Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Proteome-wide identifying site non-specific cross-linking peptides with SpotLink

ABSTRACT: We developed SpotLink to identify site non-specific cross-links from the proteome scale. Here described the Abeta dataset and the HeLa dataset to evaluate SpotLink.

INSTRUMENT(S): Orbitrap Exploris 480, Q Exactive

ORGANISM(S): Homo Sapiens (human)

TISSUE(S): Cell Culture

SUBMITTER: weijie zhang

LAB HEAD: Lihua Zhang

PROVIDER: PXD030274 | Pride | 2022-08-25

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	Abeta40_fraction2_monomer_aggre.raw	Raw
	Abeta40_fraction2_monomer_aggre_HCDFT.mgf	Mgf
	Abeta40_fraction2_monomer_aggre_HCDFT_result.csv	Csv
	Abeta40_fraction2_monomer_aggre_Run2.raw	Raw
	Abeta40_fraction2_monomer_aggre_Run2_HCDFT.mgf	Mgf

Items per page:

1 - 5 of 71

Similar Datasets

Mapping protein interactions in the active TOM-TIM23 supercomplex

Project description:Nuclear-encoded mitochondrial proteins destined for the matrix have to be transported across two membranes. The TOM and TIM23 complexes facilitate the transport of precursor proteins with N-terminal targeting signals into the matrix. During transport, precursors are recognized by the TIM23 complex in the inner membrane for handover from the TOM complex. However, we have little knowledge on the organisation of the TOM-TIM23 transition zone and on how precursor transfer between the translocases occurs. Here, we designed a precursor protein that is stalled during matrix transport in a TOM-TIM23-spanning manner and enables purification of the translocation intermediate. Combining chemical cross-linking with mass spectrometric analyses and structural modelling allowed us to map the molecular environment of the intermembrane space interface of TOM and TIM23 as well as the import motor interactions with amino acid resolution. Our analyses provide a framework for understanding presequence handover and translocation during matrix protein transport.

2021-12-13 | PXD028002 | Pride

Cross-linking/mass spectrometry for the 13th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction (CASP13)

Project description:High-density cross-linking/mass spectrometry data was provided for four targets (T0957, T0968, T0975 and T0987) in the CASP13 experiment (https://www.predictioncenter.org/casp13/index.cgi).

2019-10-07 | PXD010884 | Pride

Non-covalently associated peptides are observed during liquid chromatography-mass spectrometry and affect cross-link analyses

Project description:Cross-Linking/mass spectrometry draws structural information out of covalently linked peptide pairs. When these links do not match to previous structural models they may indicate changes of protein conformation. Unfortunately, such links can also be the result of experimental errors or artefacts. Here we describe the observation of non-covalently associated peptides during liquid chromatography-mass spectrometry analysis which can easily be misidentified as cross-linked. Strikingly, they often mismatch to the protein structure or may falsely suggest protein homo-dimerization. Non-covalently associated peptides presumably form during ionization and can be distinguished from cross-linked peptides by observing co-elution of the corresponding linear peptides in MS1, as well as the presence of the individual peptide fragments in mixed MS2 spectra. Interestingly, non-covalently associated peptides seem sensitive to ionization source design as we see them more prevalently on a Q Exactive than on an Orbitrap Velos mass spectrometer. Finally we show how more disruptive ionization settings such as moderate in-source fragmentation suppresses their presence.

2019-01-25 | PXD010895 | Pride

A complimentary benzophenone cross-linking/mass spectrometry photochemistry

Project description:We introduce a complimentary, heterobifunctional, photoactivatable, benzophenone containing cross-linker and show its successful application to cross-linking/mass spectrometry, by increasing data density, when used alongside a previously developed diazirine-based heterobifunctional cross-linker.

2017-04-26 | PXD004920 | Pride

Blind testing cross-linking/mass spectrometry under the auspices of the 11th critical assessment of methods of protein structure prediction (CASP11)

Project description:We report the first blind test on the readiness of combining high-density cross-linking/mass spectrometry data in conjunction with ab initio structure prediction, through the help of Critical Assessment of protein Structure Prediction (CASP). This blind test was coordinated by the CASP organizers and utilized the experimental protocol developed in our lab for providing high-density cross-linking/mass spectrometry data in a matter of days. The CASP organizing committee identified and acquired suitable targets and published resulting data on the CASP web page for the community of structure predictors. We provided high-density cross-linking/mass spectrometry data for four targets in CASP11, revealing to us some of the current limitations of cross-linking. These are areas where the method must now develop. With CASP taking place biannually into the future, blind testing low-resolution structure analysis tools is a worthwhile and feasible undertaking.

2016-12-02 | PXD003643 | Pride

Structural basis for the assembly of Mis18a/b core modules

Project description:The centromere, defined by the enrichment of CENP-A (a Histone H3 variant) containing nucleosomes, is a specialised chromosomal locus that acts as a microtubule attachment site. To preserve centromere identity, CENP-A levels must be maintained through active CENP-A loading during the cell cycle. A central player mediating this process is the Mis18 complex (Mis18a, Mis18b and Mis18BP1), which recruits the CENP-A specific chaperone HJURP to centromeres for CENP-A deposition. Here, using a multi-pronged approach, we characterise the structure of the Mis18 complex and show that multiple hetero- and homo-oligomeric interfaces facilitate the hetero-octameric Mis18 complex assembly composed of 4 Mis18a, 2 Mis18b and 2 Mis18BP1. Evaluation of structure-guided/separation-of-function mutants reveals structural determinants essential for Mis18 complex assembly and centromere maintenance. Our results provide new mechanistic insights on centromere maintenance, highlighting that while Mis18a can associate with centromeres and deposit CENP-A independently of Mis18b, the latter is indispensable for the optimal level of CENP-A loading required for preserving the centromere identity.

2024-05-15 | PXD047345 | Pride

Protein Structure Determination in Biological Matrices by Mass Spectrometry and Computational Biology

Project description:We have implemented the use of a heterobifunctional, UV photoactivatable cross-linker, which greatly increases the number of identified cross-links compared with homobifunctional, NHS-ester based cross-linkers. We have cross-linked human serum albumin in the context of human blood serum. We present a novel methodology that combines the use of this high-resolution cross-linking with conformational space search to investigate the structure of proteins in their native environment.

2015-09-22 | PXD001692 | Pride

Different Oligomeric States of the Tumor Suppressor p53 Show Identical Binding Behavior Towards the S100β Homodimer

Project description:The tumor suppressor protein p53 is a transcription factor that is referred to as the “guardian of the genome” and plays an important role in cancer development. P53 is active as a tetramer; the S100β homodimer binds to the intrinsically disordered C-terminus of p53, affecting its transcriptional activity. The p53/S100β complex is regarded as highly promising therapeutic target in cancer. It has been suggested that S100β exerts its oncogenic effects by altering the p53 oligomeric state. Our aim was to study the structures and oligomerization behavior of different p53/S100β complexes by electrospray ionization mass spectrometry (ESI-MS), cross-linking mass spectrometry (XL-MS), and surface plasmon resonance (SPR). For this, wild-type p53 and single amino acid variants, representing different oligomeric states of p53 (tetrameric wild-type, dimeric L344A variant, and monomeric L344P variant) were individually investigated regarding their binding behavior towards S100β. The stoichiometry of the different p53/S100β complexes were determined by ESI-MS showing that tetrameric, dimeric, and monomeric p53 variants all bind to an S100β dimer. In addition, XL-MS revealed the topologies of the p53/S100β complexes to be independent of p53’s oligomeric state. With SPR, the thermodynamic parameters were determined for S100β binding to tetrameric, dimeric or monomeric p53 variants. Our data prove that the S100β homodimer binds to different oligomeric states of p53 with identical stoichiometries and similar binding affinities. This emphasizes the need for alternative explanations to describe the molecular mechanisms underlying p53/S100β interaction.

2022-10-14 | PXD029914 | Pride

Proteome-wide cross-linking mass spectrometry of human K562 cells

Project description:Proteome-wide cross-linking mass spectrometry was performed on human K562 cell lysates. MS2-MS3 fragmentation strategy was used to aquire the XL-MS data. The raw files in this dataset are a subset of PXD013928.

2020-07-01 | PXD018771 | 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