DrawAlignR

DrawAlignR visualizes and aligns raw mass spectrometry chromatograms to establish analyte correspondence across multiple proteomic runs for accurate peptide quantification and comparison.

Key Features:

• Chromatogram visualization: Visualizes aligned chromatographic traces and peak alignments for Data-Independent Acquisition (DIA) and SWATH-MS experiments.
• Workflow integration: Accepts extracted ion chromatogram data and feature scoring data typically produced by OpenMS, OpenSWATH, and PyProphet for multi-run analysis.
• C++ alignment implementation: Implements raw chromatogram alignment in C++ with a reported ~35-fold speed improvement over previous methods.

Scientific Applications:

• Multi-run peptide quantification: Establishes analyte correspondence across runs to support accurate peptide abundance comparison and quantification in proteomics studies.
• Alignment quality assessment: Enables interpretation and inspection of cumulative alignment scores to evaluate peak matching and peptide behavior across conditions.

Methodology:

Performs raw chromatogram alignment implemented in C++ using extracted ion chromatogram inputs and feature scores from OpenMS, OpenSWATH, or PyProphet, with an observed ~35× speed improvement.