SWATH2stats

SWATH2stats converts OpenSWATH SWATH-MS output into formats compatible with MSstats, mapDIA, and aLFQ and provides annotation, filtering, false discovery rate estimation, and reproducibility assessment for targeted proteomics datasets.

Key Features:

• Data Transformation: Converts OpenSWATH output into formats compatible with MSstats, mapDIA, and aLFQ for downstream quantitative analysis.
• Annotation and Filtering: Provides annotation capabilities and advanced filtering options to refine dataset quality prior to analysis.
• False Discovery Rate (FDR) Estimation: Implements FDR estimation for peptides and proteins to assess identification confidence.
• Variation Analysis and Reproducibility Assessment: Enables analysis of measurement variation and reproducibility across samples and experimental conditions.

Scientific Applications:

• Large-scale proteomics: Processes extensive SWATH-MS datasets for high-throughput quantitative studies.
• Biomarker discovery: Prepares quantitative data for comparative analyses aimed at identifying candidate biomarkers.
• Systems biology: Supplies annotated and filtered proteomic quantifications for systems-level analyses.
• Clinical diagnostics: Supports proteomic data workflows relevant to clinical diagnostic studies.

Methodology:

Converts OpenSWATH output to downstream-tool formats and performs annotation, filtering, FDR estimation, and measurement reproducibility assessment.