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PXD006131

PXD006131 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleOptimizing the parameters governing the fragmentation of cross-linked peptides in a tribrid mass spectrometer
DescriptionWe 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.
HostingRepositoryPRIDE
AnnounceDate2017-10-24
AnnouncementXMLSubmission_2017-10-24_04:03:45.xml
DigitalObjectIdentifier
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportUnsupported dataset by repository
PrimarySubmitterSven Giese
SpeciesList scientific name: Homo sapiens (Human); NCBI TaxID: 9606;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02017-03-20 09:24:23ID requested
12017-04-21 01:06:22announced
22017-04-22 00:30:24announcedUpdated project metadata.
32017-10-24 04:03:46announcedUpdated project metadata.
Publication List
Kolbowski L, Mendes ML, Rappsilber J, Optimizing the Parameters Governing the Fragmentation of Cross-Linked Peptides in a Tribrid Mass Spectrometer. Anal Chem, 89(10):5311-5318(2017) [pubmed]
Keyword List
curator keyword: Technical
submitter keyword: LC-MS, Cross-Linking, Fusion Lumos, Fragmentation
Contact List
Juri Rappsilber
contact affiliation1. Department of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany 2. Wellcome Trust Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3JR, United Kingdom
contact emailjuri.rappsilber@tu-berlin.de
lab head
Sven Giese
contact affiliationDepartment of Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany
contact emailsven.giese@tu-berlin.de
dataset submitter
Full Dataset Link List
Dataset FTP location
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