Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

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

ABSTRACT: 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.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Escherichia Coli K-12 (ncbitaxon:83333)

SUBMITTER: Jared B. Shaw

PROVIDER: MSV000086049 | MassIVE | Mon Aug 31 22:55:00 BST 2020

REPOSITORIES: MassIVE

ACCESS DATA

Json Xml

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

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

Project description: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).

2019-06-13 | MSV000083972 | MassIVE

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

Thorough Performance Evaluation of 213 nm Ultraviolet Photodissociation for Top-down Proteomics.

Project description: Not available

| S-EPMC7000117 | biostudies-literature

mTRAQ labeled natural proteome from HeLa

Project description:To identify proteotypic peptides, HeLa cells digest labeled with mTRAQdelta0 were extensively fractionated and analyzed by LC-MS/MS.

2016-12-07 | PXD001396 | Pride

BrU-labeled nascent RNA sequencing and m6A-IP from BrU-labeled nascent RNA

Project description:BrU-labeled nascent RNA sequencing and m6A-IP from BrU-labeled nascent RNA

| PRJNA326350 | ENA

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

Extracellular vesicle labeled Granulocyte macrophage progenitors

Project description:Extracellular vesicle labeled Granulocyte macrophage progenitors

| PRJNA525660 | ENA

4sU metabolic labeled transcripts in mESCs

Project description:4sU metabolic labeled transcripts in mESCs

| PRJNA438673 | ENA

Ultraviolet Photodissociation of Tryptic Peptide Backbones at 213 nm.

Project description: Not available

| S-EPMC7273743 | biostudies-literature