PXD007250

PXD007250 is an original dataset announced via ProteomeXchange.

Title	On the reproducibility of label-free quantitative cross-linking/mass spectrometry
Description	Quantitative cross-linking/mass spectrometry (QCLMS) is an emerging approach to study conformational changes of proteins and multi-subunit complexes. Distinguishing protein conformations requires reproducibly identifying and quantifying cross-linked peptides. Here we analyzed the variation between multiple cross-linking reactions using bis[sulfosuccinimidyl] suberate (BS3)-cross-linked human serum albumin (HSA) and evaluated how reproducible cross-linked peptides can be identified and quantified by LC-MS analysis. To make QCLMS accessible to a broader research community we developed a workflow that integrates the established software tools MaxQuant for spectra pre-processing, Xi for cross-linked peptide identification and finally Skyline for quantification (MS1 filtering). Out of the 221 unique residue pairs identified in our sample, 146 (66% of those identified) could be imported into Skyline and 124 (84% of those imported) were subsequently quantified with coefficient of variation (CV) values of 14% (injection replica) and 32% (reaction replica). Thus our results demonstrate that the reproducibility of QCLMS is in line with the reproducibility of general quantitative proteomics and we establish a robust workflow for MS1-based quantitation of cross-linked peptides.
HostingRepository	PRIDE
AnnounceDate	2018-01-02
AnnouncementXML	Submission_2018-01-02_02:40:57.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fränze Müller
SpeciesList	scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2017-08-11 03:17:48	ID requested
⏵ 1	2018-01-02 02:40:58	announced

M, ü, ller F, Fischer L, Chen ZA, Auchynnikava T, Rappsilber J, On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry. J Am Soc Mass Spectrom, 29(2):405-412(2018) [pubmed]

curator keyword: Technical

submitter keyword: cross-linking, mass-spectrometry, quatitation, Skyline

Juri Rappsilber
contact affiliation	Chair of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, Scotland, United Kingdom
contact email	juri.rappsilber@tu-berlin.de
lab head
Fränze Müller
contact affiliation	TU Berlin
contact email	fraenze.mueller@tu-berlin.de
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/2018/01/PXD007250

PRIDE project URI

• PRIDE
  1. PXD007250
     1. Label: PRIDE project
     2. Name: On the reproducibility of label-free quantitative cross-linking/mass spectrometry