Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Thorough performance evaluation of 213 nm ultraviolet photodissociation for top-down proteomics

ABSTRACT: In this study we benchmark the performance of ultraviolet photodissociation (UVPD) using 213 nm photons generated by a solid-state laser applied to the study of intact proteoforms from three organisms. 213 nm UVPD was compared to the commonly employed higher-energy collisional dissociation (HCD).

INSTRUMENT(S): Orbitrap Fusion ETD

ORGANISM(S): Pseudomonas Aeruginosa (ncbitaxon:287) Homo Sapiens (ncbitaxon:9606) Mus Musculus (ncbitaxon:10090)

SUBMITTER: Neil Kelleher

PROVIDER: MSV000083972 | MassIVE | Thu Jun 13 08:52:00 BST 2019

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

2020-05-07 | PXD018176 | Pride

Application of 193 nm UVPD for phosphoproteomic analysis of HeLa and HCC70

Project description:Application of 193 nm ultraviolet photodissociation (UVPD) for phosphoproteomics analysis of IMAC enriched HeLa and HCC70 lysates. HCC70 cells were either maintained in full media or serum starved for 6 hours prior to lysis. Each sample was analyzed by three UVPD and three HCD technical replicates using an Orbitrap Fusion mass spectrometer equipped with a Coherent 193 nm excimer laser. Using UVPD, a/x, b/y, and c/z ions were generated and improved phosphate retention was observed on product ions.

2016-04-04 | MSV000079626 | MassIVE

AMCA chromophore tagging and 351 nm ultraviolet photodissociation enables de novo sequencing of E. coli proteome

Project description:Demonstration of novel experimental and computational pipeline for high performance de novo peptide sequencing. E. coli whole cell lysate is carbamylated to block lysine side chains, digested with trypsin (now active only at Arg residues), and N-terminally tagged with the chromophore AMCA. Three technical replicates were analyzed using a Thermo Velos Pro dual linear ion trap mass spectrometer coupled to a Coherent 351 nm excimer laser. 351 nm ultraviolet photodissociation (UVPD) of parent peptides produces MS2 spectra dominated by the y-type ion series. We developed the software tool UVnovo for de novo sequencing of these spectra and used Proteome Discoverer SEQUEST/Percolator to generate a dataset for training and validation. UVnovo results provided here derive from a 3-fold cross validation regime. Our methods and dataset are described in the accompanying publication.

2016-03-10 | MSV000079571 | MassIVE

Multi-Stage Native UVPD-MS to Characterize Single Amino Acid Variants of Human Mitochondrial BCAT2

Project description:We report a multi-stage approach combining collisional activation and 193 nm ultraviolet photodissociation (UVPD) to characterize single amino acid variants of the human mitochondrial enzyme branched-chain amino acid transferase 2 (BCAT2), a protein implicated in chemotherapeutic resistance in glioblastoma tumors.

2018-05-31 | PXD009447 | JPOST Repository

Characterization of disulfide linkages in proteins by 193 nm ultraviolet photodissociation (UVPD)

Project description:Inter-linked disulfide bonds connecting peptide chains are homolytically cleaved with 193 nm ultraviolet photodissociation (UVPD). Analysis of insulin demonstrates the ability for UVPD to cleave multiple disulfide bonds and provide sequence coverage of multiple peptide chains in the same MS/MS event. The information provided by UVPD of disulfide-bound peptides is comparable to information garnered from other high energy dissociation methods but requires an activation period an order of magnitude faster than these methods. This phenomenon was investigated, along with a partial reduction and alkylation sample preparation to determine disulfide connectivities of enzymatically digested proteins. The 4 disulfide bonds of lysozyme and the 19 disulfide bonds of serotransferrin were unambiguously characterized through non-reduced and partially reduced protein digestions.

2018-04-28 | PXD009460 | JPOST Repository

Complementary CID and 351 nm UVPD tandem mass spectra enable effective de novo sequencing

Project description:This dataset accompanies a publication in which we present a strategy for acquisition and effective de novo peptide sequencing of complementary CID and 351 nm ultraviolet photodissociation (UVPD) MS/MS pairs. E. coli whole cell lysate is carbamylated to block lysine side chains, digested with trypsin (now active only at Arg residues), and N-terminally tagged with the chromophore AMCA. Three technical replicates were analyzed using a Thermo Velos Pro dual linear ion trap mass spectrometer coupled to a Coherent 351 nm excimer laser. Each precursor ion is isolated twice with the mass spectrometer switching between CID and UVPD activation modes to obtain a complementary MS/MS pair. We modified our UVnovo de novo sequencing software to automatically learn from and interpret fragmentation spectra from any combination of complementary activation methods, and we used this to analyze the CID/UVPD paired spectra. This performance exceeds that of PEAKS and PepNovo on the CID spectra alone and demonstrates that CID/UPVD brings significant advantages for comprehensive and accurate de novo peptide sequencing.

2017-03-06 | MSV000080603 | MassIVE

Light-induced orthogonal fragmentation of crosslinked peptides

Project description:Crosslinking mass spectrometry provides pivotal information on the structure and interaction of proteins. MS-cleavable crosslinkers are regarded as a cornerstone for the analysis of complex mixtures. Yet they fragment under similar conditions as peptides, leading to mixed fragmentation spectra of the crosslinker and peptide. This hampers selecting individual peptides for their independent identification. Here we introduce orthogonal cleavage, using ultraviolet photodissociation (UVPD) to increase crosslinker over peptide fragmentation. We designed and synthesized a crosslinker that can be cleaved at 213 nm in a commercial mass spectrometer configuration. In an analysis of crosslinked E. coli lysate, the crosslinker-to-peptide fragment intensity ratio increases from nearly 1 for a conventionally cleavable crosslinker to 5 for the UVPD cleavable crosslinker. This largely increased the sensitivity of selecting the individual peptides for MS3, even more so with an improved doublet detection algorithm.

2023-08-28 | PXD040267 | Pride

Evaluating the performance of 193 nm ultraviolet photodissociaiton (UVPD) for tandem mass tag (TMT) labeled peptides

Project description:We evaluated 193 nm UVPD for characterization of TMT labeled peptides (HeLa digest) and N-glycopeptides (alpha-1-acid glycoprotein digest) at different conditions, and compared the results with HCD. Samples were digested with trypsin and labeled with TMT6. Instrument data files were searched with either MS-GF+ (using PNNL's DMS processing pipeline) or with Byonic.

2020-08-31 | MSV000086049 | MassIVE

Unraveling O-Glycan Diversity of Mucins: Insights from SmE Mucinase and Ultraviolet Photodissociation Mass Spectrometry

Project description:Data, figures, and tables of O-glycopeptides of TIM-1, MUC-16, and MUC-1 digested with SmE mucinase and activated with ultraviolet photodissociation.

2024-04-15 | MSV000094544 | MassIVE