We are detecting methyl methacrylate monomer using air sampling. The signal is so low, we will need to use gain factors. Can I apply gain to a certain region of the TIC or does it have to be applied to the whole chromatogram? My signal height of MMA is currently at 4E+4, other compounds in the standard are at 6E+6 height, what is the suitable gain factor for us?
This is a chromatogram of my high standard, Still haven't gotten to the low. Note that this is actually just one compound injected on the sorbent tube. The compound is methyl methacrylate. The tube is Carbopack B,X. The library identifies the compound at 3.4 mins. The other peaks are unknown and probably side-products of methyl methacrylate heating up (unsure about this). Eventually the plan is to perform air sampling for MMA during combustion of PMMA. SIM is below.
As you can see, the signal is pretty low especially in SCAN mode.
Here is the acqmeth file:
INSTRUMENT CONTROL PARAMETERS: 1
-----------------------------------
Mon Sep 18 12:19:39 2023
Control Information
------- -----------
Sample Inlet : GC
Injection Source : External Device
Mass Spectrometer : Enabled
Injection Location: Rear
No Sample Prep method has been assigned to this method.
GC
GC Summary
Run Time 16.091 min
Post Run Time 0 min
Oven
Temperature
Setpoint On
(Initial) 36 °C
Hold Time 1 min
Post Run 70 °C
Program
#1 Rate 9 °C/min
#1 Value 150 °C
#1 Hold Time 0 min
#2 Rate 33 °C/min
#2 Value 230 °C
#2 Hold Time 0 min
Equilibration Time 0.25 min
Max Temperature 230 °C
Maximum Temperature Override Disabled
Slow Fan Disabled
Front SS Inlet He
Excluded from Readiness ***Excluded from Affecting GC's Readiness State***
Mode Sleep
Heater Off
Pressure Off
Septum Purge Flow Off
Pre-Run Flow Test Off
Liner Agilent 5183-4709: 140 μL (Direct, straight (gas samples, HS, P&)
Back PTV Inlet He
Mode Solvent Vent
Pressure On 6.8361 psi
Total Flow On 14 mL/min
Septum Purge Flow On 3 mL/min
Septum Purge Flow Mode Standard
Pre-Run Flow Test Off
Gas Saver On 20 After 2 min mL/min
Purge Flow to Split Vent 10 mL/min at 0.01 min
Vent Flow 50 mL/min per min
Vent Pressure 6.83 psi Until 0 min
Liner Agilent G1544-80730: 675 μL (Direct connect, single taper, bottom )
Column
Column #3
Flow
Setpoint On
(Initial) 1 mL/min
Post Run 1.1952 mL/min
Column Information Agilent
Restek-Rxi5SilMS
Temperature Range -60 °C—350 °C (350 °C)
Dimensions 30 m x 250 μm x 0.25 μm
Column lock Unlocked
In Back PTV Inlet He
Out MSD
(Initial) 36 °C
Pressure 6.8361 psi
Flow 1 mL/min
Average Velocity 36.187 cm/sec
Holdup Time 1.3817 min
Control Mode Constant Flow
Column Outlet Pressure 0 psi
Front Detector FID
Excluded from Readiness ***Excluded from Affecting GC's Readiness State***
Makeup He
Heater On 275 °C
H2 Flow Off
Air Flow Off
Makeup Flow Off
Carrier Gas Flow Correction Constant Makeup and Fuel Flow
Flame Off
Detector Evaluation
Perform Detector Evaluation Test Off
Signal Selected No Signal Selected
Checkout Sample None
MSD Transfer Line
Temperature
Setpoint On
(Initial) 280 °C
Aux EPC 1,2,3
Aux EPC 1 N2
Pressure
Setpoint Off
(Initial) 10 psi
Post Run 10 psi
Excluded from Readiness ***Excluded from Affecting GC's Readiness State***
Aux EPC 2 N2
Pressure
Setpoint Off
(Initial) 10 psi
Post Run 10 psi
Excluded from Readiness ***Excluded from Affecting GC's Readiness State***
Aux EPC 3 N2
Pressure
Setpoint Off
(Initial) 10 psi
Post Run 10 psi
Excluded from Readiness ***Excluded from Affecting GC's Readiness State***
PSD 2
Pressure
Setpoint Off
(Initial) 10 psi
Post Run 10 psi
Excluded from Readiness ***Excluded from Affecting GC's Readiness State***
PSD Purge Off
Signals
Signal #1:
Description None
Signal #2:
Description None
Signal #3:
Description None
Signal #4:
Description None
Signal #5:
Description None
Signal #6:
Description None
Signal #7:
Description None
Signal #8:
Description None
GERSTEL MAESTRO
SYSTEM SETTINGS
Maestro Runtime : 16.09 min
GC Cool Down Time : 5.00 min
Cryo Timeout : 15.00 min
GERSTEL CIS
CIS : used
CRYO COOLING
Cryo Cooling : used
TEMPERATURE PROGRAM
Heater Mode : Standard
Liner Type : 013882-010-00 glass liner CIS4, baffled, non deactivated
Liner Max Temperature : 400 'C
Initial Temperature : -10 'C
Equilibration Time : 0.50 min
Initial Time : 0.50 min
Ramp 1
Rate : 12.00 'C/s
End Temp : 325 'C
Hold Time : 5.00 min
Ramp 2
Rate : 0.0 'C/s
Low Split : not used
GERSTEL TDU
TEMPERATURE PROGRAM
Initial Temperature : 40 'C
Delay Time : 0.50 min
Initial Time : 0.50 min
Ramp 1
Rate 1 : 720.0 'C/min
End Temp 1 : 320 'C
Hold Time 1 : 7.00 min
Ramp 2
Rate 2 : 0.0 'C/min
TDU SETTINGS
Transfer Temp : 280 'C
Transfer Temp Mode : Fixed
Desorption Mode : Splitless
Sample Mode : Remove Tube - Standby Cooling
Standby Temp : 40 'C
TDU LIQUID OPTION
Liquid Option : not used - use these parameters if it becomes 'used'
Sample Tray : Rack 1,VT54/2-CVM
Fixed Liquid Vial : used
Liquid Vial : 1
Inject into Micro vial : not used
PYROLYSIS PARAMETERS
Pyrolysis : not used - use these parameters if it becomes 'used'
Pyro Mode : Pyro in last hold (standard)
Pyrolysis Lead Time : 0.10 min
Pyrolysis Followup Time : 1.00 min
Pyrolysis Initial Time : 0.50 min
Pyrolysis Initial Temp. : 500 'C
Pyrolysis Rate 1 : 0.00 'C/s
Pyrolysis Rate 2 : 0.00 'C/s
Pyrolysis Heater : used
GERSTEL DHS
DHS : not used - use these parameters if it becomes 'used'
DHS Module : DHS
INJECTION TUBE
Tube Tray : TDUTray1,VT40t/Tube
Fixed Tube : used
Tube Number : 1
PURGE TUBE
Purge Tube : not used - use these parameters if it becomes 'used'
Purge Tube Tray :
Tube Number :
INCUBATION SETTINGS
Incubation Temperature : 30 'C
Incubation Time : 1.00 min
AGITATION SETTINGS
Agitator On Time : 60 s
Agitator Off Time : 1 s
Agitator Speed : 500 rpm
TRANSFER HEATER SETTINGS
TEMP : 75 'C
PURGE PHASE SETTINGS
Volume : 0.0 mL
TRAPPING PHASE SETTINGS
Volume : 50.0 mL
Flow : 20.0 mL/min
Trap Temperature : 25 'C
Incubation Temperature : 30 'C
DRYING PHASE SETTINGS
Volume : 0.0 mL
MS Information
-- -----------
General Information
------- -----------
Acquisition Mode : SIM/Scan
Solvent Delay (minutes) : 1
Tune file : D:\MassHunter\GCMS\1\5977\etune.u
EM Setting mode Gain : 1.000000
Number of SIM Groups : 3
Run Time (if MS only) : 16 minutes
[Scan Parameters]
Start Time : 1
Low Mass : 35
High Mass : 350
Threshold : 100
A/D Samples: : 8
[SIM Parameters]
Group 1 Group ID : Null
Resolution : 0
Group Start Time : 1
Number of Ions : 1
Ions
Dwell In Group :( Mass, Dwell) ( Mass, Dwell) ( Mass, Dwell)
( 450.00,50 )
Group 2 Group ID : MMA
Resolution : 0
Group Start Time : 3.52
Number of Ions : 5
Ions
Dwell In Group :( Mass, Dwell) ( Mass, Dwell) ( Mass, Dwell)
( 41.00,50 ) ( 69.00,50 ) ( 85.00,50 )
( 99.00,50 ) ( 100.00,50 )
Group 3 Group ID : Null
Resolution : 0
Group Start Time : 3.9
Number of Ions : 1
Ions
Dwell In Group :( Mass, Dwell) ( Mass, Dwell) ( Mass, Dwell)
( 450.00,50 )
[MSZones]
MS Source : 230 C maximum 250 C
MS Quad : 150 C maximum 200 C
Timed Events
----- ------
Number Events= 0
END OF MS ACQUISITION PARAMETERS
TUNE PARAMETERS for SN: US2018M021
---------------------------------
Trace Ion Detection is OFF.
34.593 : EMISSION
70.007 : ENERGY
0.503 : REPELLER
88.835 : IONFOCUS
12.582 : ENTRANCE_LENS
1509.614 : EMVOLTS
1752.4 : Actual EMV
1.00 : GAIN FACTOR
1869.000 : AMUGAIN
140.125 : AMUOFFSET
1.000 : FILAMENT
0.000 : DCPOLARITY
11.650 : ENTLENSOFFSET
10.002 : Ion_Body
-2.800 : EXTLENS
-244.000 : MASSGAIN
-28.000 : MASSOFFSET
END OF TUNE PARAMETERS
----------------------
END OF INSTRUMENT CONTROL PARAMETERS
------------------------------------
This is a chromatogram of my high standard, Still haven't gotten to the low. Note that this is actually just one compound injected on the sorbent tube. The compound is methyl methacrylate. The tube is Carbopack B,X. The library identifies the compound at 3.4 mins. The other peaks are unknown and probably side-products of methyl methacrylate heating up (unsure about this). Eventually the plan is to perform air sampling for MMA during combustion of PMMA. SIM is below.
As you can see, the signal is pretty low especially in SCAN mode.
Here is the acqmeth file:
INSTRUMENT CONTROL PARAMETERS: 1
-----------------------------------
Mon Sep 18 12:19:39 2023
Control Information
------- -----------
Sample Inlet : GC
Injection Source : External Device
Mass Spectrometer : Enabled
Injection Location: Rear
No Sample Prep method has been assigned to this method.
GC
GC Summary
Run Time 16.091 min
Post Run Time 0 min
Oven
Temperature
Setpoint On
(Initial) 36 °C
Hold Time 1 min
Post Run 70 °C
Program
#1 Rate 9 °C/min
#1 Value 150 °C
#1 Hold Time 0 min
#2 Rate 33 °C/min
#2 Value 230 °C
#2 Hold Time 0 min
Equilibration Time 0.25 min
Max Temperature 230 °C
Maximum Temperature Override Disabled
Slow Fan Disabled
Front SS Inlet He
Excluded from Readiness ***Excluded from Affecting GC's Readiness State***
Mode Sleep
Heater Off
Pressure Off
Septum Purge Flow Off
Pre-Run Flow Test Off
Liner Agilent 5183-4709: 140 μL (Direct, straight (gas samples, HS, P&)
Back PTV Inlet He
Mode Solvent Vent
Pressure On 6.8361 psi
Total Flow On 14 mL/min
Septum Purge Flow On 3 mL/min
Septum Purge Flow Mode Standard
Pre-Run Flow Test Off
Gas Saver On 20 After 2 min mL/min
Purge Flow to Split Vent 10 mL/min at 0.01 min
Vent Flow 50 mL/min per min
Vent Pressure 6.83 psi Until 0 min
Liner Agilent G1544-80730: 675 μL (Direct connect, single taper, bottom )
Column
Column #3
Flow
Setpoint On
(Initial) 1 mL/min
Post Run 1.1952 mL/min
Column Information Agilent
Restek-Rxi5SilMS
Temperature Range -60 °C—350 °C (350 °C)
Dimensions 30 m x 250 μm x 0.25 μm
Column lock Unlocked
In Back PTV Inlet He
Out MSD
(Initial) 36 °C
Pressure 6.8361 psi
Flow 1 mL/min
Average Velocity 36.187 cm/sec
Holdup Time 1.3817 min
Control Mode Constant Flow
Column Outlet Pressure 0 psi
Front Detector FID
Excluded from Readiness ***Excluded from Affecting GC's Readiness State***
Makeup He
Heater On 275 °C
H2 Flow Off
Air Flow Off
Makeup Flow Off
Carrier Gas Flow Correction Constant Makeup and Fuel Flow
Flame Off
Detector Evaluation
Perform Detector Evaluation Test Off
Signal Selected No Signal Selected
Checkout Sample None
MSD Transfer Line
Temperature
Setpoint On
(Initial) 280 °C
Aux EPC 1,2,3
Aux EPC 1 N2
Pressure
Setpoint Off
(Initial) 10 psi
Post Run 10 psi
Excluded from Readiness ***Excluded from Affecting GC's Readiness State***
Aux EPC 2 N2
Pressure
Setpoint Off
(Initial) 10 psi
Post Run 10 psi
Excluded from Readiness ***Excluded from Affecting GC's Readiness State***
Aux EPC 3 N2
Pressure
Setpoint Off
(Initial) 10 psi
Post Run 10 psi
Excluded from Readiness ***Excluded from Affecting GC's Readiness State***
PSD 2
Pressure
Setpoint Off
(Initial) 10 psi
Post Run 10 psi
Excluded from Readiness ***Excluded from Affecting GC's Readiness State***
PSD Purge Off
Signals
Signal #1:
Description None
Signal #2:
Description None
Signal #3:
Description None
Signal #4:
Description None
Signal #5:
Description None
Signal #6:
Description None
Signal #7:
Description None
Signal #8:
Description None
GERSTEL MAESTRO
SYSTEM SETTINGS
Maestro Runtime : 16.09 min
GC Cool Down Time : 5.00 min
Cryo Timeout : 15.00 min
GERSTEL CIS
CIS : used
CRYO COOLING
Cryo Cooling : used
TEMPERATURE PROGRAM
Heater Mode : Standard
Liner Type : 013882-010-00 glass liner CIS4, baffled, non deactivated
Liner Max Temperature : 400 'C
Initial Temperature : -10 'C
Equilibration Time : 0.50 min
Initial Time : 0.50 min
Ramp 1
Rate : 12.00 'C/s
End Temp : 325 'C
Hold Time : 5.00 min
Ramp 2
Rate : 0.0 'C/s
Low Split : not used
GERSTEL TDU
TEMPERATURE PROGRAM
Initial Temperature : 40 'C
Delay Time : 0.50 min
Initial Time : 0.50 min
Ramp 1
Rate 1 : 720.0 'C/min
End Temp 1 : 320 'C
Hold Time 1 : 7.00 min
Ramp 2
Rate 2 : 0.0 'C/min
TDU SETTINGS
Transfer Temp : 280 'C
Transfer Temp Mode : Fixed
Desorption Mode : Splitless
Sample Mode : Remove Tube - Standby Cooling
Standby Temp : 40 'C
TDU LIQUID OPTION
Liquid Option : not used - use these parameters if it becomes 'used'
Sample Tray : Rack 1,VT54/2-CVM
Fixed Liquid Vial : used
Liquid Vial : 1
Inject into Micro vial : not used
PYROLYSIS PARAMETERS
Pyrolysis : not used - use these parameters if it becomes 'used'
Pyro Mode : Pyro in last hold (standard)
Pyrolysis Lead Time : 0.10 min
Pyrolysis Followup Time : 1.00 min
Pyrolysis Initial Time : 0.50 min
Pyrolysis Initial Temp. : 500 'C
Pyrolysis Rate 1 : 0.00 'C/s
Pyrolysis Rate 2 : 0.00 'C/s
Pyrolysis Heater : used
GERSTEL DHS
DHS : not used - use these parameters if it becomes 'used'
DHS Module : DHS
INJECTION TUBE
Tube Tray : TDUTray1,VT40t/Tube
Fixed Tube : used
Tube Number : 1
PURGE TUBE
Purge Tube : not used - use these parameters if it becomes 'used'
Purge Tube Tray :
Tube Number :
INCUBATION SETTINGS
Incubation Temperature : 30 'C
Incubation Time : 1.00 min
AGITATION SETTINGS
Agitator On Time : 60 s
Agitator Off Time : 1 s
Agitator Speed : 500 rpm
TRANSFER HEATER SETTINGS
TEMP : 75 'C
PURGE PHASE SETTINGS
Volume : 0.0 mL
TRAPPING PHASE SETTINGS
Volume : 50.0 mL
Flow : 20.0 mL/min
Trap Temperature : 25 'C
Incubation Temperature : 30 'C
DRYING PHASE SETTINGS
Volume : 0.0 mL
MS Information
-- -----------
General Information
------- -----------
Acquisition Mode : SIM/Scan
Solvent Delay (minutes) : 1
Tune file : D:\MassHunter\GCMS\1\5977\etune.u
EM Setting mode Gain : 1.000000
Number of SIM Groups : 3
Run Time (if MS only) : 16 minutes
[Scan Parameters]
Start Time : 1
Low Mass : 35
High Mass : 350
Threshold : 100
A/D Samples: : 8
[SIM Parameters]
Group 1 Group ID : Null
Resolution : 0
Group Start Time : 1
Number of Ions : 1
Ions
Dwell In Group :( Mass, Dwell) ( Mass, Dwell) ( Mass, Dwell)
( 450.00,50 )
Group 2 Group ID : MMA
Resolution : 0
Group Start Time : 3.52
Number of Ions : 5
Ions
Dwell In Group :( Mass, Dwell) ( Mass, Dwell) ( Mass, Dwell)
( 41.00,50 ) ( 69.00,50 ) ( 85.00,50 )
( 99.00,50 ) ( 100.00,50 )
Group 3 Group ID : Null
Resolution : 0
Group Start Time : 3.9
Number of Ions : 1
Ions
Dwell In Group :( Mass, Dwell) ( Mass, Dwell) ( Mass, Dwell)
( 450.00,50 )
[MSZones]
MS Source : 230 C maximum 250 C
MS Quad : 150 C maximum 200 C
Timed Events
----- ------
Number Events= 0
END OF MS ACQUISITION PARAMETERS
TUNE PARAMETERS for SN: US2018M021
---------------------------------
Trace Ion Detection is OFF.
34.593 : EMISSION
70.007 : ENERGY
0.503 : REPELLER
88.835 : IONFOCUS
12.582 : ENTRANCE_LENS
1509.614 : EMVOLTS
1752.4 : Actual EMV
1.00 : GAIN FACTOR
1869.000 : AMUGAIN
140.125 : AMUOFFSET
1.000 : FILAMENT
0.000 : DCPOLARITY
11.650 : ENTLENSOFFSET
10.002 : Ion_Body
-2.800 : EXTLENS
-244.000 : MASSGAIN
-28.000 : MASSOFFSET
END OF TUNE PARAMETERS
----------------------
END OF INSTRUMENT CONTROL PARAMETERS
------------------------------------
You are running in SIM/Scan mode. The first chromatogram is TIC Scan. The peak in the second SIM time segment, 3.52 to 3.9 minutes, is still visible even at that scale. 0.1x10^7 is 1 million. Zoom in on just this portion and let's see how big that peak is in SCAN mode along with some background. That peak only needs to be 3x or 4x the noise to be valid. The other peaks are huge - 1x10^7. A spectrum of the background near the peak would be interesting, too.
The second chromatogram is TIC SIM. During that time segment it is summing five ions, 41, 69, 85, 99, and 100. Because it's SIM there is no extraneous background so the peak can be even smaller and still valid.
Method recommendations: Because of your very low initial oven temperature, increase the oven temperature equilibration time to 1 to 2 minutes for better run to run reproducibility. At Gain 1, the system is already running with the EM at ~243 volts above autotune. The Scan baseline is very low, too, maybe reduce the threshold to 50 or 75 and see how much the baseline increases first. Below 50 is not useful except for troubleshooting as you start to see electronic background below that.
I'll need to chat with someone who has Gerstel Maestro and PTV inlet experience about those parameters, but my guess would be that the MMA peak is not being transferred onto the column as well as those other peaks are. Are those other peaks there in a blank, no inject run? Are they there in a method blank with no MMA in the sample?
That retention time seems early based on other applications looking for MMA. Search in this catalog for Methyl Methacrylate::5991-5213EN_GC_Catalog_Applications.pdf (agilent.com) . I think further experimentation and method development is needed.
Now to answer your original question. A search in MassHunter Acquistion Help for SIM/Scan gives this answer.
This EM setting type and value is fixed for all Scan time segments but its value can be overridden by different values specified in timed events.
