PXD003977 is an
original dataset announced via ProteomeXchange.
Dataset Summary
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 |
Dataset History
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. |
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 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 | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD003977
- Label: PRIDE project
- Name: Expanding proteome coverage with CHarge Ordered Parallel Ion aNalysis (CHOPIN) combined with broad specificity proteolysis