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PXD003977-2

PXD003977 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleExpanding proteome coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) combined with broad specificity proteolysis
DescriptionWe 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.
HostingRepositoryPRIDE
AnnounceDate2017-02-08
AnnouncementXMLSubmission_2017-02-08_00:31:27.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterRoman Fischer
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue
InstrumentOrbitrap Fusion ETD
Dataset History
RevisionDatetimeStatusChangeLog Entry
02016-04-15 03:53:23ID requested
12017-02-07 02:16:15announced
22017-02-08 00:31:28announcedUpdated project metadata.
32017-02-16 00:30:46announcedUpdated project metadata.
42017-10-24 04:57:42announcedUpdated project metadata.
52024-10-22 03:59:03announced2024-10-22: Updated project metadata.
Publication List
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]
Keyword List
curator keyword: Technical
submitter keyword: deep proteome, Fusion Lumos
Contact List
Roman Fischer
contact affiliationTarget Discovery Institute, Nuffield Department of Medicine, University of Oxford, Roosevelt Drive, Oxford OX3 7FZ, UK
contact emailroman.fischer@ndm.ox.ac.uk
lab head
Roman Fischer
contact affiliationUniversity of Oxford
contact emailroman.fischer@ndm.ox.ac.uk
dataset submitter
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Dataset FTP location
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PRIDE project URI
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