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Related Experiment Video

Updated: Nov 9, 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

MS Annika: A New Cross-Linking Search Engine.

Georg J Pirklbauer¹, Christian E Stieger^2,3, Manuel Matzinger²

¹University of Applied Sciences Upper Austria, Bioinformatics Research Group, Softwarepark 11, 4232 Hagenberg, Austria.

Journal of Proteome Research

|April 14, 2021

Summary

MS Annika is a new search engine for cross-linking mass spectrometry (XL-MS) data. It accurately identifies cross-linked peptides and provides reliable false discovery rate (FDR) estimates, improving proteome-wide studies.

Keywords:

MS/MS PPI XL-MS bioinformatics cross-linking protein-protein-interaction search engine tandem mass spectrometry

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Published on: December 17, 2013

Area of Science:

Biochemistry
Proteomics
Structural Biology

Background:

Cross-linking mass spectrometry (XL-MS) is vital for understanding protein structure and interactions.
Cleavable cross-linkers have advanced XL-MS, enabling proteome-wide studies by reducing search space.
Existing XL-MS search engines face challenges with novel cross-linkers and accurate false discovery rate (FDR) estimation.

Purpose of the Study:

To introduce MS Annika, a novel search engine for identifying cross-linked peptides.
To address limitations in handling diverse cleavable cross-linkers and validating XL-MS data.
To improve the accuracy and efficiency of proteome-wide XL-MS studies.

Main Methods:

Development of a new search engine, MS Annika, for processing MS2 spectra.
MS Annika is designed to handle a wide variety of cleavable cross-linkers.
Implementation of robust FDR estimation without arbitrary score cutoffs.

Main Results:

MS Annika successfully identifies cross-linked peptides across various cleavable cross-linkers.
The tool provides realistic FDR estimates, enhancing data reliability.
MS Annika achieves an average of 44% more identifications than comparable tools at similar or better true FDRs.
Fast, parallelized processing enables application in proteome-wide studies.
Visualization of identified cross-links in protein 3D structures is supported.

Conclusions:

MS Annika offers a significant advancement in XL-MS data analysis.
The search engine improves the identification and validation of cross-linked peptides.
MS Annika facilitates more comprehensive and accurate proteome-wide structural and interaction studies.