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Exploration of charge reduction on sequence coverage of proteins by 193 nm ultraviolet photodissociation v2

ABSTRACT: Comparison of fragmentation of proteins with 193 nm UVPD and EThcD at high and low charge states assessed with alternative means of charge reduction

ORGANISM(S): Homo Sapiens (human) Cellular Organisms Equus Caballus Saccharomyces Cerevisiae (baker's Yeast) Bos Taurus

SUBMITTER: Jennifer S. Brodbelt

PROVIDER: PXD067806 | JPOST Repository | Wed Aug 27 00:00:00 BST 2025

REPOSITORIES: jPOST

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			Action	DRS
	5uMCA_SF45VMS1.raw	Raw
	5uMCA_SF60VMS1.raw	Raw
	5uMCA_SF75VMS1.raw	Raw
	5uMCA_SF90VMS1.raw	Raw
	5uM_CA0,025perFA_S60V.raw	Raw

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Ultraviolet Photodissociation of tryptic peptide backbones at 213 nm

Project 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

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Exploration of charge reduction on sequence coverage of proteins by 193 nm ultraviolet photodissociation

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Impact of Charge State on Characterization of Large Middle-Down Sized Peptides by Tandem Mass Spectrometry

Project description:Fragmentation trends of large peptides were characterized by five activation methods, including HCD, ETD, EThcD, 213 nm UVPD and 193 nm UVPD. Sequence coverages and scores were assessed based on charge site, peptide sequence and peptide size. Results from four model peptides, neuromedin, glucagon, galanin and amyloid B, showed a charge state dependence on sequence coverage for collision and electron-based activation methods. The effect of charge state and peptide size on sequence coverage was also explored for a Glu-C digest of E. coli ribosomal proteins, resulting in a maximum sequence coverage between 2-6 kDa depending on the activation method.

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Ultraviolet Photodissociation of ESI and MALDI generated protein ions on a Q-Exactive mass spectrometer

Project description:UVPD was implemented on an Orbitrap Q-Exactive plus equipped with a ESI/EP-MALDI. UVPD of MALDI generated ions was benchmarked against MALDI-ISD, MALDI-HCD and ESI-UVPD. MALDI UVPD outperformed MALDI HCD and ISD efficiently sequencing small proteins ions.

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Project description:CHARGE Summary Results

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Top-Down Analysis of Supercharged Proteins Using Collision-, Electron-, and Photon-Based Activation Methods

Project description:Analysis of fragmentation under standard and supercharging conditions for intact proteins using HCD, ETD, EThcD, 213 nm UVPD, 193 nm UVPD

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Impact of charge state on 193 nm ultraviolet photodissociation of protein complexes.

Project description:As applications in mass spectrometry continue to expand into the field of structural biology, there have been an increasing number of studies on noncovalent biological assemblies. Ensuring that protein complexes maintain native-like conformations and architectures during the transition from solution to the gas phase is a key aim. Probing composition and arrangement of subunits of multi-charged complexes via tandem mass spectrometry (MS/MS) may lead to protein unfolding and the redistribution of charges on the constituent subunits, leading to asymmetric charge partitioning and ejection of a high-charged monomer. Additionally, the overall dissociation efficiency of many ion activation methods is often suppressed for low charge states, hindering the effectiveness of MS/MS for complexes that have low charge density. Ultraviolet photodissociation (UVPD) of proteins using 193 nm photons is a high-energy alternative to collisional activation and demonstrates little to no charge state dependence. Here the symmetry of charge partitioning upon UVPD is evaluated for an array of multimeric protein complexes as a function of initial charge state. The results demonstrate that high laser energies (3 mJ) for UVPD induces more symmetric charge partitioning and ejection of low-charged, presumably compact monomers than higher-energy collisional dissociation (HCD).

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