Survey of metaproteomics software tools for functional microbiome analysis

Area of Science:

• Microbiome research
• Metaproteomics
• Bioinformatics

Background:

• Understanding microbiome dynamics requires characterizing expressed microbial genes and proteins.
• Metaproteomics analyzes protein expression in microbiomes, aiding functional insights.
• Several software tools exist for functional microbiome analysis, but their performance varies.

Purpose of the Study:

• To evaluate and compare the performance of six available metaproteomics software tools.
• To guide researchers in selecting appropriate software for their specific research objectives.
• To provide feedback for software developers to optimize metaproteomics analysis algorithms.

Main Methods:

• Tandem mass spectrometry-based proteomic data from dental caries plaque biofilms were used.
• Six software tools (eggNOG-mapper, MEGAN5, MetaGOmics, MPA, ProPHAnE, Unipept) were employed for functional annotation using Gene Ontology (GO) terms.
• Peptide-level comparisons and BLAST analysis against NCBI non-redundant database assessed annotation quality, sensitivity, and specificity.

Main Results:

• Significant differences in functional annotation were observed among the evaluated tools.
• eggNOG-mapper annotated the highest number of GO terms.
• Unipept demonstrated higher accuracy in GO term generation.
• Sensitivity and specificity of functional annotation varied across the tools.

Conclusions:

• Metaproteomics researchers can select software based on their specific analytical needs, balancing the number of annotations with accuracy.
• eggNOG-mapper and Unipept 4.0 have been integrated into the Galaxy platform for enhanced accessibility in metaproteomics workflows.
• The study provides valuable insights for both users and developers in the field of metaproteomics analysis.