Intact Glycopeptide Analysis — Site Occupancy & Microheterogeneity — Hands-on

Learn how to move from enriched glycopeptide LC MS MS data to quantitative views of site occupancy and glycan microheterogeneity. This module covers acquisition setup, intact glycopeptide searching, extracting site level abundances and summarizing glycoforms per site for biologics, serum glycoproteins and discovery studies.

Intact Glycopeptide Analysis — Site Occupancy & Microheterogeneity

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Session Index

Session 1 — LC-MS/MS Setup for Intact Glycopeptides Session 2 — Site Occupancy Quantification Strategies Session 3 — Microheterogeneity Profiling & Visualization Session 4 — Mini Capstone: Site Occupancy & Microheterogeneity Report

Session 1

Fee: Rs 8800

LC-MS/MS Setup for Intact Glycopeptides

Chromatography and gradient design for intact glycopeptides

reversed phase nano LC column choices and loading gradient lengths for coverage

DDA / DIA / PRM strategies for glycopeptides

DDA survey scans and inclusion lists DIA windows and libraries targeted PRM for key sites

Fragmentation and instrument parameters for intact glyco data

HCD vs EThcD settings resolution, AGC and max IT dynamic exclusion tuning

Session 2

Fee: Rs 11800

Site Occupancy Quantification Strategies

Relating glycopeptide and non-glycosylated peptide signals

paired glycopeptide / peptide concepts using deglycosylated runs normalization choices

Calculating site occupancy from intensities or areas

% occupied vs unoccupied handling multiple charge states replicates and error estimates

QC metrics for site occupancy measurements

signal to noise thresholds missing value handling technical vs biological variance

Session 3

Fee: Rs 14800

Microheterogeneity Profiling & Visualization

Aggregating glycoforms per site from intact glycopeptide IDs

grouping by peptide and site composition vs structure level intensity vs area measures

Summarizing microheterogeneity across samples or batches

relative abundance of glycoforms lot comparability views change detection for CQAs

Plots and visual summaries for reports and dashboards

stacked barplots per site heatmaps and clustering export ready figures

Session 4

Fee: Rs 18800

Mini Capstone: Site Occupancy & Microheterogeneity Report

Build a small intact glycopeptide analysis pipeline on example data

from ID table to site level summaries

Generate site occupancy and microheterogeneity summaries

per site % occupancy glycoform distributions condition or batch comparisons

Deliverables and documentation set

summary tables per site plots for a short report notes for MIRAGE and CQA tracking

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Intact Glycopeptide Analysis — Site Occupancy & Microheterogeneity Training | Quantitative Glycoproteomics

Intact Glycopeptide Analysis — Site Occupancy & Microheterogeneity — Hands-on