PXD047307-1

PXD047307 is an original dataset announced via ProteomeXchange.

Title	Peptide centric detection of cross-linked peptides using PASEF, MeroX, and Skyline
Description	Cross-linking mass spectrometry (XL-MS) has evolved into a pivotal technique for probing protein interactions, with recent ad-vancements significantly enhancing its analytical potential. This technical note presents advancements in cross-linking mass spec-trometry (XL-MS) through the implementation of Parallel Accumulation-Serial Fragmentation (PASEF) on timsTOF instruments, enhancing the detection and analysis of protein interactions. Addressing the challenges in XL-MS, such as the interpretation of complex spectra, low abundance of cross-linked peptides (XL-peptides), and data acquisition biases, the study integrates a peptide-centric approach for the analysis of XL-MS data and presents the foundation for integrating data independent acquisition (DIA) in XL-MS with a vendor neutral and open-source platform. A novel method is described for processing DDA-PASEF data using Bruker software, enabling the conversion of this data into a format compatible with MeroX and Skyline tools. This approach, demonstrated with a bovine serum albumin (BSA) case study, significantly improves the identification and understanding of protein interactions, equipping the cross-linking community to overcome current analytical limitations.
HostingRepository	PanoramaPublic
AnnounceDate	2024-05-13
AnnouncementXML	Submission_2024-05-13_21:57:41.791.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Juan Camilo Rojas Echeverri
SpeciesList	scientific name: Bos taurus; NCBI TaxID: 9913;
ModificationList	Xlink:BuUrBu[196]; Carbamidomethyl; Label:13C(6)15N(2); Label:13C(6)15N(4); Xlink:BuUrBu[214]
Instrument	timsTOF Pro

Revision	Datetime	Status	ChangeLog Entry
0	2023-11-27 22:10:49	ID requested
⏵ 1	2024-05-13 21:57:42	announced

Rojas Echeverri JC, Hause F, Iacobucci C, Ihling CH, T, ä, nzler D, Shulman N, Riffle M, MacLean BX, Sinz A, A Workflow for Improved Analysis of Cross-Linking Mass Spectrometry Data Integrating Parallel Accumulation-Serial Fragmentation with MeroX and Skyline. Anal Chem, 96(19):7373-7379(2024) [pubmed]

submitter keyword: XL-MS, PASEF, DDA, DIA, Peptide-centric

Andrea Sinz
contact affiliation	Martin-Luther-Universität Halle-Wittenberg
contact email	andrea.sinz@pharmazie.uni-halle.de
lab head
Juan Camilo Rojas Echeverri
contact affiliation	Scientific Assistant
contact email	juan-camilo.rojas-echeverri@pharmazie.uni-halle.de
dataset submitter

Panorama Public dataset URI