PXD022533-1
PXD022533 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | SubCellBarCode: Integrated workflow for robust classification and visualization of spatial proteome |
Description | We have developed a mass spectrometry (MS) and bioinformatics-based pipeline to generate a proteome-wide resource of protein subcellular localization across multiple human cancer cell lines (www.subcellbarcode.org). Here, we present a detailed wet-lab protocol spanning from subcellular fractionation to MS-sample prep, as well as a dry-lab protocol covering quantitative MS-data analysis, machine-learning-based classification, differential localization analysis and visualization of the output. For broad applicability, we evaluated the pipeline using MS-data generated by three different peptide prefractionation approaches, HiRIEF-LC-MS, High-pH reverse phase fractionation and direct analysis without pre-fractionation using long gradient LC-MS. |
HostingRepository | jPOST |
AnnounceDate | 2022-09-26 |
AnnouncementXML | Submission_2022-09-26_01:48:45.019.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | Yanbo Pan |
SpeciesList | scientific name: Homo sapiens (Human); NCBI TaxID: 9606; |
ModificationList | S-carboxamidomethyl-L-cysteine; L-methionine sulfoxide; TMT6plex reporter+balance reagent N-acylated residue; TMT6plex reporter+balance reagent acylated N-terminal |
Instrument | Q Exactive |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2020-11-15 12:49:37 | ID requested | |
⏵ 1 | 2022-09-26 01:48:45 | announced |
Publication List
Arslan T, Pan Y, Mermelekas G, Vesterlund M, Orre LM, Lehti, ö J, SubCellBarCode: integrated workflow for robust spatial proteomics by mass spectrometry. Nat Protoc, 17(8):1832-1867(2022) [pubmed] |
Keyword List
submitter keyword: Subcellular fractionation, Protein localization, Proteomics, Mass spectrometry, Classification, Visualization |
Contact List
Janne Lehtiö | |
---|---|
lab head | |
Yanbo Pan | |
contact affiliation | Karolinska Institutet |
dataset submitter |
Full Dataset Link List
jPOST 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://ftp.jpostdb.org/JPST001009/ |