Chemical Crosslinking and Structural MS — Hands-on

Build a strong conceptual understanding of chemical crosslinking and structural mass spectrometry (XL-MS) . This module focuses on crosslinker chemistry, experimental design, XL-MS data patterns and identification concepts, and how crosslink distance restraints are interpreted in the context of protein complex architecture and integrative structural models.

Chemical Crosslinking and Structural MS

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Session Index

Session 1 — Crosslinking & Structural Restraints Foundations Session 2 — Crosslinker Types & Experiment Design (Concepts) Session 3 — XL-MS Data Patterns & Identification Concepts Session 4 — Mini Capstone: From Crosslinks to Structure

Session 1

Fee: Rs 8800

Crosslinking & Structural Restraints Foundations

What is chemical crosslinking and why use XL-MS

capturing proximity information probing complexes and conformations complementing structural methods

Distance restraints and structural interpretation ideas

linker length concepts Cα–Cα distance thinking satisfied vs violated crosslinks (overview)

Overview of XL-MS workflows at conceptual level

crosslinking reaction idea digestion and LC–MS/MS readout data interpretation and mapping

Session 2

Fee: Rs 11800

Crosslinker Types & Experiment Design (Concepts)

Crosslinker families and reactive group concepts

amine reactive crosslinkers (overview) cleavable vs non cleavable ideas homo vs heterobifunctional concepts

Spacer length, flexibility and solvent accessibility thinking

approximate upper distance limits impact of protein dynamics surface exposure concepts

Conceptual experiment planning for XL-MS projects

choice of complex and conditions controls and replicate thinking high level LC–MS/MS considerations

Session 3

Fee: Rs 14800

XL-MS Data Patterns & Identification Concepts

Types of crosslinked species in XL-MS data (concepts)

monolinks and loop links inter and intra protein crosslinks uncrosslinked background peptides

MS/MS patterns and interpretation at conceptual level

precursor mass shifts ideas cleavable linker fragment concepts complex fragmentation patterns awareness

Identification thinking and FDR concepts for crosslinks

search space considerations (overview) target decoy style thinking for crosslinks confidence and site assignment ideas

Session 4

Fee: Rs 18800

Mini Capstone: From Crosslinks to Structure

Mapping crosslinks onto structures or models (conceptual)

Theory + Practical (planning style)

Interpreting satisfied and violated restraints at high level

possible causes of conflicts conformational heterogeneity ideas model refinement thinking (overview)

Mini capstone deliverables (concept and planning focused)

crosslink table layout and annotation plan distance summary and simple plots (idea level) short narrative linking crosslinks to architecture

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Chemical Crosslinking & Structural MS Training | XL-MS Concepts and Structural Restraints

Chemical Crosslinking and Structural MS — Hands-on