PASTAQ

PASTAQ performs preprocessing and quantification of liquid chromatography–tandem mass spectrometry (LC-MS/MS) data for metabolomics and proteomics by avoiding arbitrary intensity thresholds to enable detection of low-intensity signals.

Key Features:

• Threshold-Avoiding Quantification: Eliminates arbitrary intensity thresholds during early preprocessing to preserve low-intensity signals relevant to metabolomic and proteomic analyses.
• Single-Stage (MS1) Quantification: Performs compound and peptide quantification using single-stage MS1 data.
• Novel Algorithms: Implements computational algorithms for quantification, retention time alignment, feature detection, and annotation linking.
• Annotation Integration: Links and integrates annotations originating from multiple identification engines.
• Quality Control Plots: Generates quality control plots to assess data and preprocessing steps.
• Reduced Variance in Replicates: Minimizes variance when analyzing replicates of proteomes mixed at known ratios.
• Enhanced Dynamic Range Detection: Detects peptides across a broader dynamic concentration range compared with other widely used proteomics preprocessing tools.

Scientific Applications:

• Biomarker discovery: Applied to a human serum dataset to identify gender-related proteins.
• Quantitative metabolomics and proteomics: Improves detection and quantification of low-intensity compounds and peptides across a wide dynamic range.

Methodology:

Preprocessing avoids arbitrary intensity thresholds; quantification is performed on MS1 data; computational modules perform quantification, retention time alignment, feature detection, and annotation linking that integrates annotations from multiple identification engines, and the workflow produces quality control plots.