MsViz

MsViz enables manual validation and relative quantitation of post-translational modifications (PTMs) in small- to medium-scale proteomics experiments by visualizing sequence coverage, peptide–spectrum matches, tandem mass spectrometry (MS/MS) spectra, and extracted ion chromatograms to support accurate PTM localization and comparative analysis across conditions.

Key Features:

• Visualization of spectral and chromatographic data: Displays sequence coverage, peptide–spectrum matches, tandem mass spectrometry (MS/MS) spectra, and extracted ion chromatograms for integrated inspection.
• Manual validation of PTM localization: Supports manual inspection and confirmation of PTM localization on proteins to validate modification sites.
• Relative quantitation across conditions: Performs relative quantitation of modified species across multiple samples and experimental conditions for comparative analyses.
• In-depth spectral and chromatographic inspection: Enables detailed examination of spectral and chromatographic evidence to improve the reliability of PTM identification and quantitation.

Scientific Applications:

• PTM localization confirmation: Manual confirmation and refinement of PTM sites identified by mass spectrometry in proteomics datasets.
• Comparative PTM dynamics: Assessment of relative abundance changes of modified species across experimental conditions for functional studies.
• Validation-focused proteomics studies: Applied to small- to medium-sized proteomic experiments requiring per-protein validation and quantitation of modifications.

Methodology:

Computational functions explicitly include visualization of sequence coverage, peptide–spectrum matches, tandem MS/MS spectra, and extracted ion chromatograms, together with manual PTM localization validation and relative quantitation across samples and conditions.