PXD019926

PXD019926 is an original dataset announced via ProteomeXchange.

Title	Expanding the depth and sensitivity of cross-link identification by differential ion mobility using FAIMS
Description	In cross-linking mass spectrometry (XL-MS), the depth and sensitivity of cross-link detection is often limited by the low abundance of cross-links compared to non-cross-linked peptides in the digestion mixture. To improve the identification efficiency of cross-links, here we present a gas-phase separation strategy using high field asymmetric waveform ion mobility spectrometry (FAIMS) coupled to the Orbitrap Tribrid mass spectrometers. By enabling an additional peptide separation step in gas phase using the FAIMS device, we increase the number of cross-link identification by 22% for a medium complex sample and 59% for strong cation exchange-fractionated HEK293T cell lysate in XL-MS experiments using disuccinimidyl sulfoxide (DSSO) cross-linker. When disuccinimidyl suberate (DSS) cross-linker is in use, we are able to boost cross-link identification by 89% for the medium and 100% for the highly complex sample comparing to the analyses without FAIMS . Furthermore, we show that for medium complex samples, FAIMS enables the collection of single-shot XL-MS data with comparable depth to the corresponding sample fractionated by chromatography-based approaches. Altogether, we demonstrate FAIMS is highly beneficial for XL-MS studies by expanding the proteome coverage of cross-links while improving the efficiency and confidence of cross-link identification.
HostingRepository	PRIDE
AnnounceDate	2024-10-22
AnnouncementXML	Submission_2024-10-22_05:09:32.394.xml
DigitalObjectIdentifier
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Unsupported dataset by repository
PrimarySubmitter	Lennart Schnirch
SpeciesList	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	No PTMs are included in the dataset
Instrument	Orbitrap Fusion Lumos

Revision	Datetime	Status	ChangeLog Entry
0	2020-06-21 23:50:51	ID requested
1	2020-07-22 01:17:10	announced
⏵ 2	2024-10-22 05:09:34	announced	2024-10-22: Updated project metadata.

Schnirch L, Nadler-Holly M, Siao SW, Frese CK, Viner R, Liu F, Expanding the Depth and Sensitivity of Cross-Link Identification by Differential Ion Mobility Using High-Field Asymmetric Waveform Ion Mobility Spectrometry. Anal Chem, 92(15):10495-10503(2020) [pubmed]

10.1021/acs.analchem.0c01273;

ProteomeXchange project tag: deep learning, benchmarking, machine learning

submitter keyword: FAIMS, whole proteome,Cross-linking mass spectrometry, XL-MS, Orbitrap Fusion Lumos, CX-MS

Fan Liu
contact affiliation	Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125, Berlin, Germany
contact email	fliu@fmp-berlin.de
lab head
Lennart Schnirch
contact affiliation	Department of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125, Berlin, Germany
contact email	schnirch@fmp-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/2020/07/PXD019926

PRIDE project URI

• PRIDE
  1. PXD019926
     1. Label: PRIDE project
     2. Name: Expanding the depth and sensitivity of cross-link identification by differential ion mobility using FAIMS