LC-MS FOR PROTEINS AND PEPTIDES - FRAGMENTATION AND SEQUENCING TRAINING COURSE
Understanding peptide fragmentation is essential for confident sequence identification, structural characterisation, PTM analysis, and troubleshooting complex spectra. This course provides a practical, mechanism-focused approach to interpreting MS/MS data and performing de novo peptide sequencing using modern LC-MS instrumentation.
Designed for analysts working with proteins, peptides, digests, or biotherapeutics, this course guides learners from core fragmentation principles to advanced sequence deduction.
LC-MS FOR PROTEINS AND PEPTIDES - FRAGMENTATION AND SEQUENCING COURSE DETAILS
- Peptide Fragmentation Fundamentals: How ionisation sites form, how charge migration works, the effect of precursor charge state, and how to recognise key sequence and non-sequence fragments
- De Novo Peptide Sequencing: Mobile proton model, optimising precursor selection and collision energy, interpreting a/b/c and x/y/z ion series (individually and combined), plus side-chain cleavages and double-residue deletions
- Pseudo-MS³ Acquisition: How pseudo-MS³ improves confidence in complex peptide sequence assignments.
We offer flexible delivery options for this instructor-led course:
- On-site: One full-day session at your laboratory or any location of your choice.
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Online: Two half-day interactive sessions.
View our online training calendar for upcoming dates.
Experienced in small molecule LC-MS.
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MS/MS Fragmentation Mechanisms of Peptides
- Ionisation site formation and stabilisation
- Charge migration fragmentation
- Effect of ion charge state of fragmentation spectral quality
- Structurally important fragments
- Non-sequence related fragments
- Fragment abundance
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MS/MS Denovo Peptide Sequencing
- Mobile proton model of fragmentation
- Effect of charge state on fragmentation
- Optimisation of parent ion selection and Q2 energy
- a, b, c series deletions
- Individual types with workshops
- Combined types with workshops
- x, y, z series deletions
- Individual types with workshops
- Combined types with workshops
- Combined a, b, c and x, y, z series spectra
- Sidechain type effect on sequential deletions
- Side chain cleavage
- Double residue deletions
- Pseudo MS3 Acquisition
