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Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Navigating the Mass Spectrometry-Based Proteomic Data Using Free Computational Tools

Published on: August 19, 2025

Unrestricted identification of modified proteins using MS/MS.

Erik Ahrné¹, Markus Müller, Frederique Lisacek

¹Swiss Institute of Bioinformatics, Proteome Informatics Group, Geneva, Switzerland. Erik.Ahrne@isb-sib.ch

|December 24, 2009

Summary

Discovering protein modifications is crucial for understanding cellular functions. New bioinformatics tools enable unrestricted identification of post-translational modifications (PTMs) in mass spectrometry data, advancing proteome dynamics research.

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Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Detection of Protein Ubiquitination Sites by Peptide Enrichment and Mass Spectrometry

Published on: March 23, 2020

Area of Science:

Proteomics
Bioinformatics
Molecular Biology

Background:

Post-translational modifications (PTMs) are critical for protein structure and function, yet many remain undiscovered.
Mass spectrometry (MS)-based shotgun proteomics is a high-throughput method for analyzing protein mixtures.
Current MS/MS data analysis tools identify limited predefined PTMs, leaving many spectra unidentified.

Purpose of the Study:

To review software solutions for unrestricted identification of PTMs in MS/MS data, termed open modification search tools.
To provide an overview of algorithmic approaches for evaluating candidate peptides with unrestricted modifications.
To demonstrate the value of large-scale open modification search studies in PTM discovery.

Main Methods:

Focus on bioinformatics software for open modification (OM) searching in MS/MS data.
Evaluation of conceptually different algorithmic solutions for handling unrestricted modification searches.
Analysis of results from large-scale OM search studies.

Main Results:

Identified a significant portion of previously unidentified spectra likely correspond to peptides with unknown PTMs.
Demonstrated the effectiveness of open modification search tools in discovering a wider range of PTMs.
Highlighted the value of OM search studies for comprehensive proteome analysis.

Conclusions:

Open modification search tools are essential for advancing the discovery of protein modifications.
Efficient and user-friendly tools are needed to map the dynamics of proteomes through PTM identification.
This approach significantly expands our understanding of the proteome beyond currently known modifications.