Crosslinking MS — XL MS for Structural Mapping — Hands-on

Understand how crosslinking mass spectrometry (XL MS) turns covalent crosslinks into distance restraints for protein and complex level structural mapping. This module focuses on crosslinker concepts, experimental layouts, the idea of XL specific search space, and how to interpret crosslink patterns as topological information to support models and interaction hypotheses.

Crosslinking MS — XL MS for Structural Mapping

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Session Index

Session 1 — XL MS Concepts & Structural Use Cases Session 2 — Crosslinker Chemistry & Experiment Layouts Session 3 — Acquisition, Search Space & IDs Session 4 — Distance Restraints, QC & Reporting

Session 1

Fee: Rs 8800

XL MS Concepts & Structural Use Cases

What crosslinking MS measures in structural biology

covalent links between residues distance restraint concepts intra vs inter protein links

Structural questions XL MS can address (conceptual)

domain arrangements and interfaces complex organization and topology supporting models and docking

XL MS in the context of other structural methods

complementing cryo EM and X ray hybrid modeling ideas advantages and limitations overview

Session 2

Fee: Rs 11800

Crosslinker Chemistry & Experiment Layouts

Crosslinker types and reactive groups (conceptual)

amine reactive and other chemistries homo vs hetero bifunctional logic spacer length as distance upper bound

MS cleavable vs non cleavable crosslinkers (high level)

fragmentation signature ideas benefits for identification logic tradeoffs in complexity and cost

Designing XL MS experiment layouts on paper

protein vs complex vs cell lysate setups controls and quenching ideas digestion and enrichment considerations

Session 3

Fee: Rs 14800

Acquisition, Search Space & Identifications

MS/MS acquisition ideas for crosslinked peptides

complexity of XL spectra fragmentation mode considerations enrichment impact on signal

Concept of XL specific search space and scoring

paired peptide candidates idea search space explosion intuition FDR thinking for crosslinks

Classes of IDs: inter, intra and dead end links

mapping to sequence and complexes interpreting dead end modifications confidence and filtering concepts

Session 4

Fee: Rs 18800

Distance Restraints, QC & Reporting

Translating crosslinks into distance restraints (conceptual)

theory plus planning worksheet

QC for XL MS data and structural consistency checks

distance distributions vs expected ranges model violation concepts replicate and site level robustness

Summarizing XL MS for structural and biology audiences

contact maps and network style figures tables of crosslinks and distances transparent methods and parameter descriptions

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Crosslinking MS — XL MS for Structural Mapping Training | Distance Restraints for Structural Biology

Crosslinking MS — XL MS for Structural Mapping — Hands-on