QuantPipe

QuantPipe: Integrated DIA Proteomics Analysis Workflow

QuantPipe integrates and automates the OpenSWATH-PyProphet-TRIC workflow for data-independent acquisition (DIA) mass spectrometry to perform spectral library conversion, statistical validation, and peptide and protein quantification.

Key Features:

• OpenSWATH-PyProphet-TRIC Integration: Executes core functions of OpenSWATH, PyProphet, and TRIC for targeted extraction, statistical scoring, and cross-run alignment.
• Spectral Library Conversion: Converts spectral libraries into assay libraries for accurate peptide and protein quantification.
• Quantitative Output: Generates detailed peptide and protein intensity values for downstream analysis.

Scientific Applications:

• SWATH-MS Analysis: Processes SWATH-MS data from TripleTOF 5600 and TripleTOF 6600 instruments.
• Phospho-SWATH-MS Analysis: Analyzes phospho-specific DIA datasets to study protein phosphorylation dynamics.
• Orbitrap DIA Analysis: Supports DIA data acquired on Orbitrap mass spectrometers.
• diaPASEF Analysis: Processes diaPASEF data from the TimsTOF Pro instrument.

Methodology:

QuantPipe automates DIA data analysis by performing spectral library conversion to assay libraries, targeted signal extraction with OpenSWATH, statistical validation with PyProphet, cross-run alignment with TRIC, and quantitative peptide and protein intensity calculation.