PXD018176
PXD018176 is an original dataset announced via ProteomeXchange.
Dataset Summary
Title | Ultraviolet Photodissociation of tryptic peptide backbones at 213 nm |
Description | We 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 |
HostingRepository | PRIDE |
AnnounceDate | 2024-10-22 |
AnnouncementXML | Submission_2024-10-22_05:03:19.728.xml |
DigitalObjectIdentifier | https://dx.doi.org/10.6019/PXD018176 |
ReviewLevel | Peer-reviewed dataset |
DatasetOrigin | Original dataset |
RepositorySupport | Supported dataset by repository |
PrimarySubmitter | Lars 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; |
ModificationList | monohydroxylated residue; iodoacetamide derivatized residue |
Instrument | Orbitrap Fusion Lumos |
Dataset History
Revision | Datetime | Status | ChangeLog Entry |
---|---|---|---|
0 | 2020-03-24 23:18:27 | ID requested | |
1 | 2020-05-07 02:33:16 | announced | |
⏵ 2 | 2024-10-22 05:03:24 | announced | 2024-10-22: 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 affiliation | 1. 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 email | juri.rappsilber@tu-berlin.de |
lab head | |
Lars Kolbowski | |
contact affiliation | TU Berlin |
contact email | lars.kolbowski@tu-berlin.de |
dataset submitter |
Full Dataset Link List
Dataset FTP location NOTE: Most web browsers have now discontinued native support for FTP access within the browser window. But you can usually install another FTP app (we recommend FileZilla) and configure your browser to launch the external application when you click on this FTP link. Or otherwise, launch an app that supports FTP (like FileZilla) and use this address: ftp://ftp.pride.ebi.ac.uk/pride/data/archive/2020/05/PXD018176 |
PRIDE project URI |
Repository Record List
[ + ]