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PXD019926

PXD019926 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleExpanding the depth and sensitivity of cross-link identification by differential ion mobility using FAIMS
DescriptionIn 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.
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_05:09:32.394.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterLennart 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;
ModificationListNo PTMs are included in the dataset
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-06-21 23:50:51ID requested
12020-07-22 01:17:10announced
22024-10-22 05:09:34announced2024-10-22: Updated project metadata.
Publication List
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;
Keyword List
ProteomeXchange project tag: deep learning, benchmarking, machine learning
submitter keyword: FAIMS, whole proteome,Cross-linking mass spectrometry, XL-MS, Orbitrap Fusion Lumos, CX-MS
Contact List
Fan Liu
contact affiliationDepartment of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125, Berlin, Germany
contact emailfliu@fmp-berlin.de
lab head
Lennart Schnirch
contact affiliationDepartment of Chemical Biology, Leibniz-Forschungsinstitut für Molekulare Pharmakologie (FMP), Robert-Roessle-Str. 10, 13125, Berlin, Germany
contact emailschnirch@fmp-berlin.de
dataset submitter
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Dataset FTP location
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