Advanced Interpretation of CID Mass Spectra from LC/MS/MS 
Developing a Systematic Methodology for Spectral Interpretation

Two day course
Instructor: Robert D. Voyksner, Ph.D.
LCMS Limited
Durham, NC

Course Description:

This advanced 2 day course will cover generation and interpretation of Collision Induced Dissociation (CID) mass spectra generated from positive and negative ions formed from the API techniques of electrospray, APCI or APPI. The course will cover formation of ions, variables in CID mass spectra under tandem MS (triple quadrupole, q-TOF, ion trap) and API transport CID and interpretation of both the molecular ion and common molecular adduct ions and the product ion formed from these species after CID. The interpretation of the product ion mass spectra will be broken down into distinctive fragmentation mechanisms to aid the student to develop a systematic approach towards spectral interpretation. The fragmentation processes covered include single bond cleavage, multiple bond cleavage with charge retention and with charge migration, cyclization, ring opening fragmentation, hydrogen rearrangements, and charge remote fragmentation. The fragmentation mechanisms will be applied to both positive and negative ions. Additionally, CID product ion formation from adducts such as [M+Na]+ [M+NH4]+ and [M+F, Cl or Br]- will be covered. Each of the lectures have imbedded practical problems, which will allow a review of the various fragmentation mechanisms on a variety of compound types. The course will finish with a series of real world LC/MS/MS interpretation problems applicable to pharmaceuticals, clinical, industrial, and forensic and biochemical industry that the students will work on in groups and discuss at the end of the class.

The course is designed for the students who have completed a LC/MS Short Course or who have some working knowledge of LC/MS and want to improve their qualitative interpretation skills for problem solving in LC/MS. The outline for the course is given below:

Course Outline

- General information in an Electrospray mass spectrum –
- What is CID?
- CID reaction/energies

Generating CID Spectra:
- API transport CID
- Tandem MS
- Comparison of trap, triple and high-energy CID spectra.

Interpretation of API Mass Spectra:
- Identifying the molecular ion
- Using isotope abundances to gain information
- Nitrogen rule
- Identifying other adduct ions, dimers and multiply charged species.

Interpretation of Positive and Negative ion CID
- Variability of CID
- Stability of ions and neutrals
- Charge retention vs. charge migration fragmentation
- Single bond cleavages
- Cyclization reactions
- Multiple bond cleavages
- Rearrangement reactions
- Charge remote fragmentation
- Problem sets reviewing all mechanisms discussed

Interpretation of CID mass spectra generated from ions other than [M+H]+ or [M-H]-
- Interpretation of CID mass spectra from Alkali metal cations
- Interpretation of CID mass spectra from Halogen anions
- Interpretation of CID mass spectra from multiply charged ions (anions and cations)

Techniques and Tools to help with CID Interpretation:
- Isotopic labeling
- Hydrogen-deuterium exchange
- Using accurate mass for determining molecular formulas
- CID Libraries and their generation

- Real world problems in the areas of pharmaceuticals, biochemical, clinical, industrial, and forensic and environmental that aid in the development of the students systematic approach to interpretation of CID mass spectra.