{"database":"Pride","file_versions":[{"headers":{"Content-Type":["application/json"]},"body":{"files":{"Txt":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/checksum.txt"],"Raw":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/21P11080004.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/21P11080001.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/21P11080003.raw","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/21P11080002.raw"],"Fasta":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/nr_up_Homo_sapiens.fasta"],"Mgf":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/21P11080001.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/21P11080004.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/21P11080003.mgf","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/21P11080002.mgf"],"Other":["ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/21P11080003.dat","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/21P11080002.dat","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/21P11080004.dat","ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/05/PXD062704/21P11080001.dat"]},"type":"primary"},"statusCode":"OK","statusCodeValue":200}],"scores":null,"additional":{"labhead_mail":["zoubj6@mail.sysu.edu.cn"],"submitter":["Baojia Zou"],"technology_type":["Affinity purification coupled with mass spectrometry proteomics","Mass Spectrometry","Gel-based experiment"],"disease":["Liver Cancer"],"software":[""],"submitter_keywords":["Mitophagy activator","Ku80","Liver cancer"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD062704"],"tissue":["Hepatocyte","Cell Culture"],"sample_protocol":["Endogenous Ku80 was pulled down in the samples from liver cancer cell line MHCC97H treated with or without the mitophagy activator, propofol. Exogenous Ku80 was pulled down in MHCC97H stable cell lines (vector/control and Ku80 overexpression/Ku80-OE).  The identification of protein gel strips is to separate the sample proteins by gel electrophoresis, then obtain the protein gel strips at different positions on the film, extract the peptides after enzymatic digestion, and then uses mass spectrometry to obtain the mass spectrum of the proteins in these gel strips, and finally uses the protein identification software to identify the proteins in the samples. 1.1 Proteolysis (1) Soaked the gel in 50μL of pure water for 30 minutes, then took out and cut (1-2 mm gel particles, if the gel particles meet the size of 1-2 mm, then skip the process) and transferred to the corresponding EP tube; (2) Added 1mL of decolorizing solution (50mM NH4HCO3: acetonitrile = 1:1, V:V), vortexed for 10 seconds, decolorized at 37°C for 30 minutes, briefly centrifuged and dried; repeated several times until the blue faded (Silver dyed gel does not need to be decolored, it can be washed directly with 1mL of pure water for 3 times); (3) Added 500μL of acetonitrile to dehydrate the gel to completely whiten, repeat once; soaked up the acetonitrile, opened the centrifuge tube and placed it in a clean bench for 10 minutes to air-dry acetonitrile, add 10mM DTT (1M DTT: 25mM NH4HCO3=1:100) until the liquid covered the gel, then put in water bath at 56°C for 1 hour; after cooling to room temperature, soaked it up, added 55mM IAM (0.55 M IAM:25mM NH4HCO3 = 1:10) quickly until the liquid covered the gel, and put at room temperature in a dark room for 45 minutes; (4) Soaked up the liquid, washed twice with 500μL of decolorizing solution (50 mM NH4HCO3: acetonitrile = 1:1, V:V), washed once with pure water; soaked up the liquid, added 500μL of acetonitrile, vortexed for 5 minutes. Soaked up the acetonitrile, opened the centrifuge tube lid and placed it on the clean bench for 10 minutes to dry thoroughly; (5) Diluted the enzyme concentration to 0.01μg/μL with 25mM NH4HCO3, and completely covered the gel with the enzyme solution, and stood at 4°C or ice for 30 minutes. After the gel was swelled, added the corresponding buffer to the gel. Incubated overnight at 37°C. (6) Added 5 times volume of 50% ACN the next day, vortexed for 5 minutes, centrifuged at 5,000g for 1 minute, transferred the supernatant to the new centrifuge tubes of the same number; added 5 volumes of 100% ACN, vortexed for 5 minutes. After centrifugation at 5,000g for 1 minute, the supernatant was transferred to a new centrifuge tube of the same number. Finally, the resulting supernatant was centrifuged at 25,000g for 5 minutes, and the supernatant was taken for freeze-dried. 1.2 HPLC The dried peptide samples were reconstituted with mobile phase A (2% ACN, 0.1% FA), centrifuged at 20,000g for 10 minutes, and the supernatant was taken for injection. Separation was performed by Thermo UltiMate 3000 UHPLC. The sample was first enriched in trap column and desalted, and then entered a self-packed C18 column (75μm internal diameter, 3μm column size, 25cm column length) and separated at a flow rate of 300nL/min by the following effective gradient: 0~5minutes, 5% mobile phase B (98% ACN, 0.1% FA); 5~45 minutes, mobile phase B linearly increased from 5% to 25%; 45~50minutes, mobile phase B increased from 25% to 35%; 50~52 minutes, mobile phase B rose from 35% to 80%; 52~54 minutes, 80% mobile phase B; 54~60 minutes, 5% mobile phase B. The nanoliter liquid phase separation end was directly connected to the mass spectrometer. 1.3 Mass Spectrometry Detection The peptides separated by liquid phase chromatography were ionized by a nanoESI source and then passed to a tandem mass spectrometer Q-Exactive HF X (Thermo Fisher Scientific, San Jose, CA) for DDA (Data Dependent Acquisition) mode detection. The main parameters were set: ion source voltage was set to 1.9kV, MS1 scanning range was 350~1,500m/z; resolution was set to 60,000; MS2 starting m/z was fixed at 100; resolution was 15,000. The ion screening conditions for MS2 fragmentation: charge 2+ to 6+, and the top 30 parent ions with the peak intensity exceeding 10,000. The ion fragmentation mode was HCD, and the fragment ions were detected in Orbitrap. The dynamic exclusion time was set to 30 seconds. The AGC was set to: MS1 3E6, MS2 1E5."],"repository":["Pride"],"quantification_method":[""],"modification":[""],"data_protocol":["2.1 Database Selection The selection of database is an important step in MS based protein identification, and the final identified protein sequences are from the selected database. Currently databases in use can be divided into three main categories: 1) UniProt protein database UniProt is the most informative and resourceful protein database. It consists of data from three major databases, i.e. Swiss-Prot, TrEMBL and PIR-PSD. It is a data set verified by experts and consists of two parts: UniProtKB/Swiss-Prot (with reviewed, manually annotated entries) and UniProtKB/TrEMBL (with unreviewed, automatically annotated entries). In general, it is recommended to give priority using the subset of UniProtKB/Swiss-Prot for protein identification. When it aims to find novel sequences (such as alternative splicing, new transcripts) or to identify allied species, UniProtKB/TrEMBL datatbase can be considered. 2) The protein databases based on genome annotation The databaseses mainly include a series of databases derived from NCBI and Ensembl gene annotation databases. Among them, we choose protein database from reference sequence (RefSeq) of NCBI, which is a non-redundant proteome database. It is widely used in the analysis of multi-omics studies due to the importance of the NCBI annotation system. NCBI's RefSeq provides reference sequence for molecules that are naturally involved in central dogma, from chromosomes to mRNA and proteins. The RefSeq standard provides a basis for functional annotation of the human genome. It provides a stable reference for mutation analysis, gene expression studies, and polymorphic discovery. In addition, NCBI provides completed non-redundant protein sequence database (NCBI_nr), including animal, plant, microbial, bacterial and other taxonomy. Since the database is derived from various sources (including GeneBank, RefSeq, SwissProt, PDB, etc.), unless the species is without complete genome annotation, or it is necessary to search for homologous, it is not recommended to use this database for protein identification. Ensembl aims to develop a software package with automatic annotation and maintenance for the eukaryotic genome. Ensembl has relatively complete and consistent genomic, transcriptome, and proteomic annotation information, which is ideal for multi omics analysis. 3) Databases from other sources They usually refer to the protein target databases provided by the client, or new gene sequence generated from genome or transcriptome sequencing de novo assembly. They may also contain sequences of new features such as alternative splicing, mutation site, fusion genes, etc. 2.2 Mascot Search Mascot is one of the most important and widely used protein identification software in the field of proteomics. The version used in the project is Mascot 2.3.02. In the operation, the mgf file was used as the original file, and the database that has been constructed was selected, and then the database search was performed."],"omics_type":["Proteomics"],"labhead":["Baojia Zou"],"instrument_platform":[""],"labhead_affiliation":["5th Affiliated Hospital of Sun Yat-sen University"],"submission_type":["PARTIAL"],"species":["Homo Sapiens (human)"],"submitter_mail":["zoubj6@mail.sysu.edu.cn"],"publication":["Not available"],"submitter_affiliation":["5th Affiliated Hospital of Sun Yat-sen University"],"submitter_country":["China"],"additional_accession":[]},"is_claimable":false,"name":"Ku80 interaction proteins under enhanced mitophagy","description":"We reported Ku80 as a critical mitophagy protein and closely related to chemotherapy efficacy in liver cancer. The project detects the Ku80-interacted proteins under the condition of mitophagy activator or exogenously overexpression of Ku80 gene.  After immunoprecipitation pulldown via anti-Ku80 or anti-flag antibody, LC MS/MS was performed to determine Ku80-interacted mitophagy-related 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