PXD007038

PXD007038 is an original dataset announced via ProteomeXchange.

Title	SEC-SWATH-MS HEK293
Description	Increasingly, biochemical co-fractionation-based approaches are used to study interactomes and protein complexes at high throughput. The devised methods facilitate the qualitative assignment and prediction of hundreds of putative cellular assemblies in one experiment and without dependency on genetic engineering to introduce affinity tags. The present dataset consists of a native proteome extracted by mild lysis from the HEK293 cell line and fractionated into 80 fractions along high resolution size exclusion chromatography, and each fraction analyzed via bottom-up SWATH mass spectrometry. In multi-tiered targeted analysis, from this fragment ion level chromatographic data, quantitative complex assembly information of the proteome is reconstructed in three steps, (i) peptide-centric detection of peptide analytes within each SEC fraction based on fragment ion co-elution groups; (ii) protein-centric detection of protein elution in SEC based on fragment peptide co-elution groups in SEC; (iii) complex-centric detection and quantification of protein complexes and -variants based on component subunit protein co-elution groups in SEC. The data delineate a global picture of quantitative complex formation within a human proteome, including deconvolution of novel subversions and assembly intermediates of critical cellular complexes with essential functions.
HostingRepository	PRIDE
AnnounceDate	2019-01-11
AnnouncementXML	Submission_2019-08-19_07:06:57.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Moritz Heusel
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	TripleTOF 5600

Revision	Datetime	Status	ChangeLog Entry
0	2017-07-13 13:18:56	ID requested
1	2018-06-26 02:37:53	announced
2	2018-06-28 01:05:24	announced	Updated publication reference for DOI(s): 10.1101/323683.
3	2019-01-11 06:26:32	announced	Updated project metadata.
⏵ 4	2019-08-19 07:06:58	announced	Updated project metadata.

10.1101/323683;

Heusel M, Bludau I, Rosenberger G, Hafen R, Frank M, Banaei-Esfahani A, van Drogen A, Collins BC, Gstaiger M, Aebersold R, Complex-centric proteome profiling by SEC-SWATH-MS. Mol Syst Biol, 15(1):e8438(2019) [pubmed]

curator keyword: Technical, Biological

submitter keyword: Size exclusion chromatography, SWATH, Mass Spectrometry, protein complexes

Rudolf Aebersold
contact affiliation	Institute of Molecular Systems Biology D-BIOL ETH Zurich Switzerland
contact email	aebersold@imsb.biol.ethz.ch
lab head
Moritz Heusel
contact affiliation	ETHZ
contact email	heusel@imsb.biol.ethz.ch
dataset submitter

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/pride/data/archive/2019/01/PXD007038

PRIDE project URI

• PRIDE
  1. PXD007038
     1. Label: PRIDE project
     2. Name: SEC-SWATH-MS HEK293