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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 2000
3000
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 Q316000
20000
24000
28000
77 Q2
94 Q316000
20000
24000
28000Biggest ionsmode
77 Q2
94 Q316000
20000
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 Q320000
24000
28000
Macro moves 182 to tgt, replaces 77 with 83. Q t ith 182 ill b
94 Q320000
24000
28000
Macro moves 182 to tgt, replaces 77 with 83. Q t ith 182 ill b
Opt 25%
94 Q320000
24000
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
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
10
Are there any tips to using Ion Optimization?
Settings are very matrix dependant. Some suggestions:• High “constant” matrix type: Use a low threshold• High, constant matrix type: Use a low threshold• Low, varying matrix: use a high threshold and the “high mass bias”
Tip: Multiple matrix files can be processed if you are expecting different matrix conditions to appear … the optimization will use the average of the interference in all files.
Trick: Use DRS to determine if matrix files are analyte free – the ti i ti k b t if th fil d d t t i t toptimization works best if the files used do not contain target
compounds (defined in the Quant method).
11
Setting up a SIM Method with AutoSIM.
Step 1 – Select “Method / Generate AutoSIM Method’ in Data Analysis
Step 2 – Define Automatic SIM parameters
Step 3 – Select SIM or SIM/Scan method for Acquisition
Step 4 – Select if default Quantitative method is SIM or Scan
Tip: The currently loaded method must have a quantitation database (it is not necessary to have calibration). AutoSIM uses all masses in the quantitation database to automatically generate a SIM acquisition method from thedatabase to automatically generate a SIM acquisition method from the quantitation method.
Trick: Select the quantitative method type with the most compounds – this will typically be SIM for target compound analysis – it is easier to go back and h th ll t t th th dchange the smaller set to the other mode.
Note: AutoSim only looks at the largest ions for selection. Agilent has a new tool available soon – Ion Optimization
12
Your GC/MSD can do SIM/Scan – but how easy is it to set up a method?to set up a method?The impact for SIM/Scan on the analysis is minimal, but the benefits are great.• Get the best sensitivity for target compounds with SIM.• Look for unknowns and interferences in Scan.
Trick: To auto set up quantitation with a SIM/Scan method, do a dummy SIM channel in preliminary Scan run (i.e. <insert quiet m/z>).
S STip: You can assign a Target compound to either the SIM or Scan channel.
Tip: NEVER SEPARATE THE SIGNALS using File/Select Signals.Tip: NEVER SEPARATE THE SIGNALS using File/Select Signals. You must keep the data Sim/Scan to see the proper signal descriptions in the EditCompounds panel.
13
Setting up a SIM/Scan method
Step 1 – Select Acquire Scan and SIM from the instrument parameters dialogp g
Step 2 – Edit the Scan parameters for the method
Step 3 – Edit the SIM Parameters for the methodStep 3 – Edit the SIM Parameters for the method
Ti Y t dit b th SIM d S t b f d iTip: You must edit both SIM and Scan parameters before doing an analysis
Tip: The real time display and Snapshot features use the ScanTip: The real time display and Snapshot features use the Scan data.
14
How about making changes to my GC method?
Use the Agilent Method Translation software.
You can use the method translation software to precisely scale• You can use the method translation software to precisely scale a GC/MS method (or GC) to different speeds, i.e. exactly three times faster.– This has been proven time and again in the Agilent
Application labs, specifically when building the Pesticide (G1672AA) and Tox (G1674AA) RTL Libraries(G1672AA) and Tox (G1674AA) RTL Libraries.
15
Outline
1) Method Development
2) Acquisition2) Acquisitiona) Intelligent Sequencingb) Column splittingb) Column splittingc) Column Backflushing
3) Data Analysis
4) Reporting
5) Troubleshooting5) Troubleshooting
6) Macros
16
Intelligent Sequencing
Intelligent Sequencing is a feature of DrugQuantthat makes "programmed" decisions based on p gthe quantitative and qualitative results of sample analysis. The "programming" is done by editing the intelligent sequencing portion of a method tothe intelligent sequencing portion of a method to set up the intelligent sequencing parameters and then setting up a batch analysis using the S l L T blSample Log Table.
(Online Help)( p)
17
Intelligent Sequencing Requires
Criteria for Blanks
Criteria for Controls
Criteria for Negativesg
Criteria for Specimens
(Criteria User Defined Parameters In Data Analysis)( y )
18
Intelligent Sequencing Parameters
19
Intelligent Sequencing
Trick – use keywords to enhance the actions of intelligent sequence• ClockSrt – Lets you specify a starting time (in 24 hour military time) for the next sample.
The starting time is entered into the keyword string.– Example: 16:30 - The next sample will be processed at 4:30 PM.
• Seedname– automatically generate names of the format ABCDExxx or ABCxxxDE.• <Tune Type> <Interval> - Performs selected AutoTune and optionally repeats the tune
at specified intervals. This is applicable for EI mode only.– Possible tune types are AUTO: Autotune, LOWMASS: Low Mass Autotune, STD:
Standard Spectra Tune, QUICK: Quick Tune, DFTPP: DFTPP Tune, BFB: BFB Tunep , , ,– For Example BFB 08:00 will execute BFB Target Tune when that line in the sequence
is encountered, and then again every 8 hours until the sequence completes.
Tip – The sequence table can create a new data path so you could separate two sets of data files in the same sequence run.
20
Using Column splitting
MSD ChemStation can handle both GC detector and MS signals easily in the same software.y
Trick – use FID to provide good semi quantitative results for unknowns detected on the GC/MSD.
Tip - Calibrate FID to get response per ng.–FID response per ng is almost constant for all compounds.–GC/MSD response per ng is not as constant.
21
Using Backflush
• More analyses per unit time . . . – Faster and more efficient separationsp– Shorter analysis cycle time (time from injection to injection)– Reduced requirement for sample preparation
• with consistently better results . . .with consistently better results . . . – Quantitative: accuracy, precision, detection limits, linear range– Qualitative: response ratios, confirmatory retention times, library
searches (eliminate false negatives and false positives)searches (eliminate false negatives and false positives)• while using less operator time for each analysis.
– Less time performing maintenance– Extensive computer control and data processing– Simplified operator review/approval
22
Shifting Retention Time and Higher Background (Baseline Increasing) with Multiple Analyses
Abundance
4.4e+074.6e+07
A: TIC: lettuce_blank.D\data.ms
B: TIC: lettuce_blank3.D\data.ms
After only 3 samples, the background is significantly
3e+073.2e+073.4e+073.6e+073.8e+07
4e+074.2e+074.4e 07
Data provided by MSD user in Almeria, Spain
g g yhigher (increase chemical noise is every spectrum)
1.8e+072e+07
2.2e+072.4e+072.6e+072.8e+07
3e+07B
A
400000060000008000000
1e+071.2e+071.4e+071.6e+07
Overlay of two chromatograms of a blank extract injected BEFORE (A) and AFTER (B) three injections without backflush
4.00 6.00 8.00 10.00 12.00 14.00 16.00 18.00 20.00020000004000000
Time
Overlay of two chromatograms of a blank extract injected BEFORE (A) and AFTER (B) three injections without backflush
23
With Backflush: No Increased Background (Less Spectral Noise) and Consistent Retention Times
4 2e+074.4e+074.6e+07
Abundance
TIC: lettuce_10_ppb.D\data.msTIC: lettuce_100_ppb.D\data.ms
Stable retention times and baseline less3 07
3.2e+073.4e+073.6e+073.8e+07
4e+074.2e+07 TIC: lettuce_5_ppb.D\data.ms
Data provided by user in Almeria, Spain
and baseline . . . less chemical noise
2e+072.2e+072.4e+072.6e+072.8e+07
3e+07
80000001e+07
1.2e+071.4e+071.6e+071.8e+07
4.00 6.00 8.00 10.00 12.00 14.00 16.00 18.00 20.000
200000040000006000000
Time
O l f th h t f l tt t t ith 2 i f b k fl hOverlay of three chromatograms of lettuce extract run with 2 min of back flush
24
Backflush with Purged Ultimate Union: Loss of Response without BackflushResponse without Backflush
with backflushwith backflush
without backflush
App Note 5989-9359EN
25
Backflush with Purged Ultimate Union: Loss of Response without BackflushResponse without Backflush
with backflushwith backflush
These were the first backflush results; the
without backflush
system is getting clearer
App Note 5989-9359EN
26
Outline
1) Method Development2) Acquisition2) Acquisition
3) Data Analysisa) Quant Calibration informationa) Quant Calibration informationb) Extended Quantc) Mix[A] and Mix[B]d) M l i i l Qd) Multi-signal Quant
4) Reporting5) Troubleshooting5) Troubleshooting6) Macros
27
Moving calibration Information to a different instrumentinstrumentThe calibration information of a method is contained in a file:
qdb mthqdb.mth
Copy and paste this file from the old method to the new method.
The calibration information is now in the new method• Compound List
C lib ti l l• Calibration levels
28
Extended Area Quantitation (Quant method default)
Trick – Do not use this mode unless you need to use relative peak area for qualifier ratio determination or are using peak p q g psummation for quantitation.
Tip - For EAQ to work properly, all of the extracted ions must be integrated properly.• Daunting when you have 100+ compounds in your qdb.
“The other modes are simpler, give the same results, and allow faster data re ie ”faster data review.”
29
Mix [A] and Mix [B]
Useful if you can’t run all standards in one mixture. Calibration will update only those components in each mixCalibration will update only those components in each mix.
Setup is two steps:In the Sample Misc field type “Mix[A] or “Mix[B]”In the Sample Misc field type Mix[A] or Mix[B]In the calibration table under “Compound Type”, type in “A” for the Mix A components or “B” for the Mix B components.p p
Trick: Up to five (5) different mixes can be specified in theTrick: Up to five (5) different mixes can be specified in the sequence i.e. Mix[A,C,F]. This allows you to update multiple mixes in one run.
30
Mix [A] and Mix [B]
File information Method information
31
Multi signal quantitation or SIM/Scan:Dos and Don’tsDos and Don tsDo not separate the signals.• Reload the data file after viewing as a snapshot• Reload the data file after viewing as a snapshot• Do not open via File / Select Signals
DO: define the integration parameters for each signal … editing g p g gthe parameters for signal 1 will not affect signal 2
Trick: Integration parameters can be defined at different levels:• Method integration – Note, only one integrator type per method.• Per Channel / signal• Per compound• Per Ion
32
Multi signal quantitation or SIM/Scan:More Dos and Don’tsMore Dos and Don tsTip: For GC/MS use the RTE integrator, even if you have GC data•For GC only, use the Genie integrator
Trick: You can process GC and GC/MS data from differentTrick: You can process GC and GC/MS data from different channels into one set of results.• If you have GC compounds calibrated using external standard, you can
have these in the Quant list, but define them first (before first MS ISTD compound).
33
Outline
1) Method Development
2) Acquisition2) Acquisition
3) Data Analysis
4) Reportinga) CalExcel.mac
)5) Troubleshooting
6) Macros
34
Trick – use CalExcel.mac
A macro that dumps the RRFs (or RFs) from a qdb into Microsoft Excel™. Excellent tool for getting the data to where you can plot it easily.• look at curve fits • eliminate specific calibration points or levels• eliminate specific calibration points or levels.CalExcel can also report the ISTD raw area.Very useful for reproducibility studies.Very useful for reproducibility studies. “I always use this for enviro work where I’m looking at 10 cal levels of 100+ compounds/level. There just is no simpler way to d it Y ’t d th d d l t k ith t thido it. You can’t do methods development work without this macro.” (Kai Meng – Agilent Application Engineer)
35
Outline
1) Method Development
2) Acquisition2) Acquisition
3) Data Analysis
4) Reporting
5) Troubleshootinga) Tune Historyb) Signal-to-noise history
6) M6) Macros
36
How do I view a history of my tune files?y y
Tune Reports
I I t t C t l iIn Instrument Control viewView …Tune and VacuumIn Tune ViewFile … View Tunes
37
The Tune History Report
38
How do I view a history of my signal-to-noise calculations?calculations?A history of the S/N calculations for a given method can be found under <method>.m• sn.csv
39
Outline
1) Method Development
2) Acquisition2) Acquisition
3) Data Analysis
4) Reporting
5) Troubleshooting
6) Macrosa) Automate common actionsb) Shortcuts & menu itemsc) Advanced, customized, & special features
40
Some useful macros to know
Instrument Control• EDP edit acquisition parameters screen is launched• EDP – edit acquisition parameters screen is launched• Scan:• Profile:
Data Analysis• For Enhanced mode or EnviroQuant you can easily switch views• Enhanced 1 – will swap to EnviroQuant view• Enhanced 2 – will swap to EnhancedQuant view
41
Some more useful macros to know
Macro writing Etc.• Symboldump complete list of macros and variables Will also show the• Symboldump – complete list of macros and variables. Will also show the
current state of the variables.• Stack – Data Analysis Variable Watch
Very useful for editing and writing macros.• Command – Lists commands and Functions available for your mode of
operation• SLOG – Creates error log when a Macro is being run.• Endlog – View the log file. Typical syntax: Slog 1, run macro, endlog
42
Addon Macros
User customizable pull down menu itemsUser customizable pull down menu items
Undocumented feature (until now)( )
43
History
For many years, Agilent has employed 'data centric' addonmacro recognition to Enhanced Mode Data Analysis.
The original intent was so customers could ADD menu items to their Data Analysis menu that would persist past a softwaretheir Data Analysis menu that would persist past a software upgrade.
Notice we didn't say CHANGE menus - we still reserve ALL ofNotice we didn t say CHANGE menus - we still reserve ALL of the MSD ChemStation menu items, but the addon mechanism puts new ones right before the Help menu.
44
How it works
It's the application's menu bar macro that recognizes if the addon macro(s) exist or not. If they do, they are loaded AND EXECUTED so the LAST procedure will always be called.
Keep in mind this mechanism can be used to merely addKeep in mind, this mechanism can be used to merely add MACRO commands to your CP space; if there are NO menu commands and a dummy macro procedure at the end, all that happens is the macro procedures in that addon macro get loaded.
45
How it is done
Each and every DATA ANALYSIS menubar macro (EnviroQuant, y (Enhanced, DrugQuant) looks for a DATA SPECIFIC (that is, gcor ms) macro named ADDON.MAC.
You get your 'data specificity' by locating that macro in either msdchem\msmacros (for MS data) or msdchem\gcmacros (for GC data). )
Can you “guess” where it needs to be for Drug mode?
Drug mode's special folder is msdchem\drugmacs and that'sDrug mode s special folder is msdchem\drugmacs, and that s where it needs to be.
46
Here's an example of a macro
name MyAddOn
menunew “Who's Stuff"
menucmd "Start Full Log","slog 1","slog 1"
menucmd "Show Current slog","endlog","endlog"
menusep
menucmd "Show Vars","symboldump","symboldump"
menucmd "Show CMDS","commands","commands"
Return
This is ONLY a menubar macro.
47
User-controlled macro
There's also one other user-controlled macro that Data Analysis will LOAD, but NOT EXECUTE. ,
IF a file named DAEXTRA.MAC exists in the msdchem\msexefolder, it will be loaded during Data Analysis startup. It is intended to be used for storage of extra 'stuff' that the user may need to load up each time they start Data Analysis.
A ith th dd it i 't t f MSD Ch St tiAs with the addon macros, it isn't part of MSD ChemStation install so it will survive a software remove/reinstall - unless the entire msdchem folder is also removed. However, since this is a CUSTOMER macro, it should be backed up somewhere. This has been in the product since G1701CA.
48
Instrument Control
The menubar macro (the same one for all modes, (msexe\ic_menu.mac) search for a file named IC_ADDON.MAC in the INSTRUMENT FOLDER (i.e. msdchem\1). IF that file exists it's loaded AND EXECUTED just like in Data Analysisexists, it s loaded AND EXECUTED just like in Data Analysis.
49
menu commands AND a utility macro
name Doprof
• parameter full def 1 Notice here that there is a macro named Doprof at the top of the file This allows• icshow 0
• getconfig "atune.u"• profile full• gclear• icshow 1
t
Doprof at the top of the file. This allows the custom menu "do a PROFILE" to call a custom macro. Remember, the macro needs to be of the 'l d ' i t h th LASTreturn
name MyAddon
• menunew "Ken's IC addon stuff"
'load-n-go' variety, where the LAST procedure is always executed.
menunew Ken s IC addon stuff• menucmd "Show variables","remove","remove"• menucmd "Show commands","commands","commands"• menusep• menucmd "start logging","slog 1","slog 1"• menucmd "show logging","endlog","endlog"gg g g g• menusep• menucmd "do a PROFILE","Doprof 1","prof 1"return
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Quick Recap
Data Analysis will look for a file named ADDON.MAC in either msmacros, gcmacros, or drugmacs. If that file is present, it is , g , g p ,loaded and executed during the creation of the Data Analysis menubar object(s). This allows for data-specific menu additions and ALL instruments configured on that PC will haveadditions, and ALL instruments configured on that PC will have the same look for Data Analysis.
Instrument Control will look for a file named ICADDON.MAC inInstrument Control will look for a file named ICADDON.MAC in the INSTRUMENT FOLDER. If that file is present, it is loaded and executed during creation of the Instrument Control menubar object This allows for instrument specific menu additionsobject. This allows for instrument-specific menu additions.
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Adding right-click actions
You can add actions to the mouse right click:• In the DA Navigator edit “\msexe\treepopup mac”• In the DA Navigator edit \msexe\treepopup.mac• In the DA Graphics window, edit “\msmacros\PopUps.mac” or
“\gcmacros\PopUps.mac”.
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Outline
1) Method Development2) Acquisition) q3) Data Analysis4) Reporting5) Troubleshooting6) Macros7) Other Agilent tools
a) OpenLabs ECMb) Mass Profiler Professional)c) MassHunterd) Hardware options and technology
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What is OpenLAB ECM?Enterprise Content Managerp gA web-based electronic library that collects, organizes, indexes, stores, archives, and shares any electronic file.
OpenLAB ECM
• ArchiveArchive
• Automate
• Retrieve
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OpenLAB ECM – What is it in Detail?Central Data Management and Protectiong
ECM maintains all electronic data
Analytical Data– Analytical Data– Chromatographic result data– Pictures and graphic images – PDF documents und formulars– Email
Mi ft Offi fil– Microsoft Office files– Electronic reports– Any set of electronic data
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OpenLAB ECM – How can I find my Data?Fast Access to Data
Database Search for fast data retrieval:
– “Google” type quick search– “Extended” smart search– Advanced search with multiple
criteria
Example: Search for LC/MSD ChemStation data with sample name “AmoxiDegr” acquired Web Client Access to all dataAmoxiDegr acquired before 5-12-2005.
Search results in 9 data sets.
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OpenLAB ECM – What about my SOPs? Content Management Capabilitiesg p
Secure Access to Data and TraceabilityTraceability
– Complete audit trail of all changes
– “check in/check out” control prevents parallel data access
– Electronically sign documents y gand data files
– Record retention policies for all data- and archive-structuresdata and archive structures
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Advanced Differential A l i S ft
MassHunter Mass Profiler Professional Analysis Software
Solution for Mass S t l D t
Profiler Professional B.02.00 (MPP)
Spectral Data
Also includes Principle Component Analysis andAlso includes Principle Component Analysis and Hierarchical Clustering
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Target ApplicationsMetabolomics + ProteomicsMetabolomics + ProteomicsBiomarker DiscoveryTogether with Genomics in Systems Biology (GeneSpring platform)Environmental MetabolomicsPlant Metabolomics to create more resistant species
General mass spec based differential analysisGeneral mass spec based differential analysis• Food, beverages, flavors and fragrances
– Adulteration and fraud (natural products)– Origin determination and authenticity– Origin determination and authenticity– ID of compounds and degradends affecting taste, texture, smell
• Degradation Studies• Optimization of complex manufacturing processes of productsOptimization of complex manufacturing processes of products• Follow blood metabolome of athletes over time• Compare water from different wells, locations in a river
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Supported MS Instrumentation and SoftwareAgilent GC/MS and GC/MS/MS instrumentsAgilent GC/MS and GC/MS/MS instruments• AMDIS (NIST) feature finding on GC/MS single quad under MSD
ChemStationM H t Q l Ch t D l ti f f t fi di i• MassHunter Qual Chromatogram Deconvolution for feature finding in GC/MS (converted) and GC/MS/MS data (MS only)
Agilent LC/MS and LC/MS/MS instrumentsgMassHunter Qual feature finding in TOF and Q-TOF (MS only) dataID Browser for compound identification + annotation (incl. QTOF MS/MS)
MassHunter MS Quant Results (report.results.xml)• Preferential LC/QQQ and GC/QQQ in MRM mode• For discovery (incl. peptides) and validation
Support for all Agilent LC/MS and GC/MS solutions !
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Support for all Agilent LC/MS and GC/MS solutions !
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Agilent Hardware & Software optionsSoftware options
Agilent has GC and GC/MS Hardware Technologies to get the most out of your MSDto get the most out of your MSDColumn Backflush
Deconvolution Reporting Software (DRS)Deconvolution Reporting Software (DRS)
MSD Gain Normalization
Trace Ion Detection (TID)
Retention Time Locking (RTL)• Agilent RTL databases and libraries• User Contributed RTL data bases (Free)
There are seven RTL Databases available for free on Agilent com– There are seven RTL Databases available for free on Agilent.com.
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The MSD ChemStation Experts …
Nigel Cocks, Kai Meng, Mike Szelewski, Bruce
Quimby, Phil Wylie, Ken Weiner, Chas Thomson,
Stephan Baumann, John Pellerin, Jim Crabtree
“There is one near you”There is one near you
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Would you like more tips and tricks for your Agilent GC/MSD?for your Agilent GC/MSD?See the upcoming Agilent GC/MS seminar tour coming near you soon. Topics include:p• The Tool Box – Getting More Productivity from Your GC and GC/MSD• Tools for Optimizing the Inlet and Injection Parameters• Mass Spectrometer Tools: Which Tools Do You Need for the Job?
Feel free to bring the issues facing you in the lab to this event. Whether it be a contamination you can’t seem to track down, a problem that won’t seem to go away, a goofy looking chromatogram, or maybe you just want to speed up an analysis that is just taking too long. We’ll do our best to help you.
www agilent com/chem/gcmstourwww.agilent.com/chem/gcmstour
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