Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

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

INSTRUMENT(S): Orbitrap Fusion Lumos UVPD

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Jennifer Brodbelt

PROVIDER: MSV000080432 | MassIVE | Tue Dec 20 07:02:00 GMT 2016

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
		Other

Items per page:

1 - 1 of 1

Similar Datasets

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

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

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

Characterization of HLA-A*02:01 MHC Immunopeptide Antigens Enhanced by Ultraviolet Photodissociation Mass Spectrometry

Project description:Triplicate results for 193 nm UVPD, HCD, and EThcD of a mixture of 157 synthetic peptide mixture, and 193 nm UVPD, HCD, and EThcD of BB7.2 and W6/32 immunoprecipitations

2021-08-13 | PXD027830 | JPOST Repository

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

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

2023-07-01 | PXD041493 | JPOST Repository

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

Leveraging complementary ion activation methods with proton transfer charge reduction reactions for comprehensive characterization of monoclonal antibody heavy chain subunits

Project description:The use of LC-MS, 193 nm UVPD, EThcD, gas-phase fractionation, and PTCR to characterize mAbs and ADCs.

2025-03-13 | PXD060606 | JPOST Repository

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.

2019-01-24 | PXD011526 | Pride

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