• Longqin Hu, Ph.D. (Coordinator)
  Associate Professor of Medicinal Chemistry
• Ray Bakhtiar, Ph.D.
  Senior Research Fellow, Merck Research Laboratory
  

• Comprehensive Final Exam on Monday, March 21st.
  • 20% - Dr. Hu's portion
  • 80% - Dr. Bakhtiar's portion
    
• Term paper due on April 20th.
  
• Presentation Schedule: 30 min each

  Date and Time	Presenter	Title
  Monday, April 25, 4:30 pm -	Guoxiang Shen	SELDI-TOF MS for Diagnostic Proteomics
  	Kristi Cappuccio	multidimensional analysis on LC-LC or GC-GC or another combination
  	Jianying Ding	NMR Spectroscopy Tools for Structure-Aided Drug Design
  	Yu Chen	TBA
  Wednesay, April 27, 4:30 pm -	Kumar Pabbisetty	Proteomics approaches in the search for disease biomarkers
  	Prathima Surabhi	TBA
  	Liang Cheng	TBA

Course Material

• Class Schedule (pdf file)
• Course Syllabus (pdf file)
• FDA Guidance for Industry: Bioanalytical Method Validation
• Chiral Method Development Screen in Drug Discovery - Lab Wall Chart
  
• LC/MS: Why is it the fastest growinganalytical technique?
• API Optimization, Source Design, and Other Considerations of LC/MS - A Finnigan Presentation
• LC/MS - Interfacing HPLC and MS - Waters
• Applications of LC/MS in Qualitative Drug Metabolite Studies
• Adducts & Clusters formed in LC/MS
• PhotoSpray
• High Throughput Protein IDMALDI-MS/MS
• Quadrupoles vs. Ion Traps
• A Word on High Resolution and Accurate Mass Definitions
• The First Step in Solving LC-MS Method Development Challenges -New
  
• Quadrupole Ion-Trap Mass Analyzer - EAS Workshop on November 15, 2004
• High Sensitivity ESI, APCI Quantitation of Cabergoline and Pergolide in Plasma on the High Resolution TSQ Quantum
• The Thermo Finnigan TSQ Quantum - High Performance Quantitative and Qualitative Applicationson a High Resolution Triple Quadrupole Mass Spectrometer
• Finnigan™ LCQ™ Advantage MAX - Product Specifications
• Finnigan™ LCQ™ Deca XP MAX - Product Specifications
• Finnigan LTQ FT - Ultra HighPerformance Mass Spectrometer
• Finnigan LTQ
• Finnigan LTQ FT brochure
• Technology Behind the Finnigan LTQ - ASMS Users Forum 2003
• Analysis of Choline and its Metaboliteson the Finnigan LTQ
• Application of a Data Dependent™ Neutral-Loss Experiment on the Finnigan LTQ™ for the Identification of Phosphorylated Peptides
  
• Stages of LTQ MS/MS Analysis - FlashPlayer
• TSQ Quantum Technology Demonstration - FlashPlayer
  
• IonSource - A Web Site for Mass Spectrometry and Biotechnology Resource
  

  References as starting leads/themes for term papers:

1. Recent advances in chiral separation principles in capillary electrophoresis and capillary electrochromatography. Electrophoresis 2004, 23, 3981–3996. [pdf]
2. Lab-on-a-chip for drug development. Advanced Drug Delivery Reviews 55 (2003) 349–377. [pdf]
3. Analysis of benidipine enantiomers in human plasma by liquid chromatography–mass spectrometry using a macrocyclic antibiotic (Vancomycin) chiral stationary phase column. Journal of Chromatography B, 814 (2005) 75–81. [pdf]
4. The use of proteomics for the assessment of clinical samples in research. Clinical Biochemistry 37 (2004) 943– 952. [pdf]
5. Use of Metabonomics to Identify Impaired Fatty Acid Metabolism as the Mechanism of a Drug-Induced Toxicity. Chem. Res. Toxicol. 2004, 17, 165-173. [pdf]
6. Application of high-throughput Fourier-transform infrared spectroscopy in toxicology studies: contribution to a study on the development of an animal model for idiosyncratic toxicity. Toxicology Letters 146 (2004) 197–205. [pdf]
7. Depletion of the high-abundance plasma proteins. Amino Acids (2004) 27: 249–259. [pdf]
8. Ion activation methods for tandem mass spectrometry. J. Mass Spectrom. 2004; 39: 1091–1112. [pdf]
9. Triple quadrupole linear ion trap mass spectrometer for the analysis of small molecules and macromolecules. J. Mass Spectrom. 2004; 39: 845–855. [pdf]
10. Quantitative determination of a novel dual PPAR alpha/gama agonist using on-line turbulent flow extraction with liquid chromatography–tandem mass spectrometry. Journal of Chromatography B, 814 (2005) 29–36. [pdf]
11. Recent methodological advances in the mass spectrometric analysis of free and protein-associated 3-nitrotyrosine in human plasma. Journal of Chromatography B, 814 (2005) 1–9. [pdf]
12. Using NMR for ligand discovery and optimization. Current Opinion in Chemical Biology 2004, 8:387–391. [pdf]
13. Proteomic approaches in the search for disease biomarkers. Journal of Chromatography B, 814 (2005) 11–19. [pdf]
14. Bioinformatics strategies for proteomic profiling. Clinical Biochemistry 37 (2004) 636– 641. [pdf]
15. NMR Spectroscopy Tools for Structure-Aided Drug Design. Angew. Chem. Int. Ed. 2004, 43, 290 – 300. [pdf]
16. Theory and Applications of NMR-Based Screening in Pharmaceutical Research. Chem. Rev. 2004, 104, 3641-3675. [pdf]
17. FTICR-Mass Spectrometry for High-Resolution Analysis in Combinatorial Chemistry. BIOTECHNOLOGY AND BIOENGINEERING (COMBINATORIAL CHEMISTRY), VOL. 71, NO. 2, 2000/2001, 149-161. [pdf]
18. Development of a LC-LC-MS complete heart-cut approach for the characterization of pharmaceutical compounds using standard instrumentation. Journal of Pharmaceutical and Biomedical Analysis 31 (2003) 1153-1166. [pdf]
19. Delineating Novel Metabolic Pathways of DPC 963, a Non-Nucleoside Reverse Transcriptase Inhibitor, in Rats. Characterization of Glutathione Conjugates of Postulated Oxirene and Benzoquinone Imine Intermediates by LC/MS and LC/NMR. Chem. Res. Toxicol. 2002, 15, 388-399. [pdf]
20. Drug-Protein Adducts: An Industry Perspective on Minimizing the Potential for Drug Bioactivation in Drug Discovery and Development. Chem. Res. Toxicol. 2004, 17, 3-16. [pdf]
21. Detection of Covalent Adducts to Cytochrome P450 3A4 Using Liquid Chromatography Mass Spectrometry. Chem. Res. Toxicol. 2004, 17, 1356-1361. [pdf]
22. Strategies for dealing with metabolite elucidation in drug discovery and development. DDT Vol. 9, No. 7 April 2004. [pdf]
23. Fourier transform infrared evaluation of microscopic scarring in the cardiomyopathic heart: Effect of chronic AT1 suppression. Analytical Biochemistry 316 (2003) 232–242. [pdf]
24. METABOLIC PROFILES OF CANCER CELLS. Nature Reviews Cancer 2004, 4, 551-561. [pdf]
25. Proteomic Applications for the Early Detection of Cancer. Nature Reviews Cancer 2003, 3, 267-275. [pdf]
26. Peptide and protein sequence analysis by electron transfer dissociation mass spectrometry. PNAS 2004, 101(26), 9528-9533. [pdf]
27. Mass Spectrometry Sampling Under Ambient Conditions with Desorption Electrospray Ionization. Science 2004, 306, 471-473. [pdf]
28. Mass Analysis at the Advent of the 21st Century. Chem. Rev. 2001, 101, 571-606. [pdf]
29. Molecular profiling approaches for identifying novel biomarkers. Expert Opin. Drug Saf. 2004, 3(2), 137-151.[pdf]
30. Exploratory Clinical Testing of Neuroscience Drugs. Nature Neuroscience Supplement, 2002, 5, 1023-1025. [pdf]
31. Clinical biomarkers in drug discovery and development. Nature Reviews Drug Discovery, 2003, 2, 566-580. [pdf]
32. High-Throughput Method for N-Terminal Sequencing of Proteins by MALDI Mass Spectrometry. Anal. Chem. 2005, 77,645-651. [pdf]
33. Evaluation of the Orthogonal Projection on Latent Structure Model Limitations Caused by Chemical Shift Variability and Improved Visualization of Biomarker Changes in 1H NMR Spectroscopic Metabonomic Studies. Anal. Chem. 2005, 77,517-526. [pdf]
34. Direct Characterization of Enzyme–Substrate Complexes by Using Electrosonic Spray Ionization Mass Spectrometry. Angew. Chem. Int. Ed. 2005, 44, 913 –916. [pdf]
35. Critical Review of Development, Validation, and Transfer for High Throughput Bioanalytical LC-MS/MS Methods. Current Pharmaceutical Analysis, 2005, 1, 3-14. [pdf]
36. Psychoanalytical Electrochemistry: Dopamine and Behavior. Analytical Chemistry, 2003, September, 414-421. [pdf]
37. Chiral Analysis by MS: A new quantitative method that is simple and rapid and uses very little sample. Analytical Chemistry, 2003, January, 25-31. [pdf]
38. Clinical Proteomics: Are We There Yet? Analytical Chemistry, 2003, November, 472-476. [pdf]
39. Electron ionization for LC-MS. Analytical Chemistry, 2003, December, 497-503. [pdf]
40. SELDI-TOF MS for Diagnostic Proteomics. Analytical Chemistry, 2003, April, 149-155. [pdf]

Useful Links