PXD002142

PXD002142 is an original dataset announced via ProteomeXchange.

Title	Quantitative cross-linking/mass spectrometry
Description	Dynamic proteins and multi-protein complexes govern most biological processes. Cross-linking/mass spectrometry (CLMS) is increasingly successful in providing residue- resolution data on static proteinaceous structures. Here we investigate the technical feasibility of recording dynamic processes using isotope-labelling for quantitation. We cross-linked human serum albumin (HSA) with the readily available cross-linker BS3-d0/4 in different heavy/light ratios. Wefound two limitations. First, isotope labelling reduced the number of identified cross-links. This is in line with similar findings when identifying proteins. Second, standard quantitative proteomics software was not suitable for work with cross-linking. To ameliorate this we wrote a basic open source application, XiQ. Using XiQ we could establish that quantitative CLMS was technically feasible. Biological significance Cross-linking/mass spectrometry (CLMS) has become a powerful tool for providing residue- resolution data on static proteinaceous structures. Adding quantitation to CLMS will extend its ability of recording dynamic processes. Here we introduce a cross-linking specific quantitation strategy by using isotope labelled cross-linkers. Using a model system, we demonstrate the principle and feasibility of quantifying cross-linking data and discuss challenges one may encounter while doing so.We then provide a basic open source application, XiQ, to carry out automated quantitation of CLMS data. Ourwork lays the foundations of studying themolecular details of biological processes at greater ease than this could be done so far.
HostingRepository	PRIDE
AnnounceDate	2015-06-08
AnnouncementXML	Submission_2015-06-08_06:29:22.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Sven Giese
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	LTQ Orbitrap Velos

Revision	Datetime	Status	ChangeLog Entry
0	2015-05-05 07:05:48	ID requested
⏵ 1	2015-06-08 06:29:23	announced

Fischer L, Chen ZA, Rappsilber J, Quantitative cross-linking/mass spectrometry using isotope-labelled cross-linkers. J Proteomics, 88():120-8(2013) [pubmed]

curator keyword: Technical

submitter keyword: Quantitation, Cross-linking, structual biology, protein dynamics

Juri Rappsilber
contact affiliation	1. Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany, 2. Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom;
contact email	juri.rappsilber@tu-berlin.de
lab head
Sven Giese
contact affiliation	Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
contact email	sven.giese@tu-berlin.de
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD002142
     1. Label: PRIDE project
     2. Name: Quantitative cross-linking/mass spectrometry