Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks

ABSTRACT: Here, we present a novel trioxane-based MS-cleavable homotrifunctional cross-linker TSTO, which can target three proximal lysine residues simultaneously. Owing to its unique structure and MS-cleavability, TSTO enables fast and unambiguous identification of cross-linked peptides using LC-MSn analysis. Importantly, we have demonstrated that the TSTO-based XL-MS platform is effective for mapping PPIs of protein complexes and cellular networks.

INSTRUMENT(S): Orbitrap Fusion Lumos

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Clinton Yu

LAB HEAD: Lan Huang

PROVIDER: PXD054551 | Pride | 2025-05-30

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Compiled_InVivo.xlsx	Xlsx
	Compiled_Rpn1.xlsx	Xlsx
	OrbitrapLUMOS_20181016_01_UCI_01.raw	Raw
	OrbitrapLUMOS_20181016_02_UCI_02.raw	Raw
	OrbitrapLUMOS_20181017_05_UCI_03.raw	Raw

Items per page:

1 - 5 of 137

Similar Datasets

Trioxane-based MS-cleavable Cross-linking Mass Spectrometry for Profiling Multimeric Interactions of Cellular Networks

Project description:Here, we present a novel trioxane-based MS-cleavable homotrifunctional cross-linker TSTO, which can target three proximal lysine residues simultaneously. Owing to its unique structure and MS-cleavability, TSTO enables fast and unambiguous identification of cross-linked peptides using LC-MSn analysis. Importantly, we have demonstrated that the TSTO-based XL-MS platform is effective for mapping PPIs of protein complexes and cellular networks.

2025-05-30 | PXD063825 | Pride

Enabling Photoactivated Cross-linking Mass Spectrometric Analysis of Protein Complexes by Novel MS-cleavable Cross-linkers

Project description:Cross-linking mass spectrometry (XL-MS) is a powerful tool for studying protein-protein interactions and elucidating architectures of protein complexes. While residue-specific XL-MS studies have been very successful, accessibility of interaction regions non-targetable by specific chemistries remain difficult. Photochemistry has shown great potential in capturing those regions due to nonspecific reactivity, but low yields and high complexities of photocross-linked products have hindered their identification, limiting current studies predominantly to single proteins. Here, we describe the development of three novel MS-cleavable heterobifunctional cross-linkers, namely SDASO (Succinimidyl diazirine sulfoxide), to enable fast and accurate identification of photocross-linked peptides by MSn. The MSn-based workflow allowed SDASO XL-MS analysis of the yeast 26S proteasome, demonstrating the feasibility of photocross-linking of large protein complexes for the first time. Comparative analyses have revealed that SDASO cross-linking is robust and captures interactions complementary to residue-specific reagents, providing the foundation for future applications of photocross-linking in complex XL-MS studies.

2021-05-07 | PXD022690 | Pride

Developing In Vivo Cross-linking Mass Spectrometry (XL-MS) to Decipher Protein Interaction Landscapes at the Proteome Scale

Project description:We have developed a new and robust in vivo cross-linking mass spectrometry (XL-MS) that utilizes a multifunctional MS-cleavable cross-linker to enable the efficient capture, enrichment, and identification of in vivo cross-linked peptides at the whole proteome scale.

2021-07-30 | PXD012788 | Pride

Integrative Structural Characterization of the Human Canonical and Non-canonical Cop9 Signalosome Complexes

Project description:The COP9 signalosome (CSN) is an evolutionarily conserved protein complex that functions as a deneddylase to inactivate Cullin-RING E3 ligases for controlling protein ubiquitination. CSN possesses structural flexibility that is important for its activation upon binding to a diverse array of CRLs. The canonical and non-canonical CSN complexes consist of 8 (CSN1-8) and 9 (CSN1-9) subunits, respectively. Although CSN9 is not essential for CSN assembly and function, it appears to be important in non-catalytic regulation of CRLs by CSN. Here we employed a combinatory cross-linking mass spectrometry (XL-MS) approach to generate the largest PPI maps of human CSN complexes, which significantly enhanced the precision of integrative structural modeling. The resulting integrative structures allowed us not only to elucidate architectures of both complexes, but also to assess CSN structural dynamics that was not described in the crystal structure. In addition, we have determined CSN9 docking sites and its impact on the CSN structure. While CSN9 binding did not induce global conformational changes, it triggered subunit local reorientations that may be associated with CSN9 involvement in CSN-mediated steric regulation of CRLs.

2020-02-04 | PXD014673 | Pride

Kinetic principles of chemical cross-link formation for protein-protein interactions

Project description:Proteins play a central role in most biological processes within the cell and deciphering how they interact is key to understand their function. Cross-linking coupled to mass spectrometry is an essential tool for elucidating protein-protein interactions. Despite its importance, we still know surprisingly little about the principles that underlie the process of chemical cross-link formation itself and how it is influenced by different physicochemical factors. To understand the molecular details of cross-link formation, we have set-up a comprehensive kinetic model and carried out simulations of protein cross-linking on large protein complexes. We dissect the contribution on the cross-link yield of parameters such as amino acid reactivity, cross-linker concentration, and hydrolysis rate. Our model can compute cross-link formation based solely on the structure of a protein complex, thereby enabling realistic predictions for a diverse set of systems. We quantitatively show how cross-links and mono-links are in direct competition and how the hydrolysis rate and abundance of cross-linker and proteins directly influence their relative formation. We show how cross-links and mono-links exist in a “all-against-all” competition due to their simultaneous formation, resulting in a non-intuitive network of interdependence. We show that this interdependence is locally confined and mainly limited to direct neighbors or residues in direct vicinity. These results enable us to identify the optimal cross-linker concentration at which the maximal number of cross-links are formed. Taken together, our study establishes a comprehensive kinetic model to quantitatively describe cross-link formation for protein-protein interactions.

2024-10-10 | PXD053500 | Pride

Digestion of a variety of synthetic peptides by proteasomes

Project description:Proteasomes are large multi-subunit enzymes that act as the main producers of antigenic peptides presented at the cell surface to CD8+ T cells. They can simply cut proteins or recombine their fragments thereby generating novel sequences, i.e. spliced peptides via a process called proteasome-catalysed peptide splicing (PCPS). In order to gain more insight into these processes, we here perform in vitro digestions of 55 synthetic polypeptide substrates by proteasome isoforms followed by LC-MS/MS measurements using different Mass Spectrometers.

2020-04-14 | PXD016782 | Pride

Defining the cellular proteolytic landscape

Project description:Mass spectrometry analysis of cellular targets of protein degradation

2018-10-16 | PXD009092 | Pride

Defining the cellular proteolytic landscape cross time points

Project description:Mass spectrometry analysis of cellular targets of protein degradation

2018-10-11 | PXD007263 | Pride

Defining the cellular proteolytic landscape in systemic lupus erythematosus – nonspecific digest

Project description:Mass spectrometry analysis of cellular targets of protein degradation

2018-10-11 | PXD009438 | Pride

An integrated workflow for cross-linking/mass spectrometry

Project description:We present a concise workflow to enhance the mass spectrometric detection of cross-linked peptides by introducing sequential digestion and the database search software Xi. We use sequential digestion to reduce the peptide size and increase identification rates. The methodology is independent of samples complexity, cross-linker choice, method acquisition and can be used with multiple digestion steps.

2019-08-27 | PXD008550 | Pride