PXD011036

PXD011036 is an original dataset announced via ProteomeXchange.

Title	Data independent acquisition cross-linking/mass spectrometry
Description	Quantitative cross-linking/mass spectrometry (QCLMS) provides increasing structural detail on altered protein states in solution. Accurate quantitation is a value in itself but may also be central to elucidating small differences between protein states. Hence, QCLMS could benefit from data independent acquisition (DIA) which generally provides higher reproducibility than data dependent acquisition (DDA) and higher throughput than targeted methods. Therefore we here open DIA to QCLMS by extending a widely used DIA software, Spectronaut to now also accommodate cross-link data. A mixture of seven proteins cross-linked with bis[sulfosuccinimidyl] suberate (BS3) was used to evaluate this workflow. Out of the 414 identified unique residue pairs, 292 (70%) were quantifiable across triplicates with a coefficient of variation (CV) of 9.8%, with manual correction of peak selection and boundaries for PSMs in the lower quartile of individual CV values. This compares favourably to DDA where we previously quantified only 63% of the identified cross-links across triplicates with a CV of 14%, for a single protein and complete manual data curation. DIA QCLMS is promising to detect differential abundance of cross-linked peptides in complex mixtures despite the encountered ratio compression when increasing sample complexity through the addition of E. coli cell lysate as matrix. In conclusion, DIA software Spectronaut can now be used in cross-linking and DIA is indeed able to improve QCLMS.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_04:48:24.884.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Fränze Müller
SpeciesList	scientific name: Oryctolagus cuniculus (Rabbit); NCBI TaxID: 9986; scientific name: Bos taurus (Bovine); NCBI TaxID: 9913; scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Equus caballus (Horse); NCBI TaxID: 9796;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2018-09-10 00:04:04	ID requested
1	2019-01-25 07:34:19	announced
⏵ 2	2024-10-22 04:48:25	announced	2024-10-22: Updated project metadata.

10.1074/mcp.tir118.001276;

M, ü, ller F, Kolbowski L, Bernhardt OM, Reiter L, Rappsilber J, Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry. Mol Cell Proteomics, 18(4):786-795(2019) [pubmed]

curator keyword: Technical

submitter keyword: Xi, Reproducibility, Spectronaut, Data independent acquisition, Label-free, Mass spectrometry,Quantitation, Cross-linking

Juri Rappsilber
contact affiliation	1 Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany 2 Wellcome Centre for Cell Biology, School of Biologic 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/2019/01/PXD011036

PRIDE project URI

• PRIDE
  1. PXD011036
     1. Label: PRIDE project
     2. Name: Data independent acquisition cross-linking/mass spectrometry