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Due to system maintenance, the application system, application review by the Data Access Committee will be unavailable during the following period.
Schedule: October 5th (Mon), 2026, 9:00 - October 7th (Wed), 2026, 15:00 (JST)
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We are currently receiving a large number of applications for data submission, and the review process is taking longer than usual.We sincerely apologize for the delay and kindly ask for your understanding. When submitting an application, we would greatly appreciate it if you could allow sufficient time for the processing.

Following a change to our organizational structure effective April 1, 2026, this division has been renamed from the "Database Center for Life Science, Joint Support-Center for Data Science Research" to the "Database Division for Life Science (DBCLS), BioData Science Initiative (BSI), National Institute of Genetics (NIG)". Where the former name still appears in the guidelines, please read it as the new name.

Dataset ID

JGAD000314

Type of data
Mass Spectrometry
Access criteria
Controlled-access (Type I)
Total data volume
321 MB
File formats
  • WIFF
Research
hum0220
Date published
2020-09-28
Date modified
2021-04-19
DDBJ Search
JGAD000314 (opens in a new tab)
JGA Study
JGAS000223 (opens in a new tab)

Analysis method

質量分析

Materials and participants
Plasma: 18 samples from 3 heathy individuals
Serum: 3 samples from 3 heathy individuals
  • Health status
    Healthy
  • Subject count
    21 (Sample)
Sample description
Plasma and serum samples
  • Tissue
    Plasma, Serum
  • Tumor / normal
    Normal
Sample processing
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.
Platform
Sciex TripleTOF 5600
Measurement condition
MS: Sciex TripleTOF 5600
LC: DIONEX Ultimate 3000 RSLC nano system
Trap column: 100 μm ID, 2 cm length, packed with 5 μm Acclaim PepMap100 C18
Analytical Column: 75 μm ID, 25 cm length, packed with 2 μm Acclaim PepMap C18
Solvent A: 0.1% formic acid in water
Solvent B: 0.1% formic acid in acetonitrile
Gradient: 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
Acquisition Method for Identification: Information Dependent Acquisition
Acquisition Method for Quantification: SWATH (Data Independent Acquisition)
Analysis method
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.
Processed data type
Identified protein list
Peak list
jPOST Accession
JPST000553
Data use policy
NBDC data sharing policy (JGAP000001)