Glycan Identification, Annotation & FDR Control — Hands-on

Learn how to go from raw LC MS glycomics data to confident, standards compliant identification tables. This module focuses on search spaces, libraries, scoring, decoy generation and FDR control for released glycans and glycopeptides, together with practical annotation workflows and export formats suitable for downstream quantitation and FAIR sharing.

Glycan Identification, Annotation & FDR Control

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Session Index

Session 1 — Search Space, Libraries & Formats Session 2 — Search Engines, Matching & Scoring Session 3 — Decoys, FDR & Manual Validation Session 4 — Mini Capstone: Identification & FDR Pipeline

Session 1

Fee: Rs 8800

Search Space, Libraries & Formats

Defining search spaces for released glycans and glycopeptides

composition vs structure lists organism and tissue specific filters linking to databases and IDs

Library concepts and reference spectra

retention time and GU scaling MS/MS libraries and templates using vendor and community libraries

Result table formats and core columns for annotation

m/z and RT columns composition, structure and ID fields scores, q values and comments

Session 2

Fee: Rs 11800

Search Engines, Matching & Scoring

Overview of glycan and glycopeptide search engines

released glycan matchers glycopeptide oriented engines integrated vendor workflows

Matching logic and score components

mass accuracy and ppm windows fragment coverage and ion types retention and GU support metrics

Exporting and parsing search engine outputs

vendor formats to tabular files joining quant and ID tables basic R / Python parsing tips

Session 3

Fee: Rs 14800

Decoys, FDR & Manual Validation

Decoy generation strategies for glycans and glycopeptides

shuffled or mass shifted decoys decoy search spaces target decoy competition logic

FDR estimation and threshold selection

global vs level based FDR q value interpretation protein and site level roll up

Manual review, spectrum checks and confidence tiers

spot checking key identifications diagnostic ion verification assigning confidence levels

Session 4

Fee: Rs 18800

Mini Capstone: Identification & FDR Pipeline

Build a simple identification and FDR workflow on example data

from search space to q value filtered table

Create an annotated identification table ready for quant and sharing

composition and ID columns scores, FDR and evidence fields links to spectra and raw files

Deliverables and documentation set

cleaned identification spreadsheet short FDR and QC summary notes aligned with MIRAGE and MSI levels

PDF

Glycan Identification, Annotation & FDR Control Training | Search Engines, Decoys & QC

Glycan Identification, Annotation & FDR Control — Hands-on