PXD037652 is an
original dataset announced via ProteomeXchange.
Dataset Summary
Title | Real-time library search assisted identification of cross-links increases resolution for structural modeling and interactome mapping |
Description | Cross-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. |
HostingRepository | PRIDE |
AnnounceDate | 2023-03-20 |
AnnouncementXML | Submission_2023-03-20_04:18:41.736.xml |
DigitalObjectIdentifier | |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Unsupported dataset by repository |
PrimarySubmitter | MaxRuwolt |
SpeciesList | scientific name: Escherichia coli; NCBI TaxID: 562; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
0 | 2022-10-24 00:56:37 | ID requested | |
⏵ 1 | 2023-03-20 04:18:42 | announced | |
2 | 2023-11-14 08:44:21 | announced | 2023-11-14: 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
FanLiu |
contact affiliation | Leibniz-Forschungsinstitut für Molekulare Pharmakologie, Berlin |
contact email | fliu@fmp-berlin.de |
lab head | |
MaxRuwolt |
contact affiliation | Leibniz-Forschungsinstitut for Molecular Pharmacology |
contact email | ruwolt@fmp-berlin.de |
dataset submitter | |
Full Dataset Link List
Dataset FTP location
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PRIDE project URI |
Repository Record List
[ + ]
[ - ]
- PRIDE
- PXD037652
- Label: PRIDE project
- Name: Real-time library search assisted identification of cross-links increases resolution for structural modeling and interactome mapping