Get the Most Out of Your MSDYour MSD ChemStation the Most Out of Your MSDYour MSD ChemStation Tips...

download Get the Most Out of Your MSDYour MSD ChemStation the Most Out of Your MSDYour MSD ChemStation Tips and Tricks for GC/MS Anthony Gray Product Manager GC/MS SoftwareGC/MS Software November

of 65

  • date post

    30-Apr-2018
  • Category

    Documents

  • view

    234
  • download

    2

Embed Size (px)

Transcript of Get the Most Out of Your MSDYour MSD ChemStation the Most Out of Your MSDYour MSD ChemStation Tips...

  • Get the Most Out of Your MSD ChemStationYour MSD ChemStation

    Tips and Tricks pfor GC/MS

    Anthony GrayProduct ManagerGC/MS SoftwareGC/MS SoftwareNovember 17, 2009

    Agilent Experts EverywhereAgilent Experts Everywhere

  • Who really did this

    Agilent MSD ChemStation experts everywhere. Your local service engineer application engineer and Agilent ChemAssist Your local service engineer, application engineer, and Agilent ChemAssist GC/MS Software Developers Other ChemStation users

    Without the above, there would be no tricks and tips to

    b tt tili MSDbetter utilize your MSD ChemStation

    2

  • Outline

    1) Method Developmenta) AutoQuant setup (do before AutoSIM)a) AutoQuant setup (do before AutoSIM)b) SIMOptimizationc) AutoSIMd) S h SIM/Sd) Synchronous SIM/Scan

    2) Acquisition3) Data Analysis3) Data Analysis

    4) Reporting5) Troubleshooting5) Troubleshooting6) Macros

    3

  • AutoQuant

    An easy Four step process to build your Quant method.1 Load a data file that contains a measured standard of the compounds1. Load a data file that contains a measured standard of the compounds

    you want to calibrate.2. Enter the common information for all compounds you will list in your

    quantitation database on the Quantitation Global parameters page andquantitation database on the Quantitation Global parameters page, and click OK.AutoQuant automatically begins looking for significant peaks in the data fil F h k it fi d it th d t ith th ifi d libfile. For each peak it finds, it compares the data with the specified library, and displays the compound on the Choose Compound Name screen.

    3. Select Compound options Add, Skip, ISTD.

    Do you want to Quantitate Now?

    4

  • How does AutoQuant Setup work?

    AutoQuant Setup identifies the compounds in your data file using the spectral library you specify and chooses the target ion g p y y p y gand qualifying ions for each compound based on their abundance in the compound. Once you agree to the choices, AutoQuant Setup will automatically complete the necessaryAutoQuant Setup will automatically complete the necessary entries in your quantitation database.

    Tip: AutoQuant will allow you to specify a compound as a ISTD, but you must associate target compounds manually.y g p y

    Tip: Run AutoQuant, IonOptimization, and AutoSim in series for easy method creation.

    5

  • Ion How do I know what the Quant ions to use? IonOptimization can make these decisions easier.IonOptimization can make these decisions easier.

    Largest Ion Mode Ion Optimized280002800028000

    77 Q220000

    24000

    28000

    77 Q220000

    24000

    28000

    77 Q220000

    24000

    28000

    12000

    14000

    182 T12000

    14000

    182 T12000

    14000

    12000

    14000

    182 TQ

    94 Q3

    12000

    16000

    20000 Q

    94 Q3

    12000

    16000

    20000 Q

    94 Q3

    12000

    16000

    20000

    6000

    8000

    10000

    198 Q3

    272 Q2

    303 Q1

    6000

    8000

    10000

    198 Q3

    272 Q2

    303 Q1

    6000

    8000

    10000

    6000

    8000

    10000

    198 Q3

    272 Q2

    303 Q1

    82 T

    400

    8000

    82 T

    400

    8000

    82 T

    400

    8000

    2000

    4000

    6000 272 Q2

    2000

    4000

    6000 272 Q2

    2000

    4000

    6000

    2000

    4000

    6000 272 Q2

    182 Q1

    8.6 8.8 9.0 9.2 9.4 9.6

    00

    182 Q1

    8.6 8.8 9.0 9.2 9.4 9.6

    00

    182 Q1

    8.6 8.8 9.0 9.2 9.4 9.6

    00

    0

    8.6 8.8 9.0 9.2 9.4 9.6

    0

    8.6 8.8 9.0 9.2 9.4 9.6

    00

    8.6 8.8 9.0 9.2 9.4 9.6

    6

  • What is Ion Optimization?

    A mechanism for optimizing the selection of ions used for quantitation based on similar

    l d b i d Abundance

    Cocaine Reference SpectrumBig 4 ions in red

    Abundancerules used by experienced method developers.

    Method detection limits can be improved, and the occurrence

    8000

    9000

    Abundance82 (Target)

    182 (Q1)

    8000

    9000

    Abundance82 (Target)

    182 (Q1)

    of both false positives and negatives can be reduced.

    For methods with large numbers of analytes, the

    5000

    6000

    7000

    8000

    94 (Q3)

    77 (Q2)

    5000

    6000

    7000

    8000

    94 (Q3)y ,macro can do in seconds what would have required days by previous means.

    Available as macro prior to 20003000

    4000

    5000

    105

    42

    3032000

    3000

    4000

    5000

    105

    42

    303Available as macro prior to E.02.01.

    Will be included as product feature in E.02.01

    40 60 80 100 120 140 160 180 200 220 240 260 280 3000

    1000

    2000

    m/z -- >

    303

    122 198272

    40 60 80 100 120 140 160 180 200 220 240 260 280 3000

    1000

    2000

    m/z -- >

    303

    122 198272

    m/zm/z

    7

  • B h i th it i f77 Q2

    94 Q31600020000

    24000

    28000

    77 Q2

    94 Q31600020000

    24000

    28000Biggest ionsmode

    77 Q2

    94 Q31600020000

    24000

    28000Example of Ion Optimization

    By changing the criteria for selecting a SIM ion, the effect of interferences can be minimized. Chooses the ions based on b d d f i t f

    82 T

    182 Q1

    94 Q3

    8.6 8.8 9.0 9.2 9.4 9.60

    4000

    8000

    12000

    16000

    82 T

    182 Q1

    94 Q3

    8.6 8.8 9.0 9.2 9.4 9.60

    4000

    8000

    12000

    16000

    82 T

    182 Q1

    94 Q3

    8.6 8.8 9.0 9.2 9.4 9.60

    4000

    8000

    12000

    16000

    abundance, degree of interference, and mass.

    Seen here is an example of how changing which ions are considered

    94 Q32000024000

    28000

    Macro moves 182 to tgt, replaces 77 with 83. Q t ith 182 ill b

    94 Q32000024000

    28000

    Macro moves 182 to tgt, replaces 77 with 83. Q t ith 182 ill b

    Opt 25%

    94 Q32000024000

    28000

    Macro moves 182 to tgt, replaces 77 with 83. Q t ith 182 ill bchanging which ions are considered

    for SIM can change the performance. This example shows the interference of arachidonic acid with the analysis of cocaine (fatty

    83 Q2182 T

    82 Q1

    0

    4000

    8000

    12000

    16000 Quant with 182 will be much cleaner

    83 Q2182 T

    82 Q1

    0

    4000

    8000

    12000

    16000 Quant with 182 will be much cleaner

    83 Q2182 T

    82 Q1

    0

    4000

    8000

    12000

    16000 Quant with 182 will be much cleaner

    with the analysis of cocaine (fatty acid interference is a common problem in blood extracts).

    Trick: The ions selected using Ion

    8.6 8.8 9.0 9.2 9.4 9.68.6 8.8 9.0 9.2 9.4 9.68.6 8.8 9.0 9.2 9.4 9.68.6 8.8 9.0 9.2 9.4 9.6

    10000

    12000

    14000

    182 T303 Q1

    Macro replaces 82, 77, and 94 with 303, 198, 10000

    12000

    14000

    182 T303 Q1

    Macro replaces 82, 77, and 94 with 303, 198,

    Opt 7%

    10000

    12000

    14000

    10000

    12000

    14000

    182 T303 Q1

    Macro replaces 82, 77, and 94 with 303, 198, g

    Optimization can also be transferred to a acquisition SIM method . further enhancing the sensitivity and robustness of the

    0

    20004000

    6000

    800010000

    198 Q3272 Q2

    303 Q1 , ,and 272. Target and qualifiers are now much cleaner.

    0

    20004000

    6000

    800010000

    198 Q3272 Q2

    303 Q1 , ,and 272. Target and qualifiers are now much cleaner.

    0

    20004000

    6000

    800010000

    0

    20004000

    6000

    800010000

    198 Q3272 Q2

    303 Q1 , ,and 272. Target and qualifiers are now much cleaner.

    yGC/MSD method.

    08.6 8.8 9.0 9.2 9.4 9.6

    08.6 8.8 9.0 9.2 9.4 9.6

    008.6 8.8 9.0 9.2 9.4 9.6

    8

  • What does Ion Optimization do?

    Chooses the best ions (highest signal to noise) from the allowable ions in the target

    Signal/Noise Ratio

    InterferenceNoise

    Cocaine abd

    Cocainem/zg

    spectrum.

    Options:

    Cutoff mass (the minimum

    821827794

    1058342 (out)

    10000844951764624414435132632

    173180

    6588395984031582885

    5.78105.610.791.170.492.222 97

    25%

    T

    Q3

    Q2

    Q1TQ2

    T

    Cutoff mass (the minimum relative abundance for an ion, i.e. 25%, 10%, 7%.Minimum Mass: The mass threshold no masses below

    42 (out)96

    303518197

    122

    263224821852159111311131971

    885149276

    55268641097805

    2.971.66

    24.432.880.161.031.21

    Cutoff

    Q1Q3

    10% Cutoff

    Q1

    threshold no masses below this will be considered despite what the S/N ration may be.U M W i hti Add

    1981835541 (out)

    2726867

    961931831781751721651

    945127027872936

    167512884

    10.281.820.120.09

    20.750.430 05

    7% Cutoff

    Q3

    Q2

    Use Mass Weighting: Adds a mass factor to the S/N ratio favors higher masses in the decision.

    67 651 12884 0.05Cutoff

    9

  • Ion Optimization clearly better quantitation

    Largest Ion Mode Ion Optimized280002800028000

    77 Q220000

    24000

    28000

    77 Q220000

    24000

    28000

    77 Q220000

    24000

    28000

    12000

    14000

    182 T12000

    14000

    182 T12000

    14000

    12000

    14000

    182 TQ

    94 Q3

    12000

    16000

    20000 Q

    94 Q3

    12000

    16000

    20000 Q

    94 Q3

    12000

    16000

    20000

    6000

    8000

    10000

    198 Q3

    272 Q2