WOMBAT-P: Benchmarking Label-Free Proteomics Data Analysis Workflows

The inherent diversity of approaches
in proteomics research has
led to a wide range of software solutions for data analysis. These
software solutions encompass multiple tools, each employing different
algorithms for various tasks such as peptide-spectrum matching, protein
inference, quantification, statistical analysis, and visualization.
To enable an unbiased comparison of commonly used bottom-up label-free
proteomics workflows, we introduce WOMBAT-P, a versatile platform
designed for automated benchmarking and comparison. WOMBAT-P simplifies
the processing of public data by utilizing the sample and data relationship
format for proteomics (SDRF-Proteomics) as input. This feature streamlines
the analysis of annotated local or public ProteomeXchange data sets,
promoting efficient comparisons among diverse outputs. Through an
evaluation using experimental ground truth data and a realistic biological
data set, we uncover significant disparities and a limited overlap
in the quantified proteins. WOMBAT-P not only enables rapid execution
and seamless comparison of workflows but also provides valuable insights
into the capabilities of different software solutions. These benchmarking
metrics are a valuable resource for researchers in selecting the most
suitable workflow for their specific data sets. The modular architecture
of WOMBAT-P promotes extensibility and customization. The software
is available at https://github.com/wombat-p/WOMBAT-Pipelines.