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PXD006131

DataSet Summary

  • HostingRepository: PRIDE
  • AnnounceDate: 2017-04-22
  • AnnouncementXML: Submission_2017-04-22_00:30:23.xml
  • DigitalObjectIdentifier:
  • ReviewLevel: Peer-reviewed dataset
  • DatasetOrigin: Original data
  • RepositorySupport: Unsupported dataset by repository
  • PrimarySubmitter: Sven Giese
  • Title: Optimizing the parameters governing the fragmentation of cross-linked peptides in a tribrid mass spectrometer
  • Description: We compared the five different ways of fragmentation available on a tribrid mass spectrometer and optimized their collision energies with regard to optimal sequence coverage of cross-linked peptides. We created a library of bis(sulfosuccinimidyl)suberate (BS3/DSS) cross-linked precursors, derived from the tryptic digests of three model proteins (Human Serum Albumin, creatine kinase and myoglobin). This enabled in-depth targeted analysis of the fragmentation behavior of 1065 cross-linked precursors using the five fragmentation techniques: collision-induced dissociation (CID), beam-type CID (HCD), electron-transfer dissociation (ETD), and the combinations ETciD and EThcD. EThcD gave the best sequence coverage for cross-linked m/z species with high charge-density, while HCD was optimal for all others. We tested the resulting data-dependent decision tree against collision energy-optimized single methods on two samples of differing complexity (a mix of eight proteins and a highly complex ribosomal cellular fraction). For the high complexity sample the decision tree gave the highest number of identified cross-linked peptide pairs passing a 5% false discovery rate (on average ~21% more than the second best, HCD). For the medium complexity sample the higher speed of HCD proved decisive. Currently, acquisition speed plays an important role in allowing the detection of cross-linked peptides against the background of linear peptides. Enrichment of cross-linked peptides will reduce this role and favor methods that provide spectra of higher quality.
  • SpeciesList: scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
  • ModificationList: monohydroxylated residue; iodoacetamide derivatized residue
  • Instrument: Orbitrap Fusion Lumos

Dataset History

VersionDatetimeStatusChangeLog Entry
02017-03-20 09:24:23ID requested
12017-04-21 01:06:22announced
22017-04-22 00:30:24announcedUpdated project metadata.

Publication List

  1. Kolbowski L, Mendes ML, Rappsilber J, Optimizing the parameters governing the fragmentation of cross-linked peptides in a tribrid mass spectrometer. Anal Chem, ():(2017) [pubmed]

Keyword List

  1. curator keyword: Technical
  2. submitter keyword: LC-MS, Cross-Linking, Fusion Lumos, Fragmentation

Contact List

    Juri Rappsilber
    • contact affiliation: 1. Department of Bioanalytics, Institute of Biotechnology, Technische Universitšt Berlin, 13355 Berlin, Germany 2. Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
    • contact email: juri.rappsilber@tu-berlin.de
    • lab head:
    Sven Giese
    • contact affiliation: Department of Bioanalytics, Institute of Biotechnology, Technische Universitšt Berlin, 13355 Berlin, Germany
    • contact email: sven.giese@tu-berlin.de
    • dataset submitter:

Full Dataset Link List

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  2. PRIDE project URI
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