PXD018176

PXD018176 is an original dataset announced via ProteomeXchange.

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

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.

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;

submitter keyword: LC-MSMS, E. coli, ovotransferrin, Fusion Lumos, Dual MS2,UVPD 213 nm, HSA, myoglobin, creatine kinase

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

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PRIDE project URI

• PRIDE
  1. PXD018176
     1. Label: PRIDE project
     2. Name: Ultraviolet Photodissociation of tryptic peptide backbones at 213 nm