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PXD037652

PXD037652 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleReal-time library search assisted identification of cross-links increases resolution for structural modeling and interactome mapping
DescriptionCross-linking mass spectrometry (XL-MS) is a universal tool of molecular and structural biology for probing structural dynamics and protein-protein interactions in vitro and in vivo. Although cross-linked peptides are naturally less abundant than their unlinked counterparts, recent experimental advances improved cross-link identification by enriching the cross-linker modified peptides chemically with the use of enrichable cross-linkers. However, mono-links (i.e., peptides modified with a hydrolyzed cross-linker) still hinder efficient cross-link identification because a large proportion of measurement time is spent on MS2 acquisitions of mono-links. Currently, cross-links and mono-links cannot be separated by sample preparation techniques or chromatography because they are chemically almost identical. Here, we found that based on the intensity ratios of four diagnostic peaks when using PhoX/tert-butyl-PhoX cross-linkers, cross-links and mono-links can be partially distinguished. Harnessing their characteristic intensity ratios for real-time library search (RTLS)-based triggering of full scans increased the number of cross-link identifications from both single protein samples and intact E. coli cells. Furthermore, RTLS improves cross-link identification from unenriched samples and short gradients, which is beneficial in high-throughput approaches and when instrument time or sample amount is limited.
HostingRepositoryPRIDE
AnnounceDate2023-11-14
AnnouncementXMLSubmission_2023-11-14_08:44:17.282.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterMax Ruwolt
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02022-10-24 00:56:37ID requested
12023-03-20 04:18:42announced
22023-11-14 08:44:21announced2023-11-14: Updated project metadata.
Publication List
Ruwolt M, He Y, Borges Lima D, Barshop W, Broichhagen J, Huguet R, Viner R, Liu F, Real-Time Library Search Increases Cross-Link Identification Depth across All Levels of Sample Complexity. Anal Chem, 95(12):5248-5255(2023) [pubmed]
Keyword List
submitter keyword: RTLS, E coli,Cross-linking, diagnostic peaks, XL-MS, PhoX
Contact List
Fan Liu
contact affiliationLeibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin
contact emailfliu@fmp-berlin.de
lab head
Max Ruwolt
contact affiliationLeibniz-Forschungsinstitut for Molecular Pharmacology
contact emailruwolt@fmp-berlin.de
dataset submitter
Full Dataset Link List
Dataset FTP location
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