PXD011182

PXD011182 is an original dataset announced via ProteomeXchange.

Title	EPIC: Software Toolkit for Elution Profile-Based Inference of Protein Complexes
Description	Heteromeric protein complexes are key macromolecular machines of the cell, but their description remains incomplete. We previously reported an experimental strategy for global characterization of native protein assemblies based on chromatographic fractionation of biological extracts coupled to precision mass spectrometry analysis (CF/MS), but the resulting data can be challenging to process and interpret. Here, we describe EPIC (Elution Profile-based Inference of Complexes), a software toolkit for automated scoring of CF/MS data for large-scale determination of high-confidence physical interaction networks and macromolecular assemblies from diverse biological specimens. As a case study, we used EPIC to map the global interactome of Caenorhabditis elegans, defining 590 putative worm protein complexes linked to diverse biological processes, including assemblies unique to nematodes. The EPIC software is freely available as a Jupyter notebook packaged in a Docker container (https://hub.docker.com/r/baderlab/bio-epic/), and the open source code is available via GitHub (https://github.com/BaderLab/EPIC).
HostingRepository	PRIDE
AnnounceDate	2019-07-16
AnnouncementXML	Submission_2019-07-18_00:47:58.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sadhna Phanse
SpeciesList	scientific name: Caenorhabditis elegans; NCBI TaxID: 6239;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Elite

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-24 08:14:06	ID requested
1	2019-07-16 03:18:23	announced
⏵ 2	2019-07-18 00:55:06	announced	Updated publication reference for PubMed record(s): 31308550.

Hu LZ, Goebels F, Tan JH, Wolf E, Kuzmanov U, Wan C, Phanse S, Xu C, Schertzberg M, Fraser AG, Bader GD, Emili A, EPIC: software toolkit for elution profile-based inference of protein complexes. Nat Methods, 16(8):737-742(2019) [pubmed]

curator keyword: Technical

submitter keyword: CF/MS

EPIC

Biochemical fractionation

Worm interaction network

Mass Spectrometry

Proteomics

Protein complexes

Andrew Emili
contact affiliation	1Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, 160 College Street, Toronto, Ontario M5S 3E1, Canada 2Department of Molecular Genetics, University of Toronto, 1 King's College Circle, Toronto, Ontario M5S 1A8, Canada Departments of Biochemistry and Biology, Boston University, 71 E. Concord St, Boston, MA 02118, USA
contact email	andrew.emili@utoronto.ca
lab head
Sadhna Phanse
contact affiliation	University of Toronto; University of Regina
contact email	srphanse@gmail.com
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/2019/07/PXD011182

PRIDE project URI

• PRIDE
  1. PXD011182
     1. Label: PRIDE project
     2. Name: EPIC: Software Toolkit for Elution Profile-Based Inference of Protein Complexes