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SCU LC-MS Agilent 6100 training_060710


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Agilent 6100 training course

Agilent 6100 training course

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  • 1. Introduction to LC-MS using the
    SCU Agilent 6100 Single Quadrupole
  • 2. Introduction
    Training outline
    LC-MS introduction
    Basics of LC-MS as Analytical Technique
    Introduction to the Agilent 6100
    Running a sample
    Data Analysis : Qualitative and Quantitative analysis
    Best Practices: Operating/Troubleshooting
    What does LC-MS stand for??
    Liquid Chromatography
    – Mass Spectroscopy
  • 3. Introduction
  • 4. Introduction
    Requirements of an Analytical technique:
    What are the questions we expect an Analytical technique to answer?
    What is in the sample? Qualitative analysis
    e.g. Was there really caffeine in that coffee?
    2) How much is present? Quantitative analysis
    e.g. How much caffeine is present?
    Analytical technique needs to identify the component unambiguously, needs to be sensitive, reproducible and needs to complete analysis within a reasonable time cost and ease of use.
  • 5. Introduction
    Pharmaceutical sciences
    -Metabolic Profiling
    -Identification and purity
    -Pharmacokinetic profiling
    Forensic sciences
    Performance enhancing drugs: cortiosteroids
    -Adulterants in consumer products: Bisphenol A
    Clinical Sciences
    -Metabolic Disorders
    -Therapeutic Drug monitoring
    Environmental Chemistry
    -EPA Appendix VIII
    -Pollutants : chlorophenoxy herbicides
    Biochemistry and Biotechnology
    -Post translational modifications
    -Non covalent complexes
    -Peptide mapping
    Synthetic Chemistry
    -Combinatorial Libraries
    -Reaction products
    Food Chemistry
    -Drug residues: Bovine hormones
    -Artificial Sweeteners
    -Flavor components: wine antioxidants
    -Fungal metabolites: mycotoxins
    Petroleum Chemistry
    -Oil exploration
    - Fractionation of oil : Polycyclic aromatics
  • 6. Basics of LC-MS
    MS (Mass Spectrometry)
    Mass spectrometry is the study of systems causing the formation of gaseous ions, with or without fragmentation, which are then characterized by their mass to charge ratios (m/z) and relative abundances.
    LC (Liquid Chromatography)
    • HPLC is a method of separating and identifying the components of a complex mixture by differential movement through a two-phase system, in which the movement is effected by a flow of a liquid (mobile phase) which percolates through an adsorbent (stationary phase) at high pressure.
  • Basics of LC-MS
    HPLC : High Pressure Liquid Chromatography – forerunner and component of LC-MS detection
    • A Liquid (mobile phase) is forced through a column containing a stationary phase.
    • 7. A small amount of sample introduced by injector will separate into discrete components
    based on their affinity for stationary or mobile phase.
    • Most common means of detecting components eluting from column is by
    Ultra-violet (UV) detection.
    • > 80% of HPLC is Reverse phase HPLC.
    • 8. > 80% of Reverse phase HPLC utilizes buffered mobile phases which may or may not be
     > 80% of Reverse phase separations are on 150- 50 x 4.6 mm columns with a flow
    Rate of 1.5-0.5 ml/min.
    • Many Reverse phase separations are by gradient high % Aqueous (Mobile phase A)
    to high % Organic (Mobile phase B).
  • 9. LC-MS-UV
    Basics of LC-MS
    Ion source:makes ions
    HPLC:provides separation
    Mass Analyzer:
    Separates ions
    Detection Device
    Time of Flight
    Ion Trap
    Reverse Phase
    Ion Chromatography
    Aqueous Normal Phase
    Mass spectrum
    LC-MS Chromatogram
    Providing separation
    of components and
    mass spectrum of each.
  • 10. Basics of LC-MS
    Making ions: Process of Ionization
    If a quantity of energy is supplied to a molecule equivalent to the ionization energy of the molecule, a molecule ion is formed M+.
    Mechanism of LC-MS Electrospray ionization
    • HPLC outlet usually 0.5-1.5 ml/min is split (1:9) to enter capillary into MS source.
    • 11. Stream of solution sprayed out of capillary at high voltage (ca. 3 – 5 kV).
    • 12. Charged droplets formed by spray.
    • 13. Solvent evaporated by stream of warm N2.
    • 14. As droplet shrinks, charge density increases until analyte ions ejected.
    • 15. Pseudomolecular [M+H]+ - positive mode or [M-H]-ions formed or water adducts.
    • 16. Solvent pumped away and ions admitted to mass spectrometer.
  • Basics of LC-MS
    Mechanism of LC-MS Electrospray ionization
    • HPLC outlet usually 0.5-1.5 ml/min is split (1:9) to enter capillary into MS source.
    • 17. Stream of solution sprayed out of capillary at high voltage (ca. 3 – 5 kV).
    • 18. Charged droplets formed by spray.
    • 19. Solvent evaporated by stream of warm N2.
    • 20. As droplet shrinks, charge density increases until analyte ions ejected.
    • 21. Pseudomolecular [M+H]+ - positive mode or [M-H]-ions formed or water adducts.
    • 22. Solvent pumped away and ions admitted to mass spectrometer.
  • Separating the ions
    Basics of LC-MS
    Mass analyzers scan or select ions over a particular m/z range. The key feature of all mass analyzers is their measurement of m/z, not mass.
    The Quadrupole
    But how does a Single Quad work anyway?
    It is a filter. The ions are passed through a time varying field generated by opposing potentials
    on a set of opposing rods (the quadrupole). This creates a “mass filter” where ions of different
    Mass/charge ratio are sequentially focused on a detector. A complete Scan through a mass
    Range e.g. (100-1000 amu) takes usually <1 sec. Single Quads are usually operated in
    Full Scan mode and produce a chromatogram referred to as a TIC- Total Ion Chromatogram.
    However they can be operated in SIM mode – Single Ion Monitoring where the quadrupole
    only allows a small number of preselected m/z values to reach the detector generating a
    SIC- Single Ion Chromatogram.
  • 23. Basics of LC-MS
    In general TIC data is more favored than SIM data since it contains all the m/z values
    For the eluting components. TIC’s are often processed to give Extracted Ion Chromatograms
    -EIC – where the trace for only one m/z value is “extracted” from the TIC highlighting the
    presence of a component of interest.
    TIC and EICs of carbamate pesticides spiked in a tomato extract
  • 24. Basics of LC-MS
    So why all the fuss?
    LC-MS with Electrospray detection is
    - Very Selective, 2 stages of separation – chromatography and mass analyzer.
    It can find the needle in the haystack.
    • Very Sensitive: in best conditions and most sensitive detection mode
    LC-MS quadrupole can detect at 0.1 -1.0 pg levels. VERY SENSITIVE.
    Weight of 3 cell of E. Coli = 3 pg; 1 pollen grain (Alder tree) =9,700 pg;
    1 typical fingerprint = 50, 000, 000 pg; Average amount of erythromycin
    in surface water (as per USGS) = 1 pg/uL.
    • Electrospray ionization can produce multiply charged ions – protein analysis.
    • 25. Is concentration dependant- can be used for quantitative analysis.
    • 26. Can be coupled to Reverse phase HPLC separations – amenable to analysis of
    a wide range of compounds.
    - It is an “Active” detection method.
  • 27. Basics of LC-MS
    LC-MS is an “Active” detection mode as opposed to LC-UV.
    The interface accomplishes the physiochemical process of ionization, evaporation, pressure reduction, and in some cases molecular fragmentation.
    These can be affected profoundly by Solution phase chemistry –pH, and mobile phase composition.
  • 28. Intro to Agilent 6100
    Agilent LC-MS 6100 : where do I start?
    UV detector
    Solvent reservoirs
    Column compartment
    Mass Spectrometer
    Mass Analyzer and detector
    Data System
    Ion Source
    Reference: Agilent 6100 Series Quadrupole LC/MS system,
    Concepts guide.pdf, Quickstart guide.pdf, Familiarization guide.pdf
  • 29. Intro to Agilent 6100
    Introduction to the Chemstation software
    Method and Run control tab
  • 30. Intro to Agilent 6100
    • Start up and place the instrument in standby
    • 31. Set up methods to control LC, ion source and MS
    • 32. Run single samples
    Run a sample set – a “sequence”
    View data in real time
    • View chromatograms and spectra from the
    MS and UV detectors
    • Integrate chromatographic peaks
    • Perform quantitation
    • Check peak purity
    • Deconvolute multiply charged spectra
    • Generate reports
    • Design custom report templates
    • Verify system performance
    • Perform tests to demonstrate compliance with regulatory requirements
    • Perform diagnostic tests
    • Vent and pump down Mass spectrometer
    • Optimize and calibrate the MS
  • 33. Intro to Agilent 6100
    1 Ensure that you are wearing your PPE and Lab glasses.
    2. Observe instrument and workspace - Did previous operator complete shutdown?
    Are all the components present- e.g. HPLC column? Is LC connected to MS through a split?
    Are solvent reservoirs for HPLC full with appropriate mobile phase? Are the Autosampler wash bottles full?
    Is workspace clean? Are all components powered up? Any visible red lights on instrument?
    3. In the software ensure that you are in the in the Method and Run Control Tab
    4. From the Method and Run Control view, click the button on the system
    status bar to activate the system.
    5. Ensure all components are “green” - Autosampler, Pump, UV, MS.
    6. Depending on how long the system has been idle, one can warm up/
    “equilibrate” the system by turning on the HPLC pump – Instrument/Pump at a low
    flow- ca. 0.5 ml/min- for 15 min. And/or one can run 1-2 blanks.
    - standby mode
    Suggested exercises:
    Startup instrument and observe at rest values for LC pressure and MS vacuum. Equilibrate system for 10 minutes and observe values. Are those values normal? – Refer Familiarization guide.
  • 34. Method and Run Control
    Running the 6100
    Agilent 6100: loading methods and running a single sample
    Ensure that you have completed LC-MS Startup procedure.
    Activate the single sample toolset by clicking the button on the toolbar.
    Load a method by selecting Method/Load method or by clicking the the
    3. If you need to create new method, load “DEF_LC.M” and save as a new name, e.g. “pc061010_sulfa_analysis_1.M”
    4. To edit the method use Method/Edit entire method or icon. A series of dialog boxes
    will appear allowing you to set and save desired parameters for Autosampler, LC, UV and MS. Make changes and save method.
    5. Place the sample vial in position as you specified in the autosampler method parameters
    and click the Start button
    Suggested exercises:
    - Create a method with your initials and date e.g. PC060710_1 using suggested parameters given in Sample Experiment 1
  • 35. Data Analysis
    Agilent 6100 Data Analysis view
  • 36. Data Analysis
    Agilent 6100: loading data files
  • 37. Data Analysis
    Agilent 6100: Qualitative information from your loaded chromatogram
    m/z 271
    Mass Spectrum of
    component eluting at 1.885 min
    Fragment ion
    m/z 156
    m/z 156
    1. Use the cursor to expand the chromatogram in the Data Analysis view.
    2. Use the Spectrum Icon from the tool bar to click on the peak to obtain a Mass
    Spectrum of the component eluting at that time point.
    3. This provides Qualitative information – molecular ion and characteristic fragment
    Of the component eluting at 1.85 minutes- Sulfamethiozole.
  • 38. Data Analysis
    Agilent 6100: Generating EIC (Extracted ion chromatogram) data
    Use File/Load signal to load your initial TIC
    Use File/Extract Ions to extract ions
    Enter the desired m/z values in the dialog box and click OK
    EIC’s will be displayed within same window as TIC as shown below
    Qualitative Analyses suggested exercises:
    1) Complete exercises 1-3 Pages 30-41 6100 Familiarization guide for analysis of sulfonamide
  • 39. Data Analysis
    Agilent 6100: Quantitative Analysis
    Quantitation is the process of determining how much compound is present in a sample.
    In LC-MS this is achieved usually by comparing Peak areas of component in your sample
    with the area generated by a standard or set of standards of known concentrations. Peak
    Areas are generated by integration for which the correct parameters must be set
    Use File/Load signal to load the TIC for your lower level standard.
    Use File/Extract Ions to generate EIC suitable for quantitation.
    Click on the icon to activate Integration tool set.
    Click on the auto integrate tool to complete initial integration.
    Click on the Icon Edit Integration table which displays below screen and
    Adjust integration events manually if auto integration is unsuitable.
    6. Save this integration method as part of your overall LC-MS method.
  • 40. Data Analysis
    Agilent 6100: Quantaitative Analysis
    Quantitation of samples may be done by activating the calibration
    Icon and tool set.
    2. A calibration curve table may then be constructed by loading signals for standards
    and entering the known concentrations as shown below for caffeine.
    3. This generated calibration may then be used to quantitate samples ran within the
    Sample set for which peak areas have been calculated
    Qualatative Analyses suggested exercises:
    1) Complete exercises 1 & 2 Pages 63-76 Agilent 6100 Familiarization guide quantitation of caffeine.
  • 41. Best practices
    Operational Best Practices
    - Ensure your sample is soluble in the diluent you use for preparation.
    - Filter you sample.
    - Make up your sample in as close to 100% Mobile phase A as possible.
    • Do not inject “dirty” samples onto LC-MS without a sample preparation e.g. plasma, plant extract etc.
    • 42. Do not inject too concentrated sample, 1-5 μg/ml (ca. 10 μM, MW 350-500) is normal for single quad operating in full scan mode.
    • Use only HPLC grade solvents and deionized water.
    • 43. Use only LC-MS “friendly solvents”!- 0.05% HCOOH/H2O Mobile phase A and 0.05% HCOOH/CAN Mobile phase B as your default mobile phase.
    - Designate a performance standard, Inject weekly and keep a performance
    log of instrument.
    • Make sure your system is equilibrated, run 2 blanks if beginning from a
    cold system.
    - Flush the system with 50:50 ACN: H2O if leaving in standby for a longer period.
    - Ensure that the split deliver flow rate to the electrospray source of 0.08-0.15 ml/min.
  • 44. Best practices
    Trouble shooting
    No Signal- no peaks? Or very low signal?
    - Check that LC flow is normal and back pressure is normal and steady.
    - Check that there is spray from the nebulizer.
    - Check that you have vial in correct position and that enough sample is present.
    - Check LC-UV chromatogram, are peaks present?
    - Check that ion Source parameters – Capillary Voltage, Drying gas flow and temp
    are set to normal ranges.
    - Check that you are running a full scan method in the expected range for your analyte.
    - Check that your sample is fresh- prepare fresh standard if in doubt.
    - Consider your solution phase chemistry. Are you providing sample to MS in a volatile
    solvent at a pH which promotes ionization?
    - Remove source and check orifice entrance. Has it become blocked?
  • 45.
  • 46. 29
    • Amu—atomic mass unit/Dalton
    • 47. M+˙, molecular ion—the ionized molecule; the molecular ion peak is the peak representing the ionized molecule that contains only the isotopes of natural abundance
    • 48. Base Peak—the peak in the spectrum that represents the most abundant ion
    • 49. Daughter Ion—the product produced by some sort of fragmentation of a larger ion
    • 50. Isotopic Peak—a peak in the spectrum that corresponds to the presence of one or more heavier isotopes of an ion
    • 51. “A” Element—an element that is monoisotopic
    • 52. “A + 1” Element—an element with an isotope that is 1 amu above that of the most abundant isotope, but which is not an ‘A + 2’ element
    • 53. “A + 2” Element—an element with an isotope that is 2 amu above that of the most abundant isotope
  • Sample Experiment 1: Separation and Qualitative Analysis of Sulfonamide compounds by LC-MS in Full Scan positive ion mode
    Sulfonamide drugs were the first antimicrobial drugs, and paved the way for the antibiotic revolution in medicine.
    To implement an LC-MS full scan method which is capable of separating and
    Identifying four sulfonamide drugs. To report method sensitivity.
    Figure 1. Four sulfonamides present in of Electrospray LC Demo kit sample
  • 54. General Instructional Objective
    Students shall gain the basic competency of Agilent 6100 hardware and software to
    complete an LC-MS Electrospray separation of a multi-component mixture according
    to an established procedure. Students shall further develop the skills to identify the
    components and determine the method sensitivity with established parameters.
    Specific Instructional Objectives
    Students will learn how to prepare and LC-MS sample.
    Students will learn how to prepare the 6100 for operation.
    Students will learn how to create and save a method given the parameters.
    Students will learn how to inject successive samples as per established method.
    Students will learn how to process data to produce mass spectra and identify
    components in a mixture.
    Students will learn how to process data and plan further injections and dilutions to
    determine the limits of sensitivity of a method.
    Students will have completed initial 30 minute training session and 20 minute laboratory
    familiarization with the instrument.
    Future Objectives
    Depending on time constraints this experiment can be easily extended to investigate the
    effect of key ion source parameters (e.g. fragmentor voltage) on qualitative data or the
    effect of solution phase chemistry (different pH) on separation and sensitivity.
  • 55. Preparatory work.
    1. Fill mobile Phase A reservoir with deionized water/5 mM Ammonium Formate and
    mobile phase B with Methanol/5 mM Ammonium Formate .
    Place the Betasil C8, 50 x 2.1 mm, 3 micron HPLC column in correct position in the
    column compartment.
    Start up LC-MS-UV as described in initial training section.
    Experimental Procedure:
    Prepare a 1: 10 dilution of Electrospray LC Demo kit sample (which contains
    the four sulfonamides. Dilute 100 μL of the sample with 900 μL of
    90:10 Merhanol:water/5 mM Ammonium Formate. Filter this sample into a 1 ml
    autosampler vial. Concentration of the samples is then 10 ng/ml.
    Prepare a solvent blank by filtering 1 ml of 90:10 Methanol:Water
    /5 mM Ammonium Formate into a 1 ml autosampler vial.
    Load DEF_LC.M in Method and Run control tab .
    4 Save this method as SULFA_MS_SCAN_1.M
    Go to Set up Instrument method and click on Autosampler tab. Click Injection
    Volume and enter a value of 1uL into dialog box. Save.
    Click on the Pump tab in Set up Method and set up the following gradient
    parameters Flow = 0.4 ml/ml, Stop time = 10.0 min.
  • 56. Experimental Procedure- continued
    7. Set up the following gradient table:
    Time %A %B
    0.0 88 12
    1.0 88 12
    3.0 0 95
    6.0 0 95
    7.0 88 12
    10.0 88 12
    8. Leave DAD (UV) settings in Set up instrument method tab at default settings.
    9. Right click MSD icon and select Set Up MSD signals. Enter signal 1 in Scan mode,
    positive polarity. Enter the following parameters Scan range: 100-500;
    Fragmentor: 100 V; Gain: 1.0; Threshold: 150; Stepsize: 0.1.
    10. Set up Ion Source by right clicking MSD icon and Select Spray Chamber. Set Drying gas
    to 9L/min, Nebulizer to 40 psi, Drying gas to 300°C and Capillary voltage to 3000V.
    11. Save method and print for your experimental report.
    12. Place blank vial on position 1 of autosampler and run blank in single sample mode
    as described in your Initial training material.
    13. Place sulfonamide sample in position 2 and inject sample.
  • 57. 14. Post run Open data file in Data Analysis tab as described in initial training document.
    Print out TIC (as shown in Figure 1) and the Mass spectrum associated with each peak.
    Assign each peak in the TIC to determined sulfonamide.
    16. Dilute Sulfonamide sample and determine by subsequent injections the LOD
    Limit of detection (defined as 3 x Signal/noise) of each sulfonamide by this method.
    Figure 1: TIC of sulfonamide mixture in Fullscan positive mode at 10 ng/ml
    Reference: Agilent 6100 series Familiarization guide, Sections 2 and 3.
  • 58. Sample Experiment 2: LC-MS methods to support QbD (Quality by Design) approaches to Active Pharmaceutical Ingredient manufacturing.
    Gabapentin is an anticonvulsant medication indicated in the treatment of epilepsy and neuropathic pain. Since October 2004, It has been launched as a generic drug. This compound is an γ-amino acid which under the right circumstances may form a lactam as shown in Figure 1. The study of conditions which favor this process is of importance since the lactam displays a certain toxicity and must therefore be avoided as far as possible in the formulated drug. Recent FDA initiatives have suggested a Quality by Design (QbD) approach to minimizing the occurrence of such impurities in Drug products1. These studies have contrasted conventional approaches to minimizing such impurities (reduced expiration dates for batches, modified packaging, reduced storage temperatures) with a QbD approach (greater understanding of drug substance degradation pathways, and incorporating this understanding into formulating and manufacturing processes). This QbD approach stresses the need for more selective and sensitive Analytical methods to be applied to gain understanding of the conditions which lead to impurity formation.
    Figure 1. Gabapentin lactamization
  • 59. Introduction continued
    Pregabalin a related compound has also shown effectiveness as an anticonvulsant and is similarly capable of lactamization as shown in Figure 2.
    Figure 2. Pregabalin lactamization
    Previous analytical methods for assaying the kinetics have established that two acid base
    equilibria are involved as shown in Figures 3 and 4. These methods have relied on
    Fluorometric detection which required a derivatization step or NMR monitoring which
    lacked sensitivity
    Aim of Experiment
    To develop sensitive direct LC-MS methods capable of detecting and quantitating
    the lactam of Gabapentin and Pregabalin. To apply these methods to determine the
    rate of Lactam formation at pH 3.0 and 10.0 and at 37°C and 80°C
  • 60. Introduction continued
    Figure 3. Equilibrium between different forms of Gabapentin as a function of pH2.
    Figure 4. pH-rate profile for the lactamization of Gabapentin at 80°C
    and 0.5 M concentration3.
    FDA Advisory committee for Pharmaceutical Science and Clinical pharmacology meeting, April 14, 2010 meeting.
    2. Zambon et al, Tetrahedron, 2008, 64, 6739-6743
    3. Kearney et al, Int. J. of Pharm, 1992, 78, 25-34.
  • 61. General Instructional Objective
    Student will use previously developed expertise to develop sensitive LC-MS methods capable of detecting and quantitating the lactam of Gabapentin and Pregabalin. Student will apply these methods to determine the rate of Lactam formation at at pH 3.0 and 10.0 and at 37°C and 80°C and concentration of 0.5 M for both compounds.
    Specific Instructional Objectives
    Students will develop and optimize an LC-MS method to obtain best separation and
    sensitivity for the Gabapentin and Pregabalin lactam.
    Student will set up an experiment at two pH values and two temperatures investigating lactam formation from Gabapentin and Pregabalin.
    Student will sample the experiment at set time points and run the samples using the
    developed LC-MS method.
    Students will process the data and quantitate the amount of lactam formed over time at each condition.
    Student will use this data to determine First order rate constants.
    Of the conditions investigated, student will determine those which lead to a greater than 1% lactam formation and which should be avoided in a manufacturing process.
    Student will determine difference in lacatam formation between both amino acids under given conditions and account for this.
    Students will have completed LC-MS basic training and LC-MS experiment set 1
    as well as Pre reqs for Chem 111 and Chem 154
  • 62. Experiment Design
    Gabapentin/Pregabalindissolved in pH buffer at 0.5 M
    Incubation @ at pH 3.0 and 10.0
    and at 37°C and 80°C
    Reaction quenched at 10, 20, 40 and 60 minutes in ice bath
    10 x Dilution with 50:50 = H2O:ACN at neutral pH
    Analyzed with LC/MS method
  • 63. Preparatory work.
    1. Set up LC-MS as in Experiment 1.
    Obtain pH buffers and set up incubator at 37 and 80°C.
    Obtain 5M stock of Gabapentin and Pregabalin from Freezer.
    Obtain 0.5 M stock of Gabapentin lactam and pregabalin lactam from freezer.
    Install LC-MS divert valve.
    Set Autosampler to low temperature within sample method.
    Experimental Procedure:
    Dilute lactam stocks 10X and develop LC-MS fullscan positive mode separation as
    in Experiment 1. Determine Retention times to set divert valve switching time.
    Prepare standard setofGabapentin and Pregabalinlactam for quantitation.
    Dilute Gabapentin and Pregablin 10X into pH buffers and set on incubator.
    Sample at 10, 20, 40 and 60 minutes. Quench and dilute 10X as per scheme.
    4 Analyze standard set and time point samples by LC-MS method.
    Determine concentration of lactam present in each sample.
    Complete plot of ln [lactam] versus time and determine slope, which is equal to –k.
    Hint: LOD for both lactams on LC-MS should be in the region of 1-10 ug/ml.
    Notes: Depending on time constraints this experiment may be need to be divided into a
    Number of lab sessions- method development, experiment completion, analysis. It can also
    easily be simplified to 1 compound, 1 pH value or expanded to form a more detailed study.
  • 64. Acknowledgements
    Xenoport Analytical research team:
    Quincey Wu Senior Director Analytical Research.
    Bernd Jandeleit, Associate Director, Medicinal Chemistry.
    Mark Gallop, Senior Vice president, Research.
    Mark Gao, Staff Scientist, Analytical Research.