Proteomics

Dataset Information

0

Quantitative cross-linking/mass spectrometry reveals subtle protein conformational changes

ABSTRACT: We have developed quantitative cross-linking/mass spectrometry (QCLMS) to interrogate conformational rearrangements of proteins in solution. Our workflow was tested using a structurally well-described reference system, the human complement protein C3 and its activated cleavage product C3b. We found that small local conformational changes affect the yields of cross-linking residues that are near in space while larger conformational changes affect the detectability of cross-links. Distinguishing between minor and major changes required robust analysis based on replica analysis and a label-swapping procedure. By providing workflow, code of practice and a framework for semi-automated data processing, we lay the foundation for QCLMS as a tool to monitor the domain choreography that drives binary switching in many protein-protein interaction networks.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Homo Sapiens (human)

SUBMITTER: Zhuo Chen  

LAB HEAD: Juri Rappsilber

PROVIDER: PXD001675 | Pride | 2016-06-16

REPOSITORIES: Pride

Json Xml

Dataset's files

Source:
Action DRS
Chen_Rappsilber_QCLMS_xC3-C3b_PeakList.zip Other
Chen_Rappsilber_QCLMS_xC3-C3b_SearchResults.csv Csv
Chen_Rappsilber_QCLMS_xC3d0C3bd4_I.raw Raw
Chen_Rappsilber_QCLMS_xC3d0C3bd4_II.raw Raw
Chen_Rappsilber_QCLMS_xC3d0C3bd4_III.raw Raw
Items per page:
1 - 5 of 8
altmetric image

Publications

Quantitative Cross-linking/Mass Spectrometry Using Isotope-labeled Cross-linkers and MaxQuant.

Chen Zhuo A ZA   Fischer Lutz L   Cox Jürgen J   Rappsilber Juri J  

Molecular & cellular proteomics : MCP 20160614 8

The conceptually simple step from cross-linking/mass spectrometry (CLMS) to quantitative cross-linking/mass spectrometry (QCLMS) is compounded by technical challenges. Currently, quantitative proteomics software is tightly integrated with the protein identification workflow. This prevents automatically quantifying other m/z features in a targeted manner including those associated with cross-linked peptides. Here we present a new release of MaxQuant that permits starting the quantification proces  ...[more]

Similar Datasets

Proteomics Quantitative cross-linking/mass spectrometry analysis revealed unknown structure of complement iC3
2016-06-17 | PXD003486 | Pride
Proteomics On the reproducibility of label-free quantitative cross-linking/mass spectrometry
2018-01-02 | PXD007250 | Pride
Proteomics A model dataset for quantitative cross-linking/mass spectrometry using isotope-labeled cross-linkers
2016-05-06 | PXD004107 | Pride
Proteomics Data independent acquisition cross-linking/mass spectrometry
2019-01-25 | PXD011036 | Pride
Proteomics Quantitative cross-linking/mass spectrometry
2015-06-08 | PXD002142 | Pride
Proteomics Cross-linking mass spectrometry of yeast mitochondria grown on different carbon sources reveal Ndi1, Min8 and Pet9 associated with the electron transport chain
2020-04-27 | PXD017620 | Pride
Proteomics XL-MS and Native MS for CSN-CRL2 complexes
2019-09-13 | PXD013018 | Pride
Proteomics Structure of transcribing RNA polymerase II-Elongin complex
2023-10-11 | PXD045446 | Pride
Proteomics An integrated workflow for cross-linking/mass spectrometry
2019-08-27 | PXD008550 | Pride
Proteomics A folded conformation of MukBEF and Cohesin
2019-03-01 | PXD012377 | Pride