NBDC Research ID: hum0220.v1
SUMMARY
Aims: To clarify the stability of blood proteins during pre-analytical blood processing and storage, to compare the proteomes of similarly treated serum and plasma samples.
Methods: We compared plasma samples prepared by centrifugation after storage of blood at room temperature for 0, 15 or 30 minutes, or under refrigeration at 0-5°C for 1, 4 or 8 hours. We also compared protein levels between plasma and serum. The plasma and serum samples were digested by trypsin and analyzed by mass spectrometer.
Participants/Materials: Plasma and serum samples from heathy individuals
| Dataset ID | Type of Data | Criteria | Release Date |
|---|---|---|---|
| JGAS000223 | Mass Spectrometry | Controlled-access (Type I) | 2020/06/02 |
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MOLECULAR DATA
| Participants/Materials |
Plasma: 18 samples from 3 heathy individuals Serum: 3 samples from 3 heathy individuals |
| Targets | Mass Spectrometry |
| Source | Plasma and serum samples |
| Sample Preparation Method | 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. |
| Measurement Conditions |
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) |
| Peak Detection / Protein Identification 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. |
| Japanese Genotype-phenotype Archive Dataset ID | JGAD000314 |
| JPOST ID | JPST000553 |
| Total Data Volume |
306 MB wiff: meta data (measument conditions) wiff.scan: raw spectral data amf: a list of peaks txt: a list of proteins |
| Comments (Policies) | NBDC policy |
DATA PROVIDER
Principal Investigator: Sumio Ohtsuki
Affiliation: Faculty of Life Sciences, Kumamoto University
Project / Group Name: Laboratory of Pharmaceutical Microbiology
URL: http://ohtsuki-lab.jp/en/
Funds / Grants (Research Project Number):
| Name | Title | Project Number |
|---|---|---|
| Core Research and Evolutional Science and Technology, Advanced Research & Development Programs for Medical Innovation, Japan Agency for Medical Research and Development (AMED-CREST) | Cancer diagnosis/drug efficiency evaluation biomarker research by comprehensive metabolomics/targeted proteomics and establishment of innovative integrated clinical diagnosis network | JP19gm0710013 |
PUBLICATIONS
| Title | DOI | Dataset ID | |
|---|---|---|---|
| 1 | Effects of Differences in Pre-Analytical Processing on Blood Protein Profiles Determined With SWATH-MS | doi: 10.1016/j.jprot.2020.103824 | JGAD000314 |
| 2 |
USRES (Controlled-access Data)
| Principal Investigator | Affiliation | Country/Region | Research Title | Data in Use (Dataset ID) | Period of Data Use |
|---|---|---|---|---|---|
