PXD022533

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]

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

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/

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/