-dependent acquisition (DDA) mode, acquiring MS1 scans from 375-1500 m/z with lock mass off, norm. AGC target of 300%, resolution of 120,000. The 25 most intense precursor ions (charge states +2 to +6) were selected within a 1.4 m/z window for HCD fragmentation with norm. collision energy of 28%, a max. fill time of 100 ms, norm. AGC of 100%, and resolution of 30,000. Peptide match was set to “preferred”, the intensity threshold to 8.0E4, dynamic exclusion to 30 sec with isotope exclusion enabled. Rep2: LC-MS analysis was performed on a Vanquish Neo UHPLC system coupled to an Orbitrap Eclipse Tribrid mass spectrometer equipped with a FAIMS Pro interface, a Nanospray Flex ion source (all Thermo Scientific), and a Column Heater connected to a Heater Controller (both IonOpticks). Peptides were loaded onto a trap column (PepMap Neo C18 5µm 300µmx5mm, Thermo Scientific) using 0.1% TFA as mobile phase, and separated on an analytical column (Aurora Ultimate XT C18, 25 cm × 75 µm, 1.7 µm, IonOpticks), applying a linear 2h gradient as in Rep1 at a flow rate of 300 nl/min. The analytical column was heated to 50°C. The mass spectrometer was operated in DDA mode with FAIMS compensation voltage (CV) set to -45, -60 and -75, with 0.6 s cycle time per CV. Survey scans were acquired from 375-1500 m/z, with norm. AGC target of 100% and resolution of 60,000. The most intense precursor ions (charge states +2 to +6) were selected for fragmentation using an isolation window of 1.4 m/z, max. fill time of 25 ms and norm. AGC target of 100%. After HCD fragmentation with norm. collision energy of 30%, fragment ions were analyzed in the linear ion trap. MIPS was set to “peptide”, the intensity threshold to 1.0E4, dynamic exclusion to 30 sec with isotope exclusion enabled."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Rep1 : MS raw data were analyzed with MaxQuant 1.6.17.0. MS2 spectra were searched against the against the human canonical database from uniprot (www.uniprot.org, 2020.01_UP000005640_9606_Homo_sapiens_canonical.fasta) and a database of common laboratory contaminants. Cleavage specificity was set to Trypsin/P, with two missed cleavages allowed. Carbamidomethyl was used as fixed cysteine modification; methionine oxidation and protein N-terminal acetylation were specified as variable modifications. All data were filtered at 1% PSM+protein+site FDR. Raw intensity values were median normalized and missing values were replaced by 16 (in log space) after filtering out contaminants and proteins with less than 2 razor &unique peptides. Rep2 : MS raw data were analyzed with FragPipe (23.1), using MSFragger (4.3), IonQuant (1.11.11), and Philosopher (5.1.2). The default FragPipe workflow for label free quantification (LFQ-MBR) was used, except “Normalize intensity across runs” was turned off. Cleavage specificity was set to Trypsin/P, with two missed cleavages allowed. Carbamidomethyl was used as fixed cysteine modification, methionine oxidation and protein N-terminal acetylation were specified as variable modifications. MS2 spectra were searched against the H. sapiens 1 protein per gene reference proteome from Uniprot (Proteome ID: UP000005640, release 2025_01), concatenated with a database of 379 common laboratory contaminants (release 2025.01, https://github.com/maxperutzlabs-ms/perutz-ms-contaminants). The protein FDR was set to 1%.  Computational analysis was performed using Python and the in-house developed Python library MsReport (0.0.30, https://github.com/hollenstein/msreport). Only non-contaminant proteins identified with a minimum of two peptides were considered for further analysis. LFQ protein intensities were log2-transformed and normalized across samples using the ModeNormalizer from MsReport. Missing LFQ values were replaced by 14 (in log space) after filtering out contaminants and proteins with less than 2 total peptides."],"omics_type":["Proteomics"],"labhead":["Sascha Martens"],"instrument_platform":[""],"labhead_affiliation":["Max Perutz Labs, Department of Biochemistry and Cell Biology, University of Vienna, Vienna BioCenter, Austria"],"submission_type":["PARTIAL"],"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":"Isolation and mass spectrometry analysis of ATG9A vesicles from HAP1 cells.","description":"Autophagy is a conserved cellular degradation pathway involving the formation of double-membrane autophagosomes that engulf cytoplasmic material for delivery to the lysosome. Autophagy-related (ATG) proteins orchestrate the steps of autophagosome formation and maturation, among which ATG9A is unique as the only integral membrane protein essential for autophagy progression. ATG9A localizes to Golgi-derived vesicles/compartments that constitute a seed for membrane nucleation. In this dataset we show proteomics analysis of mammalian ATG9A vesicles. To isolate and characterize native mammalian ATG9A-containing compartments, we generated a CRISPR/Cas9-engineered HAP1 knock-in cell line expressing ATG9A endogenously tagged ATG9A with a C-terminal GFP and FLAG tag. The FLAG-tag enabled the purification of native ATG9A vesicles via FLAG-based affinity isolation, while GFP-tag was used to submit the vesicles for mass spectrometry analysis. Both WT and ATG9A-GFP-FLAG expressing HAP1 cell lines were cultured under nutrient-rich conditions to prevent the induction of starvation-mediated 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