PXD013913-1
PXD013913 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Molecular Dynamics Simulation-directed Ionic Liquid Screening for Deep Coverage Proteome Analysis |
| Description | In-depth coverage of proteomic analysis could enhance our understanding to the mechanism of the protein functions. Unfortunately, many highly hydrophobic and low-abundance proteins are easily lost during sample preparation, mainly attributed to the fact that very few extractants can simultaneously satisfy the requirements on strong solubilizing ability to membrane proteins and enzyme compatibility. Thus, it is urgent to screen ideal extractants from the huge compound libraries. Herein, molecular dynamics simulation was established to elucidate the underlying effects of different extractants on the solubilization of membrane proteins and the maintenance of trypsin activity. Taking this tool, the interaction mechanism between ionic liquids and proteins was elucidated for the first time. And 1-dodecyl-3-methylimidazolium chloride (C12Im-Cl) was found to be the suitable candidate, in accordance with our previous empirical result. Furthermore, inspired by the advantages of C12Im-Cl, an ionic liquid-based filter-aided sample preparation (i-FASP) method was developed. Using this strategy, over 3,300 proteins were confidently identified from 103 HeLa cells (~100 ng proteins) in a single run, an improvement of 53% over the conventional FASP method. Then the i-FASP method was further successfully applied to the label-free relative quantitation of human liver cancer and para-carcinoma tissues with obviously improved accuracy, reproducibility and coverage than the commonly used urea-based FASP method. All above results demonstrate i-FASP is a versatile tool for the in-depth coverage proteomic analysis of biological samples. |
| HostingRepository | MassIVE |
| AnnounceDate | 2020-07-20 |
| AnnouncementXML | Submission_2020-07-20_19:05:38.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Non peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Fei Fang |
| SpeciesList | scientific name: Homo sapiens; common name: human; NCBI TaxID: 9606; |
| ModificationList | unknown modification; unknown modification; unknown modification |
| Instrument | Q Exactive; Orbitrap Fusion |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2019-05-19 16:11:39 | ID requested | |
| ⏵ 1 | 2020-07-20 19:05:39 | announced |
Publication List
| no publication |
Keyword List
| submitter keyword: ionic liquid, deep coverage proteome analysis |
Contact List
| Lihua Zhang | |
|---|---|
| contact affiliation | Dalian Institute of Chemical Physics |
| contact email | lihuazhang@dicp.ac.cn |
| lab head | |
| Fei Fang | |
| contact affiliation | University of Pittsburgh |
| contact email | fef13@pitt.edu |
| dataset submitter | |
Full Dataset Link List
| MassIVE dataset URI |
| Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://massive.ucsd.edu/MSV000083818/ |
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