Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Impact of internal fragments on top-down analysis of intact proteins by 193 nm UVPD

ABSTRACT: Project contain UVPD and HCD spectra collected for the study at various charge states. Spectra without and without PTCR are included as well

ORGANISM(S): Oryctolagus Cuniculus Equus Caballus Saccharomyces Cerevisiae (baker's Yeast) Bos Taurus

SUBMITTER: Jennifer Brodbelt

PROVIDER: PXD037298 | JPOST Repository | Fri Dec 09 00:00:00 GMT 2022

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	5uMMyo15+HCD20NCE1e5AGC.raw	Raw
	5uMMyo15+HCD20NCE1e5AGC_2.raw	Raw
	5uMMyo15+HCD20NCE1e5AGC_3.raw	Raw
	5uMMyo20+HCD20NCE1e5AGC.raw	Raw
	5uMMyo20+HCD20NCE1e5AGC_2.raw	Raw

Items per page:

1 - 5 of 20

Similar Datasets

Online Weak Cation Exchange-HILIC × Reversed Phase LC UVPD-HRMS of intact HeLa Histones

Project description:Intact HeLa core Histones were analyzed using an online two-dimensional liquid chromatographic separation as well as one dimensional LC (RPLC and WCX-HILIC) coupled with UVPD-MS

2018-09-19 | PXD008978 | Pride

Histone Middle Down UVPD

Project description:Middle Down UVPD MS of purified HeLa Histones analyzed using 193 nm Ultra violet photo dissocaiton on a Thermo Fisher Scientific Orbitrap Fusion Lumos

2019-05-03 | PXD009653 | JPOST Repository

Expanding the mass range for UVPD-based native top-down mass spectrometry.

Project description:Native top-down mass spectrometry is emerging as a methodology that can be used to structurally investigate protein assemblies. To extend the possibilities of native top-down mass spectrometry to larger and more heterogeneous biomolecular assemblies, advances in both the mass analyzer and applied fragmentation techniques are still essential. Here, we explore ultraviolet photodissociation (UVPD) of protein assemblies on an Orbitrap with extended mass range, expanding its usage to large and heterogeneous macromolecular complexes, reaching masses above 1 million Da. We demonstrate that UVPD can lead not only to the ejection of intact subunits directly from such large intact complexes, but also to backbone fragmentation of these subunits, providing enough sequence information for subunit identification. The Orbitrap mass analyzer enables simultaneous monitoring of the precursor, the subunits, and the subunit fragments formed upon UVPD activation. While only partial sequence coverage of the subunits is observed, the UVPD data yields information about the localization of chromophores covalently attached to the subunits of the light harvesting complex B-phycoerythrin, extensive backbone fragmentation in a subunit of a CRISPR-Cas Csy (type I-F Cascade) complex, and sequence modifications in a virus-like proteinaceous nano-container. Through these multiple applications we demonstrate for the first time that UVPD based native top-down mass spectrometry is feasible for large and heterogeneous particles, including ribonucleoprotein complexes and MDa virus-like particles.

| S-EPMC6764275 | biostudies-literature

High-throughput analysis of intact human proteins using UVPD and HCD on a Fusion Lumos mass spectrometer

Project description:High-throughput top down analysis of HeLa cell lysates using 193 nm UVPD and HCD on a Orbitrap Fusion Lumos mass spectrometer.

2016-12-20 | MSV000080432 | MassIVE

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

High-Throughput Analysis of Intact Human Proteins Using UVPD and HCD on an Orbitrap Mass Spectrometer.

Project description:The analysis of intact proteins (top-down strategy) by mass spectrometry has great potential to elucidate proteoform variation, including patterns of post-translational modifications (PTMs), which may not be discernible by analysis of peptides alone (bottom-up approach). To maximize sequence coverage and localization of PTMs, various fragmentation modes have been developed to produce fragment ions from deep within intact proteins. Ultraviolet photodissociation (UVPD) has recently been shown to produce high sequence coverage and PTM retention on a variety of proteins, with increasing evidence of efficacy on a chromatographic time scale. However, utilization of UVPD for high-throughput top-down analysis to date has been limited by bioinformatics. Here we detected 153 proteins and 489 proteoforms using UVPD and 271 proteins and 982 proteoforms using higher energy collisional dissociation (HCD) in a comparative analysis of HeLa whole-cell lysate by qualitative top-down proteomics. Of the total detected proteoforms, 286 overlapped between the UVPD and HCD data sets, with 68% of proteoforms having C scores greater than 40 for UVPD and 63% for HCD. The average sequence coverage (28 ± 20% for UVPD versus 17 ± 8% for HCD, p < 0.0001) was found to be higher for UVPD than HCD and with a trend toward improvement in q value for the UVPD data set. This study demonstrates the complementarity of UVPD and HCD for more extensive protein profiling and proteoform characterization.

| S-EPMC5549616 | biostudies-literature

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

Increasing the Separation Capacity of Intact Histone Proteoforms Chromatography Coupling Online Weak Cation Exchange-HILIC to Reversed Phase LC UVPD-HRMS.

Project description:Top-down proteomics is an emerging analytical strategy to characterize combinatorial protein post-translational modifications (PTMs). However, sample complexity and small mass differences between chemically closely related proteoforms often limit the resolution attainable by separations employing a single liquid chromatographic (LC) principle. In particular, for ultramodified proteins like histones, extensive and time-consuming fractionation is needed to achieve deep proteoform coverage. Herein, we present the first online nanoflow comprehensive two-dimensional liquid chromatography (nLC×LC) platform top-down mass spectrometry analysis of histone proteoforms. The described two-dimensional LC system combines weak cation exchange chromatography under hydrophilic interaction LC conditions (i.e., charge- and hydrophilicity-based separation) with reversed phase liquid chromatography (i.e., hydrophobicity-based separation). The two independent chemical selectivities were run at nanoflows (300 nL/min) and coupled online with high-resolution mass spectrometry employing ultraviolet photodissociation (UVPD-HRMS). The nLC×LC workflow increased the number of intact protein masses observable relative to one-dimensional approaches and allowed characterization of hundreds of proteoforms starting from limited sample quantities (?1.5 ?g).

| S-EPMC6220366 | biostudies-literature

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.

2023-11-20 | MSV000093440 | MassIVE

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data