BI-793 Spring 2012 Lecture 9 Assignment

Name___________________________

1. MS of glycoconjugates

a. Go to www.lipidmaps.org.

b. Select five lipids or glycolipids from the data

standards, from different classes.

c. Go to the experimental results section for each.

d. Print the structure and MS/MS spectrum.

e. Assign the major fragments.

Note: You should avoid selecting the same examples as a classmate.

2. Please read R. Chan et al., J. Virology, 2008, 82, 11228–11238. Retroviruses Human Immunodeficiency Virus and Murine Leukemia Virus Are Enriched in Phosphoinositides.

a. What lipids are associated with the virus particles?

b. Which lipids would be detected with the highest sensitivity in the positive ion mode? Which in the negative ion mode?

c. Select an example of each of the classes which appear in the MS spectra presented in Fig. 2, draw the structures and assign the major predicted fragment ions.

d. What are three challenges presented by this type of analysis and how did the authors address each difficulty?

3. Please read H. Park, et al., J. Lipid Res. 2010, 51, 480-489. Transcript profiling and lipidomic analysis of ceramide subspecies in mouse embryonic stem cells andembryoid bodies.

a. What procedure was used for lipid isolation?

b. Why LC conditions and mass spectrometer were used? Why were these chosen?

c. What could be the advantages or disadvantages of using MALDI-MS instead of ESI-MS for the analyses described here?

d. What standards were used for quantification? What were the ranges over which quantitative data was obtained and how accurate were the results? Do you have suggestions for improvement?