Existing bioinformatics tools for the quantitation of post-translational modifications

Area of Science:

• Proteomics
• Mass Spectrometry
• Post-Translational Modification Analysis

Background:

• Mass spectrometry (MS)-based proteomics is complex, with quantitation, especially of post-translational modifications (PTMs), posing significant challenges.
• The vast data output from MS necessitates specialized software for practical data interpretation.
• Various quantitation strategies exist, with potential adaptation for differential PTM expression analysis.

Purpose of the Study:

• To review currently available free software for the quantitation of PTMs in mass spectrometry-based proteomics.
• To focus on liquid chromatography coupled with mass spectrometry (LC-MS) techniques for PTM quantitation.
• To highlight the capabilities in PTM quantitation, with an emphasis on phosphoproteomics.

Main Methods:

• Review of free software tools applicable to PTM quantitation.
• Focus on liquid chromatography followed by one or more stages of mass spectrometry (LC-MS/MS).
• Analysis of selected studies, particularly in phosphoproteomics, to demonstrate quantitation abilities.

Main Results:

• Identification and brief review of free software suitable for PTM quantitation.
• Demonstration of current capabilities in quantifying PTMs using LC-MS/MS approaches.
• Highlighting the utility of these tools in specific applications like phosphoproteomics.

Conclusions:

• Specialized software is crucial for the practical quantitation of PTMs in large-scale MS-based proteomics datasets.
• Free software tools offer viable solutions for analyzing differential PTM expression.
• The field, particularly phosphoproteomics, shows significant progress in PTM quantitation capabilities.