{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD063347/ID75049_01_FSN20560_6116_121622.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD063347/ID75048_01_FSN20560_6116_121622.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD063347/ID75049_03_FSN20560_6116_121622.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD063347/ID75047_01_FSN20560_6116_121622.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD063347/ID75046_01_FSN20560_6116_121622.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD063347/ID75045_01_FSN20560_6116_121622.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD063347/ID75044_01_FSN20560_6116_121622.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD063347/ID75043_01_FSN20560_6116_121622.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD063347/ID75049_02_FSN20560_6116_121622.raw"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/06/PXD063347/ID75043_01_FSN20560_6116_121622.pdResult"]},"type":"primary"},"statusCodeValue":200,"statusCode":"OK"}],"scores":null,"additional":{"labhead_mail":["cagla.eroglu@duke.edu"],"submitter":["Erik Soderblom"],"technology_type":["Mass Spectrometry","Bottom-up proteomics"],"software":["Not available"],"submitter_keywords":["Bioid","Lamp1","Label free"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD063347"],"sample_protocol":["Samples were spiked with undigested bovine casein at a total of either 1 or 2 pmol as an internal quality control standard. Next, they were reduced for 15 min at 80C, alkylated with 20 mM iodoacetamide for 30 min at room temperature, then supplemented with a final concentration of 1.2% phosphoric acid and 588 µL of S-Trap (Protifi) binding buffer (90% MeOH/100mM TEAB). Proteins were trapped on the S-Trap micro cartridge, digested using 20 ng/µL sequencing grade trypsin (Promega) for 1 hr at 47C, and eluted using 50 mM TEAB, followed by 0.2% FA, and lastly using 50% ACN/0.2% FA. All samples were then lyophilized to dryness. Samples were resuspended in 12 µL of 1% TFA/2% acetonitrile with 12.5 fmol/µL of yeast ADH. A study pool QC (SPQC) was created by combining equal volumes of each sample."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["Quantitative LC/MS/MS was performed on 3 µL of each sample, using an MClass UPLC system (Waters Corp) coupled to a Thermo Orbitrap Fusion Lumos high resolution accurate mass tandem mass spectrometer (Thermo) equipped with a FAIMSPro device via a nanoelectrospray ionization source. Briefly, the sample was first trapped on a Symmetry C18 20 mm × 180 µm trapping column (5 μl/min at 99.9/0.1 v/v water/acetonitrile), after which the analytical separation was performed using a 1.8 µm Acquity HSS T3 C18 75 µm × 250 mm column (Waters Corp.) with a 90-min linear gradient of 5 to 30% acetonitrile with 0.1% formic acid at a flow rate of 400 nanoliters/minute (nL/min) with a column temperature of 55C. Data collection on the Fusion Lumos mass spectrometer was performed for three difference compensation voltages (-40v, -60v, -80v). Within each CV, a data-dependent acquisition (DDA) mode of acquisition with a r=120,000 (@ m/z 200) full MS scan from m/z 375 – 1500 with a target AGC value of 4e5 ions was performed. MS/MS scans with HCD settings of 30% were acquired in the linear ion trap in “rapid” mode with a target AGC value of 1e4 and max fill time of 35 ms. The total cycle time for each CV was 0.66s, with total cycle times of 2 sec between like full MS scans. A 20s dynamic exclusion was employed to increase depth of coverage. The total analysis cycle time for each sample injection was approximately 2 hours."],"omics_type":["Proteomics"],"labhead":["Cagla Eroglu, PhD"],"instrument_platform":[""],"labhead_affiliation":["Professor of Cell Biology  Professor of Neurobiology Duke University School of Medicine"],"submission_type":["PARTIAL"],"species":["Mus Musculus (mouse)"],"submitter_mail":["es114@duke.edu"],"publication":["Not available"],"submitter_affiliation":["Duke University"],"submitter_country":["United States"],"additional_accession":[]},"is_claimable":false,"name":"Lamp1 BioID Protein Interaction Analysis","description":"LC-MS/MS analysis of BioID-Lamp1 to characterize 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