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Updated: Jun 18, 2025

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Combining Chemical Cross-linking and Mass Spectrometry of Intact Protein Complexes to Study the Architecture of Multi-subunit Protein Assemblies

Published on: November 28, 2017

Rescuing error control in crosslinking mass spectrometry.

Lutz Fischer¹, Juri Rappsilber^2,3,4

¹Technische Universität Berlin, Chair of Bioanalytics, 10623, Berlin, Germany.

Molecular Systems Biology

|August 2, 2024

Summary

This summary is machine-generated.

Crosslinking mass spectrometry (CMS) can misidentify protein-protein interactions by biasing search results. Refining data analysis is crucial for accurate error estimation and reliable interaction identification in complex biological samples.

Keywords:

Crosslinking Mass Spectrometry Data Analysis Data Reliability Error Estimation Proteomics

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Published on: October 20, 2021

Area of Science:

Biochemistry
Proteomics
Bioinformatics

Background:

Crosslinking mass spectrometry (CMS) is vital for studying protein-protein interactions (PPIs) in complex biological systems.
Accurate error estimation is essential for reliable PPI identification using CMS.

Purpose of the Study:

To investigate how biased search controls in CMS data analysis can affect error estimation.
To demonstrate the impact of biased results on identifying interspecies PPIs.
To develop methods for refining data analysis to ensure the integrity of PPI identification.

Main Methods:

Utilized novel search controls in CMS data analysis.
Performed synthetic mixing experiments with data from different species.
Assessed the decoy-false positive relationship in CMS data analysis.

Main Results:

Biasing search controls towards likely correct proteins subtly undermines error estimation of crosslinks.
An average of 260 interspecies PPIs were misidentified across 16 analyses due to biased results.
Demonstrated that data analysis procedures can be tested and refined to restore the integrity of the decoy-false positive relationship.

Conclusions:

Biased search controls in CMS can lead to significant misidentification of PPIs, particularly interspecies interactions.
Refined data analysis strategies are necessary to ensure the reliability of CMS for PPI studies.
Restoring the integrity of the decoy-false positive relationship is critical for accurate PPI discovery.