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Updated: Oct 10, 2025
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An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
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Accurate Prediction of Protein Sequences for Proteogenomics Data Integration
Yanick Paco Hagemeijer1,2, Victor Guryev2, Peter Horvatovich3
1Department of Analytical Biochemistry, University of Groningen, Groningen Research Institute of Pharmacy, Groningen, The Netherlands.
Methods in Molecular Biology (Clifton, N.J.)
|December 14, 2021
Summary
This chapter explores proteogenomics, integrating genomic and transcriptomic data to understand protein variations. It details how genome variability and sequencing technologies impact proteome analysis, aiding accurate protein identification.
Area of Science:
- Proteogenomics
- Genomics
- Transcriptomics
- Mass Spectrometry
Background:
- The proteome, an organism's complete protein set, is influenced by genomic variations.
- Understanding these variations is crucial for accurate protein identification and functional studies.
Purpose of the Study:
- To provide an overview of proteogenomics data integration.
- To discuss the impact of genome variability on protein sequence and abundance.
- To introduce sequencing technologies and bioinformatics tools for proteogenomics.
Main Methods:
- Review of genome variability effects (SNVs, structural variants) on protein level.
- Introduction to short- and long-read sequencing technologies for variant prediction.
- Discussion of bioinformatics tools for DNA/RNA data processing.
Main Results:
- Genomic variability, including single-nucleotide variants and structural variants, directly impacts protein sequence and abundance.
- Short- and long-read sequencing offer complementary advantages for predicting protein variants.
- Bioinformatics tools enable the generation of accurate, sample-specific protein sequences.
Conclusions:
- Accurate prediction of sample-specific protein sequences is achievable through integrated omics data analysis.
- These predicted sequences can be seamlessly used with existing mass spectrometry search engines.
- Proteogenomics offers a powerful framework for comprehensive proteome definition.
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