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PXD018176

PXD018176 is an original dataset announced via ProteomeXchange.

Dataset Summary
TitleUltraviolet Photodissociation of tryptic peptide backbones at 213 nm
DescriptionWe analyzed the backbone fragmentation behavior of tryptic peptides of a four protein mixture and of E. coli lysate subjected to Ultraviolet Photodissociation (UVPD) at 213 nm on a commercially available UVPD-equipped tribrid mass spectrometer. We obtained 15,178 high-confidence peptide-spectrum matches by additionally recording a reference beam-type collision-induced dissociation (HCD) spectrum of each precursor. Type a, b and y ions were most prominent in UVPD spectra and median sequence coverage ranged from 5.8% (at 5 ms laser excitation time) to 45.0% (at 100 ms). Overall sequence fragment intensity remained relatively low (median: 0.4% (5 ms) to 16.8% (100 ms) of total intensity) and remaining precursor intensity high. Sequence coverage and sequence fragment intensity ratio correlated with precursor charge density, suggesting that UVPD at 213 nm may suffer from newly formed fragments sticking together due to non-covalent interactions. UVPD fragmentation efficiency therefore might benefit from supplemental activation, as was shown for ETD. Aromatic amino acids, most prominently tryptophan, facilitated UVPD. This points at aromatic tags as possible enhancers of UVPD. Data are available via ProteomeXchange and on spectrumviewer.org/db/UVPD_213nm_trypPep
HostingRepositoryPRIDE
AnnounceDate2024-10-22
AnnouncementXMLSubmission_2024-10-22_05:03:19.728.xml
DigitalObjectIdentifierhttps://dx.doi.org/10.6019/PXD018176
ReviewLevelPeer-reviewed dataset
DatasetOriginOriginal dataset
RepositorySupportSupported dataset by repository
PrimarySubmitterLars Kolbowski
SpeciesList scientific name: Escherichia coli; NCBI TaxID: 562; scientific name: Oryctolagus cuniculus (Rabbit); NCBI TaxID: 9986; scientific name: Gallus gallus (Chicken); NCBI TaxID: 9031; scientific name: Homo sapiens (Human); NCBI TaxID: 9606; scientific name: Equus caballus (Horse); NCBI TaxID: 9796;
ModificationListmonohydroxylated residue; iodoacetamide derivatized residue
InstrumentOrbitrap Fusion Lumos
Dataset History
RevisionDatetimeStatusChangeLog Entry
02020-03-24 23:18:27ID requested
12020-05-07 02:33:16announced
22024-10-22 05:03:24announced2024-10-22: Updated project metadata.
Publication List
10.6019/PXD018176;
Kolbowski L, Belsom A, Rappsilber J, Ultraviolet Photodissociation of Tryptic Peptide Backbones at 213 nm. J Am Soc Mass Spectrom, 31(6):1282-1290(2020) [pubmed]
10.1021/jasms.0c00106;
Keyword List
submitter keyword: LC-MSMS, E. coli, ovotransferrin, Fusion Lumos, Dual MS2,UVPD 213 nm, HSA, myoglobin, creatine kinase
Contact List
Juri Rappsilber
contact affiliation1. Bioanalytics, Institute of Biotechnology, Technische Universität Berlin, 13355 Berlin, Germany 2. Wellcome Centre for Cell Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH93BF, United Kingdom
contact emailjuri.rappsilber@tu-berlin.de
lab head
Lars Kolbowski
contact affiliationTU Berlin
contact emaillars.kolbowski@tu-berlin.de
dataset submitter
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Dataset FTP location
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