Mass Spectrometry Course

Lesson 1 • Units, Nomenclature, and Notation

Standardises the vocabulary and units used throughout the course. Prevents misinterpretation of spectra and literature values.

Lesson 2 • History and Scope of Mass Spectrometry

Traces the development of MS from early ion physics to modern applications. Establishes context for why each instrumental component exists.

Lesson 3 • Core Physical Principles

Covers the physics of charged particles in electric and magnetic fields. Provides the quantitative basis for understanding mass separation.

Lesson 1 • Matrix-Assisted Laser Desorption Ionisation

Teaches MALDI matrix selection, sample preparation, and laser parameters. Connects pulsed ionisation to time-of-flight analyser compatibility.

Lesson 2 • Electrospray Ionisation

Explains the electrospray process for polar, nonvolatile, and large molecules. Links spray conditions to charge state distributions observed in spectra.

Lesson 3 • Gas-Phase Ionisation Methods

Covers electron ionisation and chemical ionisation for volatile analytes. Connects ionisation energy to fragmentation extent and spectral complexity.

Lesson 4 • Ambient and Emerging Ionisation Sources

Surveys DESI, DART, and related open-air ionisation techniques. Highlights minimal sample preparation as a key analytical advantage.

Lesson 1 • Time-of-Flight Analysers

Derives flight-time equations and explains reflectron design for improved resolution. Connects TOF to MALDI and high-throughput applications.

Lesson 2 • Orbitrap and FT-ICR Analysers

Explains electrostatic trapping in Orbitrap and magnetic trapping in FT-ICR. Establishes the basis for ultra-high-resolution and exact-mass measurement.

Lesson 3 • Ion Trap Analysers

Covers 3D and linear ion trap trapping, isolation, and fragmentation. Links ion storage capability to MSn experiments introduced later.

Lesson 4 • Quadrupole Mass Filters

Explains RF/DC voltage operation and ion stability diagrams for quadrupoles. Connects scan speed and unit resolution to routine quantitative workflows.

Lesson 1 • Functional Group Fragmentation Patterns

Catalogues characteristic losses and fragment ions for common functional groups. Enables rapid structural hypothesis generation from unknown spectra.

Lesson 2 • De Novo Structure Elucidation Workflow

Integrates isotope, exact-mass, and fragmentation data into a stepwise elucidation strategy. Prepares students for unknown compound identification tasks.

Lesson 3 • Isotope Patterns and Exact Mass

Explains natural isotope abundances and their effect on spectral patterns. Connects exact-mass measurement to molecular formula determination.

Lesson 4 • Reading and Annotating Mass Spectra

Teaches identification of molecular ion, base peak, and isotope clusters. Establishes a consistent annotation workflow used throughout the course.

Lesson 1 • GC-MS Fundamentals and Interface

Covers column selection, carrier gas, and direct capillary interface to the ion source. Links chromatographic resolution to spectral quality and identification confidence.

Lesson 2 • Qualitative Identification in Hyphenated MS

Covers library searching, retention time matching, and spectral scoring for compound identification. Establishes identification confidence criteria used in regulated workflows.

Lesson 3 • Troubleshooting Hyphenated MS Systems

Diagnoses common chromatographic and MS performance issues in coupled systems. Builds practical maintenance skills essential for laboratory productivity.

Lesson 4 • LC-MS Interface Technologies

Explains ESI and APCI interfaces for coupling reversed-phase and HILIC columns to MS. Addresses mobile phase compatibility and ion suppression challenges.

Lesson 1 • SRM and MRM Workflow Design

Guides transition selection, collision energy optimisation, and dwell time balancing for MRM. Produces a complete quantitative method ready for validation.

Lesson 2 • Method Validation Parameters

Covers accuracy, precision, LOD, LOQ, selectivity, and stability as validation parameters. Aligns validation design with internationally recognised bioanalytical guidelines.

Lesson 3 • Calibration Strategies and Curve Fitting

Teaches external calibration, matrix-matched calibration, and weighted regression. Connects calibration design to accuracy across the dynamic range.

Lesson 4 • Internal Standards and Isotope Dilution

Covers stable isotope-labelled internal standards and isotope dilution MS theory. Demonstrates how internal standards correct for matrix effects and recovery variability.

Lesson 1 • Peptide Fragmentation and Sequence Ions

Explains b- and y-ion series, a-ions, and neutral losses from peptide backbone cleavage. Enables manual validation of automated peptide identifications.

Lesson 2 • Bottom-Up Proteomics Workflow

Teaches LC-MS/MS data acquisition, database searching, and peptide-spectrum matching. Connects peptide identifications to protein inference and false discovery control.

Lesson 3 • Quantitative Proteomics Strategies

Covers label-free quantitation, SILAC, TMT, and iTRAQ approaches. Connects quantitation strategy to experimental design and statistical power.

Lesson 4 • Top-Down and Native MS of Proteins

Introduces intact protein analysis, native MS, and gas-phase protein complex characterisation. Extends proteomics skills to structural and systems biology questions.

Lesson 1 • Ion Mobility Spectrometry Coupled to MS

Explains drift tube, travelling wave, and trapped ion mobility separation principles. Adds a collision cross-section dimension to structural characterisation workflows.

Lesson 2 • Mass Spectrometry Imaging

Teaches MALDI-MSI, DESI-MSI, and SIMS for spatially resolved molecular mapping of tissues. Connects pixel-level spectra to histological and pharmacological interpretation.

Lesson 3 • Metabolomics and Lipidomics by MS

Covers untargeted and targeted metabolomics workflows, lipid class annotation, and pathway mapping. Integrates MS data with bioinformatics tools for biological interpretation.

Lesson 4 • Environmental and Food Safety MS Applications

Applies high-resolution MS and multi-residue methods to contaminant screening in complex matrices. Demonstrates regulatory-aligned reporting and suspect screening workflows.