Specter

Specter deconvolutes data-independent acquisition (DIA) mass spectrometry proteomics mixture spectra by directly comparing them to a spectral library to enable sensitive and reproducible peptide identification and quantification.

Key Features:

• Deconvolution via linear algebra: Employs linear algebra to deconvolute complex mixture spectra directly.
• Direct spectral library comparison: Directly compares DIA mixture spectra against a spectral library, bypassing fragment-correlation-based approaches.
• Systematic precursor measurement: Systematically measures all peptide precursors in a biological sample.
• Resolution of highly similar peptides: Resolves convoluted spectra to discriminate peptides with highly similar sequences, including SNP-derived variants and closely related phosphopeptides.
• Validated sensitivity and performance: Comparative studies demonstrate sensitivity and performance in analyses involving highly similar peptides.

Scientific Applications:

• Discrimination of highly similar peptides: Differentiates peptides with closely related sequences that produce overlapping DIA spectra.
• Detection of single-nucleotide polymorphisms (SNPs): Enables detection of peptide sequence variants arising from SNPs.
• Phosphoproteomics site localization: Identifies alternative phosphorylation site localizations within phosphopeptides.

Methodology:

Specter measures all peptide precursors and deconvolutes DIA mixture spectra by direct comparison to a spectral library using linear algebra.