PXD003977-5

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	The "deep" proteome has been accessible by mass spectrometry for some time. However, the number of proteins identified in cells of the same type has plateaued at ~8,000-10,000 without ID transfer from reference proteomes/data. Moreover, limited sequence coverage hampers the discrimination of protein isoforms when using trypsin as standard protease. Multi-enzyme approaches appear to improve sequence coverage and subsequent isoform discrimination. Here, we expanded proteome and protein sequence coverage in MCF-7 breast cancer cells to an as yet unmatched depth, by employing a workflow that addresses current limitations in deep proteome analysis at multiple stages: We used i) Gel-aided sample preparation (GASP) and combined trypsin/elastase digests to increase peptide orthogonality, ii) concatenated high pH pre-fractionation and iii) CHarge Ordered Parallel Ion aNalysis (CHOPIN)- available on an Orbitrap Fusion (Lumos) mass spectrometer- to achieve 57% median protein sequence coverage in 13,728 protein groups (8,949 Unigene IDs) in a single cell line. CHOPIN allows the use of both detectors in the Orbitrap on predefined precursor types that optimizes parallel ion processing, leading to the identification of a total of 179,549 unique peptides covering the deep proteome in unprecedented detail.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_03:58:57.576.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]

10.1021/acs.jproteome.6b00915;

ProteomeXchange project tag: benchmarking, machine learning

curator keyword: Technical

submitter keyword: Fusion Lumos,deep proteome

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