XGlycScan

XGlycScan maps peptide-spectrum matches to N-linked glycosites to assign, quantify, and assess the quality of glycosite identifications in mass spectrometry-based glycoproteomic analysis.

Key Features:

• PSM-to-glycosite mapping: Maps peptide spectrum matches (PSMs) of varying lengths from bottom-up proteomics directly to corresponding N-linked glycosites.
• Glycosite quantification: Quantifies glycosite-associated spectra counts to provide site-centric abundance measures.
• Technical replicate consistency: Reduces variability in glycosite identification across technical replicates.
• Protein inference simplification: Focuses on glycosites rather than individual peptides to simplify protein inference.
• Search-engine identification assessment: Provides quality assessment of search-engine identifications for glycosite assignments.
• Implementation: Implemented in Java and applicable to mass spectrometry-based glycoproteomic datasets.

Scientific Applications:

• N-linked glycosite assignment: Assigns and characterizes N-linked glycosites from mass spectrometry data.
• Glycoproteomic quantification: Enables quantification of glycosites in bottom-up proteomics workflows via spectra counts.
• Identification quality control: Assesses the reliability of search-engine identifications in glycoproteomic studies.
• Reproducibility improvement: Improves reproducibility of glycosite detection across technical replicates.
• Protein inference support: Supports clearer protein inference by consolidating peptide evidence at the glycosite level.

Methodology:

Maps PSMs of varying peptide lengths from bottom-up proteomics to N-linked glycosites, computes glycosite-associated spectra counts, and assesses search-engine identifications; implemented in Java.