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PXD023817

PXD023817 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleReverse-phase liquid chromatography (RPLC) in Combination with Tip-Based Strong Cation Exchange (SCX-Tip) Fractionation, ReST, an Alternative Approach for Cross-linked Peptides analysis
DescriptionChemical cross-linking in combination with mass spectrometry (XL-MS) has emerged as a useful method for structural elucidation of proteins and protein complexes. Efficient enrichment procedures are necessary to analyze cross-linked products due to their relatively low abundance. Currently, strong cation exchange chromatography (SCX), size exclusion chromatography (SEC), and affinity tag-based enrichment are among the widely used enrichment strategies. Herein, we present a two-dimensional enrichment strategy combining basic RPLC (bRPLC) fractionation and tip-based SCX (SCX-Tip) enrichment, termed ReST method, for the characterization of cross-linked peptides. We revealed the unbiased separation effects of the bRPLC in the cross-linked peptide fractionation. We optimized the enrichment conditions of SCX-Tip for cross-linked peptides using well-designed cross-linked peptides. Taking advantage of the high resolution of bRPLC fractionation and the high enrichment efficiency of SCX-Tip, we were able to identify 43.6% more cross-links than the conventional SCX approach. The presented ReST approach is an effective fractionation method for XL-MS analysis, and could be beneficial for protoeme-scale protein-protein interaction studies. Moreover, more stringent data filtering was proposed in order to achieve the high confidence of cross-linked peptide identification.
HostingRepositoryPRIDE
AnnounceDate2022-06-21
AnnouncementXMLSubmission_2022-06-21_06:25:56.171.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterZhen Wu
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02021-01-26 01:41:19ID requested
12022-06-21 06:25:56announced
Publication List
Wu Z, Li J, Huang L, Zhang X, Basic pH reversed-phase liquid chromatography (bRPLC) in combination with tip-based strong cation exchange (SCX-Tip), ReST, an efficient approach for large-scale cross-linked peptide analysis. Anal Chim Acta, 1179():338838(2021) [pubmed]
Keyword List
submitter keyword: SCX-Tip, Chemical cross-linking, Mass spectrometry, Fractionation
Contact List
Xumin Zhang
contact affiliationState Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University, Shanghai 200438, China
contact emailxumin_zhang@fudan.edu.cn
lab head
Zhen Wu
contact affiliationState Key Laboratory of Genetic Engineering, Department of Biochemistry, School of Life Sciences, Fudan University
contact emailwuz16@fudan.edu.cn
dataset submitter
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