PXD002987

PXD002987 is an original dataset announced via ProteomeXchange.

Title	xIP-MS: topological analysis of chromatin-associated protein complexes using single affinity purification
Description	In recent years, cross-linking mass spectrometry (XL-MS) has proven to be a robust and effective method of interrogating macromolecular protein complex topologies at peptide resolution. Traditionally, XL-MS workflows have utilized homogenous complexes obtained through time-limiting reconstitution, tandem affinity purification, and conventional chromatography workflows. Here, we present cross-linking immunoprecipitation-MS (xIP-MS), a simple, rapid, and efficient method for structurally probing chromatin-associated protein complexes using small volumes of mammalian whole cell lysates, single affinity purification, and on-bead cross-linking followed by LC-MS/MS analysis. We first benchmarked xIP-MS using the structurally well-characterized phosphoribosyl pyrophosphate synthetase (PRPP) complex. We then applied xIP-MS to the chromatin-associated cohesin (SMC1A/3), XRCC5/6 (Ku70/86), and MCM complexes, and we provide novel structural and biological insights into their architectures and molecular function. Of note, we use xIP-MS to perform topological studies under cell cycle perturbations, showing that the xIP-MS protocol is sufficiently straightforward and efficient to allow comparative cross-linking experiments. This work, therefore, demonstrates that xIP-MS is a robust, flexible, and widely applicable methodology for interrogating chromatin-associated protein complex architectures.
HostingRepository	PRIDE
AnnounceDate	2015-11-17
AnnouncementXML	Submission_2015-11-17_03:35:30.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Matthew Makowski
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	No PTMs are included in the dataset
Instrument	Q Exactive; Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2015-09-29 01:42:14	ID requested
⏵ 1	2015-11-17 03:35:31	announced

Makowski MM, Willems E, Jansen PW, Vermeulen M, Cross-linking immunoprecipitation-MS (xIP-MS): Topological Analysis of Chromatin-associated Protein Complexes Using Single Affinity Purification. Mol Cell Proteomics, 15(3):854-65(2016) [pubmed]

submitter keyword: Chemical cross-linking mass-spectrometry, chromatin, affinity purification

Michiel Vermeulen
contact affiliation	Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, Geert Grooteplein 28, 6525 GA Nijmegen, the Netherlands
contact email	M.Vermeulen@ncmls.ru.nl
lab head
Matthew Makowski
contact affiliation	Radboud University
contact email	matthew.makowski.m@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/2015/11/PXD002987

PRIDE project URI

• PRIDE
  1. PXD002987
     1. Label: PRIDE project
     2. Name: xIP-MS: topological analysis of chromatin-associated protein complexes using single affinity purification