Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Crosslinking Mass Spectrometry

ABSTRACT: Crosslinking mass spectrometry collected on Lumos Orbitrap elite with HCD and UVPD. BS3 and DMTMM were used for crosslinking separately.

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Jennifer Brodbelt

PROVIDER: PXD008935 | JPOST Repository | Wed Feb 13 00:00:00 GMT 2019

REPOSITORIES: jPOST

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	03022017_BSA_DMTMM_tryp_1_UVPD.raw	Raw
	03022017_BSA_DMTMM_tryp_2_UVPD.raw	Raw
	03022017_BSA_DMTMM_tryp_3_UVPD.raw	Raw
	03062017_BSA_DMTMM_tryp_1_HCD.raw	Raw
	03062017_BSA_DMTMM_tryp_2_HCD.raw	Raw

Items per page:

1 - 5 of 20

Similar Datasets

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

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

NALCN crosslinking experiments by BS3 crosslinker

Project description:We used BS3 as the crosslinker to identify the crosslinking sites between NALCN and other interacted proteins.

2020-12-04 | PXD022119 | Pride

Breaking Barriers in Crosslinking Mass Spectrometry: Enhanced Throughput and Sensitivity with the Orbitrap Astral Mass Analyzer

Project description:Crosslinking mass spectrometry (XL-MS) has become a key technique for investigating protein-protein interactions and the architecture of biological systems. This study compares the Orbitrap Astral and Eclipse mass spectrometers in XL-MS workflows, emphasizing their performance in detecting low-abundance crosslinked peptides. Using Cas9 crosslinked with PhoX and DSSO, the Astral demonstrated over 40% higher crosslink identifications due to its superior ion transmission and sensitivity, enabled by its multi-reflection time-of-flight analyzer. Single higher-energy collisional dissociation (HCD) fragmentation was more effective than stepped HCD on the Astral, while the Eclipse showed similar results for both methods. Gradient optimization revealed that extended separation times improved crosslink identifications. These findings highlight the critical role of instrumentation and workflow optimization in advancing XL-MS for structural proteomics.

2025-12-15 | PXD059096 | Pride

Crosslinking RNF168(1-113) to Nucleosome core particels

Project description:The project aimed to identify interaction sites of RNF168 with the Nucleosomes. RNF168 interaction with the Nucleosome was probed by BS3 crosslinking to support structure modeling based on NMR and mutagenesis experiments

2019-04-02 | PXD012723 | Pride

Crosslinking experiment of the RAGE-S100B complex

Project description:XL-MS of RAGE-100B complex. The Crosslinking agent is BS3. Samples were subjected to sequential digestion. 91212_AM_2_2_1_HCDFT, 91212_AM_2_2_2_HCDFT, 91212_AM_5_2_2_HCDFT, 91212_AM_5_2_2_HCDFT - Tryp-Chym; 91212_AM_2_3_1_HCDFT, 91212_AM_2_3_2_HCDFT, 91212_AM_5_3_2_HCDFT, 91212_AM_5_3_2_HCDFT - Tryp-Gluc; 91212_AM_2_1_1_HCDFT, 91212_AM_2_1_2_HCDFT, 91212_AM_5_1_2_HCDFT, 91212_AM_5_1_2_HCDFT - Tryp-Tryp.

2020-11-11 | MSV000086437 | MassIVE

Crosslinking experiment of the RAGE oligomeric complexes

Project description:XL-MS of RAGE oligomeric complexes. The Crosslinking agent is BS3. Samples were subjected to sequential digestion. 91212_AM_1_3_1_HCDFT, 91212_AM_1_3_2_HCDFT, 91212_AM_4_3_1_HCDFT, 91212_AM_4_3_2_HCDFT - Tryp-Gluc; 91212_AM_1_2_1_HCDFT, 91212_AM_1_2_2_HCDFT, 91212_AM_4_2_1_HCDFT, 91212_AM_4_2_2_HCDFT - Tryp-Chym; 91212_AM_1_1_1_HCDFT, 91212_AM_1_1_2_HCDFT, 91212_AM_4_1_1_HCDFT, 91212_AM_4_1_2_HCDFT - Tryp-Tryp.

2020-11-11 | MSV000086438 | MassIVE

An optimised fragmentation regime for cross-linking/mass spectrometry

Project description:In this study we compared three different fragmentation techniques and two combined fragmentation schemes available on a novel tribrid mass spectrometer (Orbitrap Fusion Lumos, Themro Fisher Scientific) CID, HCD, ETD, ETD with supplemental CID (ETciD) and ETD with supplemental HCD (EThcD) on cross-linked peptides obtained by tryptic cleavage of SDA-cross-linked Human Serum Albumin (HSA). The three-dimensional structure of HSA has been resolved by X-ray crystallography [35] and is used as ground-truth to evaluate the identification results. Right choice of the fragmentation method allows increasing the number of identified linkage sites, increasing the sequence coverage of both linked peptides thereby reducing the second peptide problem, and increasing the precision of cross-link site calling.

2016-08-02 | PXD003737 | Pride

Extensive backbone cleavage coverage of intact proteoforms in a mass range of 10-70 kDa by integrating electron, collision, and photon-based fragmentation techniques during an electrophoretic timescale

Project description:Capillary zone electrophoresis (CZE) –-tandem mass spectrometry (MS/MS) has been documented as a useful tool for top-down proteomics (TDP). However, CZE-MS/MS-based TDP typically has limited backbone cleavage coverage for identified proteoforms due to the use of traditional collision-based fragmentation methods (i.e., higher-energy collisional dissociation, HCD). Here, for the first time, we coupled CZE to a high-end Orbitrap Ascend mass spectrometer to investigate the performance of collision, electron, and photon-based fragmentation methods and their combinations for boosting the backbone cleavage coverage of proteoforms during the electrophoretic timescale using a standard protein mixture covering a mass range of about 10-70 kDa. CZE-MS achieved reproducible measurement of six proteins, including three insulin-like growth factor (IGF) proteoforms with different modifications. Systematic investigations of HCD, electron-transfer dissociation (ETD), electron-transfer/HCD (EThcD), and ultraviolet photodissociation (UVPD) during CZE-MS/MS analysis revealed distinct yet complementary fragmentation characteristics. ETD, EThcD, and UVPD, in general, provided higher backbone cleavage coverage than HCD. The integration of HCD, ETD, EThcD, and UVPD data offered a 74% and 98% sequence coverage for carbonic anhydrase (a 30-kDa protein) and thioredoxin (a 12-kDa protein), which is 185% and 100% higher than that produced by HCD alone. Adding internal fragments further boosted the backbone cleavage coverage substantially, for example, from 74% to 94% for 30-kDa carbonic anhydrase, and from 35% to 94% for 50-kDa Protein AG. The results demonstrate the capability of CZE-MS/MS with the integration of various fragmentation techniques for comprehensive characterization of proteoforms in a wide mass range.

2026-02-16 | PXD070486 | Pride

Activation of Histone 3 Lysine 9 methyl writing and reading capabilities within the G9a-GLP heterodimer

Project description:BS3 Crosslinking experiments were performed on in vitro preparations of histone methyltransferase dimers. Each sample was fractionated into two size-exclusion chromatography fractions that were acquired by alternating HCD/EThcD scans of the same precursor on a Fusion-Lumos instrument. File mappings: GLP homodimer, SEC1: Z20210712-08 GLP homodimer, SEC2: Z20210712-09 G9a homodimer, SEC1: Z20210712-10 GLP homodimer, SEC2: Z20210712-11 G9aGLP heterodimer, SEC1: Z20210712-12 G9aGLP heterodimer, SEC2: Z20210712-13

2021-09-22 | MSV000088143 | 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