| Metadata |
| datasetIdentifier | PASS00756 |
| datasetType | SRM |
| submitter | Toshihiro Yoneyama <t-yoneyama@dc.tohoku.ac.jp> |
| submitter_organization | Division of Membrane Transport and Drug Targeting, Graduate School of Pharmaceutical Sciences, Tohoku University |
| lab_head_full_name | Tetsuya Terasaki |
| lab_head_email | terasaki.tetsuya@m.tohoku.ac.jp |
| lab_head_organization | Division of Membrane Transport and Drug Targeting, Graduate School of Pharmaceutical Sciences, Tohoku University |
| lab_head_country | Japan |
| datasetTag | SRM_human_plasma |
| datasetTitle | SRM analysis of human plasma for pancreatic cancer diagnosis |
| publicReleaseDate | 2015-10-13 00:00:00 |
| finalizedDate | 2016-03-06 20:04:38 |
| summary | SRM analysis in plasma of healthy controls, pancreatic cancer patients and patients of other diseases other than pancreatic cancer was performed to validate the biomarker candidates for pancreatic cancer. We quantified 594 samples using high-throughput SRM system (10 min/run). |
| contributors | Toshihiro Yoneyama, Sumio Ohtsuki, Kazufumi Honada, Yasuo Uchida, Masanori Tachikawa, Tetsuya Terasaki |
| publication | Yoneyama T et al., Identification of IGFBP2 and IGFBP3 as Compensatory Biomarkers for CA19-9 in Early –Stage Pancreatic Cancer Using a Combination of Antibody-based and LC-MS/MS-based Proteomics, PlosOne, submitted |
| growth | |
| treatment | |
| extraction | |
| separation | |
| digestion | Ten microliters of 5-fold-diluted samples, corresponding 2 μL plasma, was solubilized in 15 μL of 8 M urea in 100 mM Tris-HCl (pH 8.5), and S-carbamoylmethylated with 5 μL of 20 mg/mL dithiothreitol (DTT) in 100 mM Tris-HCl (pH 8.5) and 5 μL of 50 mg/mL iodoacetamide (IAA) in 100 mM Tris-HCl (pH 8.5). The S-carbamoylmethlated samples were diluted with 56 μL of 100 mM Tris-HCl (pH 8.5), and treated with 2 μL of lysyl endo peptidase (Lys-C, Wako Pure Chemical Industries) at 25℃ for 3h. Subsequently, samples were digested with 2 μL of trypsin (Promega) at 37℃ for 16 h. |
| acquisition | LC-MS/MS analysis was performed with an electrospray ionization-triple quadrupole mass spectrometer (QTRAP5500; AB SCIEX, Framingham, MA) coupled with a MicroLC system (expert microLC 200; Ekisigent Technologies, Dublin, CA, USA). MicroLC was performed with C18 column (HALO C18 2.7μm, 0.5 × 50 mm, Ekisigent Technologies). Mobile phase A and B consisted of 0.1% formic acid in water and 0.1% formic acid in acetonitrile, respectively. The peptides were separated and eluted from the column with linear gradient sequence (10 min rum time, with a flow rate of 20 μL/min for 0-7.5 min and 50 μL/min for 8-10 min) as follows (A : B): 99 : 1 for 0-2 min after injection, 80 : 20 at 6min, 0 : 100 at 6.5 and up to 7.5 min, 99 : 1 at 8 min and up to 10 min. The mass spectrometer was set up to run as multiplexed SRM mode for peptide detection, using a 10 msec per transition. |
| informatics | Wiff files obtained by QTRAP 5500 were converted into mzmL through ProteoWizzard. The ion counts in the chromatograms were determined by using auto analysis system established our laboratory |
| instruments | AB SCIEX QTRAP5500 |
| species | Human |
| massModifications | K+8.014199, R+10.008269 |
