PXD000168
PXD000168 is an original dataset announced via ProteomeXchange.
Dataset Summary
| Title | Mouse microglia using high pH fractionation and LC-MS/MS |
| Description | To build a reference proteome, we established a BV-2 microglial proteome to a depth of 5494 unique protein groups using a novel strategy that combined FASP, StageTip-based high pH fractionation, and high-resolution mass spectrometry quickly and cost-efficiently. By bioinformatics analysis, the BV-2 proteome is a valuable resource for studies of microglial function, such as in the immune response, inflammatory response, and phagocytosis. Raw files were processed in MaxQuant version 1.2.2.5 and the Andromeda search engine against the IPI mouse database (version 3.87, 59,534 entries) containing both forward and reverse proteins sequences. Carbamidomethylation of cysteines was set as the fixed modification. Oxidation of methionine and acetylation of protein N-term was employed as a variable modification. The first search tolerance was set to 20 ppm, followed by a main search tolerance of 6 ppm. HCD fragment ion mass tolerance was set to 20 ppm. Peptides with a minimum of 6 amino acids were considered for identification. The false discovery rate (FDR) for all peptides, modification sites, and protein identifications were set to 0.01. Gene ontology of identified proteins at FDR < 1% was annotated using the DAVID bioinformatics resource tool and UniprotKB database. Pathway analysis was performed using the KEGG pathway database and Panther pathway database. |
| HostingRepository | PRIDE |
| AnnounceDate | 2013-09-11 |
| AnnouncementXML | Submission_2013-09-11_05:53:53.xml |
| DigitalObjectIdentifier | |
| ReviewLevel | Peer-reviewed dataset |
| DatasetOrigin | Original dataset |
| RepositorySupport | Unsupported dataset by repository |
| PrimarySubmitter | Dohyun Han |
| SpeciesList | scientific name: Mus musculus (Mouse); NCBI TaxID: 10090; |
| ModificationList | iodoacetamide derivatized residue; monohydroxylated residue; N-acetylated residue |
| Instrument | Q Exactive |
Dataset History
| Revision | Datetime | Status | ChangeLog Entry |
|---|---|---|---|
| 0 | 2013-03-01 01:40:42 | ID requested | |
| 1 | 2013-09-11 05:51:32 | announced | |
| 1 | 2014-07-25 00:56:23 | announced | |
| ⏵ 2 | 2013-09-11 05:53:53 | announced | Add reference |
Publication List
| Han D, Moon S, Kim Y, Kim J, Jin J, Kim Y, In-depth proteomic analysis of mouse microglia using a combination of FASP and StageTip-based, high pH, reversed-phase fractionation. Proteomics, 13(20):2984-8(2013) [pubmed] |
Keyword List
| submitter keyword: Mouse, Microglia, High-pH fractionation, LC-MS/MS |
Contact List
| Dohyun Han | |
|---|---|
| contact affiliation | Colleage of medicine |
| contact email | hdh03@snu.ac.kr |
Full Dataset Link List
| 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://ftp.pride.ebi.ac.uk/2013/09/PXD000168 |
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