| Metadata |
| datasetIdentifier | PASS01568 |
| datasetType | SRM |
| submitter | Youdong Wei <youdongwei1966@163.com> |
| submitter_organization | The first affiliated hospital of chongqing medical university |
| lab_head_full_name | Youdong Wei |
| lab_head_email | youdongwei1966@163.com |
| lab_head_organization | The first affiliated hospital of chongqing medical university |
| lab_head_country | China |
| datasetTag | parkinsonsdisease |
| datasetTitle | proteomics profiling for patients with Parkinson's disease |
| publicReleaseDate | 2020-04-18 00:00:00 |
| finalizedDate | 2020-04-23 19:27:39 |
| summary | Fasting plasma samples were obtained and analyzed using proteomics methods. After that, differentially expressed proteins were identified for further bioinformatics analysis. No significant difference was found in clinical data between these two groups. According to the proteomics analysis, forty proteins were identified to be differentially expressed, seven of which were apolipoproteins. Furthermore, five of the six top ranking Gene Ontology terms from cellular component and eleven of the other fourteen Gene Ontology terms from biological process were directly associated with lipid metabolism. In KEGG pathway analysis, the five enriched pathways were also significantly related with lipid metabolism (p<0.05). |
| contributors | Meixue Dong, Ling Hu, Youdong Wei |
| publication | unpublished |
| growth | Fasting plasma samples were obtained by centrifugation at 2000 × g for 10 min at 4°C after collection at 6:00 am by puncture of the median cubital vein. |
| treatment | Fasting plasma samples were obtained by centrifugation at 2000 × g for 10 min at 4°C after collection at 6:00 am by puncture of the median cubital vein. |
| extraction | Abundant proteins were removed using Agilent Human 14 Multiple Affinity Removal System Column following the manufacturers’ protocol (Agilent Technologies, California, USA). |
| separation | Depleted samples were separated on a 12.5% SDS-PAGE gel, and protein bands were visualized by Coomassie Blue R-250 staining. |
| digestion | Depleted samples were then digested with trypsin (Promega, Madison, Wilconsin, USA) and labeled with TMT reagents according to the manufacturer’s instructions (Thermo Scientific, Waltham, Massachusetts, USA). |
| acquisition | After labeling, a Pierce high pH reverse-phase fractionation kit (Thermo Scientific) was used to fractionate TMT-labeled digest samples into 15 fractions by an increasing acetonitrile step-gradient elution according to the manufacturer’s instructions. Each peptide mixture fraction was loaded onto a reverse phase trap column (Thermo Scientific Acclaim PepMap100, 100 um × 2 cm, nanoViper C18) connected to the C18-reversed phase analytical column (Thermo Scientific Easy Column, 10 cm long, 75 um inner diameter, 3 um resin) for nanoLC-MS/MS analysis. LC-MS/MS analysis was performed on a Q Exactive mass spectrometer (Thermo Scientific) coupled to an Easy nLC (Thermo Fisher Scientific). |
| informatics | MS/MS spectra were searched using MASCOT engine (Matrix Science, London, UK; version 2.2) embedded into Proteome Discoverer 1.4. |
| instruments | Thermo Scientific Q Exactive |
| species | Human |
| massModifications | none |
