PXD003977-2

PXD003977 is an original dataset announced via ProteomeXchange.

Title	Expanding proteome coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) combined with broad specificity proteolysis
Description	We attempted to increase proteome and protein sequence coverage in MCF-7 breast cancer cells using CHarge Ordered Parallel Ion aNalysis (CHOPIN), available on an Orbitrap Fusion Lumos mass spectrometer. The parallel use of both detectors available in this instrument, orbitrap and linear iontrap, to generate MS/MS spectra on selected precursor ions allowed a significantly increased success rate for spectrum identification as compared to a “Universal” method, which uses orbitrap for precursor and linear ion trap for MS/MS detection in a separate fashion. Consequently, CHOPIN resulted in higher peptide and protein scores, resulting in an increased confidence of identification. Overall, using high pH based pre-fractionation, we generated 3,517,223 MS/MS spectra and identified 19,803 protein groups (including isoforms) with a total of 535,882 unique peptides, representing 9,906 Ensembl gene IDs in MCF-7 cells with a mean sequence coverage of 32%. More than 5,000 protein groups could be detected with a sequence coverage of >50% allowing to map 206 different modifications to a total of 38.895 sites in 14,434 proteins, thereby covering the deep proteome in unprecedented detail.
HostingRepository	PRIDE
AnnounceDate	2017-02-08
AnnouncementXML	Submission_2017-02-08_00:31:27.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Roman Fischer
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue
Instrument	Orbitrap Fusion ETD

Revision	Datetime	Status	ChangeLog Entry
0	2016-04-15 03:53:23	ID requested
1	2017-02-07 02:16:15	announced
⏵ 2	2017-02-08 00:31:28	announced	Updated project metadata.
3	2017-02-16 00:30:46	announced	Updated project metadata.
4	2017-10-24 04:57:42	announced	Updated project metadata.
5	2024-10-22 03:59:03	announced	2024-10-22: Updated project metadata.

Davis S, Charles PD, He L, Mowlds P, Kessler BM, Fischer R, Expanding Proteome Coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) Combined with Broad Specificity Proteolysis. J Proteome Res, 16(3):1288-1299(2017) [pubmed]

curator keyword: Technical

submitter keyword: deep proteome, Fusion Lumos

Roman Fischer
contact affiliation	Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
contact email	roman.fischer@ndm.ox.ac.uk
lab head
Roman Fischer
contact affiliation	University of Oxford
contact email	roman.fischer@ndm.ox.ac.uk
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/2017/02/PXD003977

PRIDE project URI

• PRIDE
  1. PXD003977
     1. Label: PRIDE project
     2. Name: Expanding proteome coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) combined with broad specificity proteolysis