MAGIC

MAGIC identifies N-linked glycoproteins and glycan compositions from collision-induced-dissociation (CID) mass spectrometry (MS) spectra of intact glycopeptides to enable characterization of protein N-glycosylation.

Key Features:

• Automated Identification: Automates identification of peptide sequences and glycan compositions directly from CID spectra of intact N-linked glycopeptides.
• Y1-Ion Pattern Matching (Trident): Detects the Y1 ion using the Trident algorithm by identifying triplet patterns ([Y0, Y1, Y2] or [Y0-NH3, Y0, Y1]) produced from trimannosyl core fragmentation.
• In Silico MS2 Approach: Generates in silico MS2 spectra by substituting the precursor m/z with the naked peptide m/z and removing glycan-related ions to facilitate peptide identification by standard database search engines.
• Glycan Composition Ranking: Computes and ranks potential glycan compositions for processed spectra.

Scientific Applications:

• Enhanced Peptide Fragment Intensity: In analyses of horseradish peroxidase (HRP) and a five-glycoprotein mixture, produced 2- to 31-fold increases in peptide fragment intensities, enabling identification of multiple glycopeptides.
• High-throughput Processing: Processed over a thousand MS(2) spectra from HeLa cell proteome data in three minutes, identifying numerous glycopeptides and corresponding glycoproteins.
• Accuracy and Reliability: Achieved a false discovery rate (FDR) of 0% on an N-glycosylation-free Escherichia coli dataset.

Methodology:

Identifies peptide sequences and glycan compositions from CID spectra; employs the Trident algorithm to detect Y1 ion triplet patterns ([Y0, Y1, Y2] or [Y0-NH3, Y0, Y1]) from trimannosyl core fragmentation; generates in silico MS2 spectra by substituting the precursor with the naked peptide m/z and removing glycan-related ions to enable peptide identification by standard database search engines; computes and ranks potential glycan compositions.