SAMPEI

SAMPEI identifies modified peptides from high-resolution mass spectrometry proteomics data using a spectral alignment-based approach to enable unbiased discovery of amino acid, post-translational, and non-canonical protein modifications.

Key Features:

• Spectral alignment methodology: Employs spectral alignment (Spectral Alignment-based Modified Peptide Identification) to identify modified peptides without requiring prior knowledge of modification identities.
• Detection of substoichiometric modifications: Enables identification of low-abundance, substoichiometric modifications within complex cellular extracts by aligning experimental spectra to reference signals.
• High specificity and sensitivity: Demonstrated specificity and sensitivity through validation with synthetic standards and controlled chemical labeling experiments.
• Robust parametrization and versatility: Provides parametrization that supports reliable performance across diverse experimental conditions and supports exploration of macromolecular modifications including peptides beyond canonical proteins.

Scientific Applications:

• Protein modification dynamics: Applied to investigate dynamics of protein modifications and their roles in cellular signaling and regulatory mechanisms.
• Mouse macrophage differentiation mapping: Applied to map mouse macrophage differentiation, revealing an array of post-translational modifications including distinct forms of cysteine itaconatylation.

Methodology:

SAMPEI aligns high-resolution mass spectrometry spectra to identify modified peptides and compares experimental spectra against synthetic standards and controlled chemical labeling experiments to distinguish genuine biological modifications from artifacts.