LC-MS Spectral Interpretation

1 Day Course

Chromacademy eLearning

This course provides a greater understanding of how to interpret the mass spectra produced by Electrospray Ionisation (ESI) and Atmospheric Pressure Chemical Ionisation (APCI) from low molecular weight and high molecular weight compounds.

This course is not instrument-specific.


  • We limit numbers to 20 per course so that each delegate gets the opportunity to ask questions and fully participate in tutorial exercises 
  • When delivered on-site we can design the course material to suit your specific training needs
  • Customisable written assessments are available if required


Course Overview | Download course details »

Interpretation of low molecular weight compound mass spectra considers the importance of isotope patterns and their relative signal responses, how common fragmentation series are produced through electronic effects, a mechanistic understanding of Inductive and Alpha cleavage and sample identification through first principles.

Interpretation of high molecular weight compound mass spectra considers when to report monoisotopic mass or average mass, and deconvolution of an ESI multiply-charged ion series to derive the molecular weight of a compound amongst other topics.

Who is this course for

Users of LC-MS, LC-MS/MS or LC-MSn equipment, or anyone interested in structural elucidation of compounds amenable to analysis by liquid chromatography-mass spectrometry.

Previous knowledge
Experience in reviewing mass spectra is required and previous attendance to our level 1 or 2 LC-MS courses is recommended.

What you will learn

  • Mass spectral data analysis
  • Structural elucidation
  • Product ion generation by Collision Induced Dissociation (CID) characterization
  • Common mechanisms of fragmentation


Course outline

Mass Spectrometry Fundamentals

  • The pseudomolecular ion
  • The base peak
  • Multiply charged ions
  • Isotopes
  • Mass resolution
  • Mass accuracy

LC-MS Ion Production

  • Electrospray ionisation mass spectrometry
  • Atmospheric Pressure chemical Ionisation (APcI)
  • LC considerations for LC-MS
  • Eluent pH - Positive ESI-MS
  • Eluent pH - Negative ESI-MS

Electronic Effects

  • Classification of reagents
  • Inductive effects
  • Electronegativity
  • The inductive effect
  • Ion fragmentation
  • Charge-site initiation (I-cleavage)
  • Radical-site initiation (α-cleavage)

Data Analysis

  • Protein analysis and deconvolution
  • Applications of higher resolution analysis
  • LC-MS structural information modes
  • Tandem mass spectrometry
  • Product (daughter) ion scanning
  • Peptide sequencing by MS/MS
  • Product ion scanning - Considerations
  • Precursor (parent) ion scanning
  • Single and multiple reaction monitoring
  • Constant neutral loss (CNL) ion scanning

Mass Analysers

  • Quadrupole mass spectrometry
  • Time of Flight (ToF) mass spectrometry
  • Ion Trap mass spectrometry
  • Fourier Transform-Ion Cyclotron mass spectrometry
  • Detectors
  • Intelligent systems
  • Sample analysis summary