{"id":"JGAD000314","research":"hum0220","url":"https://humandbs.dbcls.jp/dataset/JGAD000314","datePublished":"2020-09-28","dateModified":"2021-04-19","values":[{"key":"access-criteria","label":{"ja":"アクセス制限","en":"Access criteria"},"type":"vocabulary","terms":[{"code":"controlled-access-type-1","label":{"ja":"制限公開（Type I）","en":"Controlled-access (Type I)"}}]},{"key":"type-of-data","label":{"ja":"データの種類","en":"Type of data"},"type":"text","text":{"ja":"質量分析","en":"Mass Spectrometry"}}],"experiments":[{"label":"質量分析","values":[{"key":"materials-and-participants","label":{"ja":"材料と対象者","en":"Materials and participants"},"type":"text","text":{"ja":"血漿：健常人3名×6条件（計18検体）\n条件：0分室温、15分室温、30分室温、1時間氷上、4時間氷上、8時間氷上\n血清：健常人3名（計3検体）","en":"Plasma: 18 samples from 3 heathy individuals\nSerum: 3 samples from 3 heathy individuals"}},{"key":"health-status","label":{"ja":"健康状態","en":"Health status"},"type":"vocabulary","terms":[{"code":"healthy","label":{"ja":"健常","en":"Healthy"}}]},{"key":"subject-count","label":{"ja":"対象者数","en":"Subject count"},"type":"number","numbers":[{"value":21,"unit":null,"high":null}]},{"key":"subject-count-type","label":{"ja":"対象者数の数え方","en":"Counted as"},"type":"vocabulary","terms":[{"code":"sample","label":{"ja":"検体数","en":"Sample"}}]},{"key":"sample-description","label":{"ja":"試料説明","en":"Sample description"},"type":"text","text":{"ja":"静脈血採取から凍結までの放置条件を振った血漿、および血清","en":"Plasma and serum samples"}},{"key":"tissue","label":{"ja":"組織","en":"Tissue"},"type":"vocabulary","terms":[{"code":"plasma","label":{"ja":"血漿","en":"Plasma"}},{"code":"serum","label":{"ja":"血清","en":"Serum"}}]},{"key":"is-tumor","label":{"ja":"腫瘍 / 非腫瘍","en":"Tumor / normal"},"type":"vocabulary","terms":[{"code":"normal","label":{"ja":"非腫瘍","en":"Normal"}}]},{"key":"sample-processing","label":{"ja":"試料の処理","en":"Sample processing"},"type":"text","text":{"ja":"健常ボランティアから採血後に血液を氷上もしくは室温で指定時間放置し、血清もしくは血漿を調製。血清もしくは血漿検体をsodium deoxycholateおよびN-lauroylsarcosinate存在下でdithiothreitolにより還元し、iodoacetamideによってアルキル化を行った。その後lysyl endopeptideseおよびtyprinで消化した後に、液液抽出および脱塩を行うことによって質量分析試料を調製した。","en":"Blood samples collected from three healthy Japanese volunteers were completely coagulated at room temperature and centrifuged to prepare serum. Matching blood samples from the same volunteers were centrifuged to obtain plasma immediately or after storage at room temperature or at 0-5°C for different periods. The serum and plasma samples were mixed with sodium deoxycholate and N-lauroylsarcosinate, reduced with dithiothreitol, alkylated with iodoacetamide, and digested with lysyl endopeptidase a and then with trypsin. The digested samples were desalted using GL-Tip GC and SDB."}},{"key":"platform","label":{"ja":"プラットフォーム","en":"Platform"},"type":"vocabulary","terms":[{"code":"sciex-tripletof-5600","label":{"en":"Sciex TripleTOF 5600"}}]},{"key":"measurement-conditions","label":{"ja":"測定条件","en":"Measurement condition"},"type":"text","text":{"ja":"質量分析：Sciex TripleTOF 5600\nLC: DIONEX Ultimate 3000 RSLC nano system\nトラップカラム：100 μm ID, 2 cm length, packed with 5 μm Acclaim PepMap100 C18\n分析カラム：75 μm ID, 25 cm length, packed with 2 μm Acclaim PepMap C18\nSolvent A: 0.1% formic acid in water\nSolvent B: 0.1% formic acid in acetonitrile\nGradient: 2% B at 0-3 min, to 25% B at 63 min, to 50% B at 78 min, 98% B at 80-85 min, then 100% A, with the flow rate of 300 nl/min\n同定用データ取得：Information Dependent Acquisition\n定量用データ取得：SWATH (Data Independent Acquisition)","en":"MS: Sciex TripleTOF 5600\nLC: DIONEX Ultimate 3000 RSLC nano system\nTrap column: 100 μm ID, 2 cm length, packed with 5 μm Acclaim PepMap100 C18\nAnalytical Column: 75 μm ID, 25 cm length, packed with 2 μm Acclaim PepMap C18\nSolvent A: 0.1% formic acid in water\nSolvent B: 0.1% formic acid in acetonitrile\nGradient: 2% B at 0-3 min, to 25% B at 63 min, to 50% B at 78 min, 98% B at 80-85 min, then 100% A, with the flow rate of 300 nl/min\nAcquisition Method for Identification: Information Dependent Acquisition\nAcquisition Method for Quantification: SWATH (Data Independent Acquisition)"}},{"key":"analysis-methods","label":{"ja":"解析方法","en":"Analysis method"},"type":"text","text":{"ja":"タンパク質の同定はInformation Dependent AcquisitionのデータをProteoinPilot 4.5で解析をする事で実施した。同定の信頼性は1% FDRを閾値とした。タンパク質の定量はSWATHのデータをSkylineを用いる事によって実施した。定量の際に用いるスペクトルライブラリは同一検体の同定情報から構築したライブラリや研究室内の蓄積したライブラリを用いた。定量の信頼性は1% FDRを閾値とし、特異的なペプチドのピーク面積の合計をタンパク質の量として計算した。","en":"For protein identification, data was acquired in a data-dependent acquisition mode, and analyzed by ProteinPilot 4.5 (Sciex) with the Uniprot human reference proteome database (release 2017_06). The peptide identification confidence for the dataset was evaluated versus the false discovery rate (FDR). For protein quantification, data was acquired in the data-independent acquisition mode (SWATH) with a variable precursor ion window, and analyzed by Skyline-daily 3.7 with an in-house spectral library. The target peptide peaks were identified with less than 1% FDR, and all peaks were manually inspected. The levels of proteins were calculated based on the sum of the peak areas of unique unmodified tryptic peptides without miscleavage."}},{"key":"processed-data-type","label":{"ja":"加工データの種類","en":"Processed data type"},"type":"vocabulary","terms":[{"code":"peak-list","label":{"en":"Peak list"}},{"code":"identified-protein-list","label":{"en":"Identified protein list"}}]},{"key":"jpost-accession","label":{"ja":"jPOST Accession","en":"jPOST Accession"},"type":"text","text":{"ja":"JPST000553","en":"JPST000553"}},{"key":"policies","label":{"ja":"利用ポリシー","en":"Data use policy"},"type":"vocabulary","terms":[{"code":"nbdc-data-sharing-policy-jgap000001","label":{"ja":"NBDC データ共有ポリシー (JGAP000001)","en":"NBDC data sharing policy (JGAP000001)"}}]}]}],"dataVolume":321192320,"fileFormats":[{"code":"wiff","label":{"en":"WIFF"}}]}