MSTopDiff

MSTopDiff visualizes and detects mass shifts in top-down proteomics data to identify artificial and biological protein modifications.

Key Features:

• Database-Independent Analysis: Operates without protein database searches to detect modifications directly from experimental data.
• Mass Difference Calculation: Calculates mass differences between observed and theoretical masses to reveal modification-induced mass shifts.
• Use of Deconvoluted MS1/MS2 Spectra: Analyzes and visualizes mass differences using deconvoluted MS1 or MS2 spectra.
• Detection of Artifacts and Biological Modifications: Identifies sample-preparation artifacts such as oxidation, alkylation, formylation, overlabeling during isobaric labeling, noncovalent adducts (e.g., detergents), cation adducts, and sodium dodecyl sulfate, as well as biological modifications including phosphorylation and acetylation.
• Visualization Modes: Provides multiple modes of data representation for inspection of mass shifts and proteoform distributions.

Scientific Applications:

• Quality Control of Top-Down Proteomics Workflows: Provides an overview of artificial and biological modifications present in samples to support workflow QC.
• Method Development and Parameter Evaluation: Aids evaluation of experimental parameters by visualizing mass shifts introduced during sample preparation or analysis.
• Proteoform Characterization and Discovery: Enables detection and characterization of novel or poorly characterized proteoforms via database-independent modification discovery.
• Detection of Sample Preparation Artifacts: Allows identification of common artifacts such as oxidation, alkylation, overlabeling, and adduct formation that can affect proteomic interpretation.

Methodology:

Uses deconvoluted mass spectrometry data to identify modifications by calculating mass differences between observed spectra and theoretical masses in a database-independent manner.