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Hwang"],"software":["Not available"],"tissue":["Cell Culture"],"sample_protocol":["LC-MS/MS analysis 0.5-1 ug of peptide samples (equal volume of each samples) were analyzed twice by Orbitrap Fusion Lumos mass spectrometry (Thermo Fisher Scientific) coupled with Easy nLC (Thermo Fisher Scientific). Samples were loaded onto Pepmap C18 column, 2 μm, 100 Å, 75 μm × 50 cm (Thermo Fisher Scientific) for 90min at flow rate 0.25μl. Peptides were separated by 5 to 7% B buffer (80% ACN in 0.1% formic acid) in the first 4 minutes and then 7 to 25% of B buffer for 58 minutes, followed by a gradient from 25 to 40 % B buffer for 8 minutes, then 40 to 95% for 8 minutes, and at 95% for 5 minutes, and washed for 10 minutes by 2% B buffer. Scan range was 400 to 2000 m/z and the MS2 scans were performed with HCD fragmentation (37.5% collision energy)."],"repository":["Pride"],"labhead":["Heeyoun Hwang"],"instrument_platform":[""],"labhead_affiliation":["Korea Basic Science Institute"],"submission_type":["COMPLETE"],"publication":["34739247 Yang Y, Hwang H, Im JE, Lee K, Bhoo SH, Yoo JS, Kim YH, Kim JY. Flashlight into the Function of Unannotated C11orf52 using Affinity Purification Mass Spectrometry. J Proteome Res. 2021 20(12):5340-5346 10.1021/acs.jproteome.1c00540"],"submitter_affiliation":["KBSI"],"labhead_mail":["heeyounh@kbsi.re.kr"],"technology_type":["Affinity purification coupled with mass spectrometry proteomics","Mass Spectrometry"],"submitter_keywords":["Human","C-hpp","Hpp","Upe1"],"full_dataset_link":["https://www.ebi.ac.uk/pride/archive/projects/PXD026986"],"quantification_method":[""],"modification":[""],"data_protocol":["Data processing and Bioinformatic analysis  Raw MS data were converted to MS2 file using raw converter and analyzed by Integrated Proteomics Pipeline (IP2) platform. Trypsin protease was set as the digestion enzyme, and a maximum of two missed cleavages were allowed. Initial precursor mass deviation was up to 5 ppm and fragment mass tolerance was 20 ppm. False positive rate for spectrum was 1% and proteins were identified with at least two unique peptides."],"omics_type":["Proteomics"],"species":["Homo Sapiens (human)"],"submitter_mail":["heeyounh@kbsi.re.kr"],"curator_keywords":["Chromosome-centric human proteome project (c-hpp)","Human proteome project"],"submitter_country":["South Korea"],"doi":["10.6019/PXD026986"],"pubmed_abstract":["For an enhanced understanding of the biological mechanisms of human disease, it is essential to investigate protein functions. In a previous study, we developed a prediction method of gene ontology (GO) terms by the I-TASSER/COFACTOR result, and we applied this to uPE1 in chromosome 11. Here, to validate the bioinformatics prediction of C11orf52, we utilized affinity purification and mass spectrometry to identify interacting partners of C11orf52. Using immunoprecipitation methods with three different peptide tags (Myc, Flag, and 2B8) in HEK 293T cell lines, we identified 79 candidate proteins that are expected to interact with C11orf52. The results of a pathway analysis of the GO and STRING database with candidate proteins showed that C11orf52 could be related to signaling receptor binding, cell-cell adhesion, and ribosome biogenesis. Then, we selected three partner candidates of DSG1, JUP, and PTPN11 for verification of the interaction with C11orf52 and confirmed them by colocalization at the cell-cell junctions by coimmunofluorescence experiments. On the basis of this study, we expect that C11orf52 is related to the Wnt signaling pathway via DSG1 from the protein-protein interactions, given the results of a comprehensive analysis of the bioinformatic predictions. The data set is available at the ProteomeXchange consortium via PRIDE repository (PXD026986)."],"pubmed_title":["Flashlight into the Function of Unannotated C11orf52 using Affinity Purification Mass Spectrometry."],"pubmed_authors":["Yang Yeji Y, Hwang Heeyoun H, Im Ji Eun JE, Lee Kyungha K, Bhoo Seong Hee SH, Yoo Jong Shin JS, Kim Yun-Hee YH, Kim Jin Young JY"],"additional_accession":[]},"is_claimable":false,"name":"C11orf52_uPE1study_for_CHPP_using_Immunoprecipitation","description":"In order to identify interactome with C11orf52, immunoprecipitation was performed in HEK293T 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