How to upgrade MS source to Extractor 350?

EhsanKhedive  What is the model number listed along with the serial number label on your system?  For example, this one is a G7077C, a 5977C system with a turbomolecular high vaccum pump and an extractor ion source.

Hi paulsalverda ,

Thank you for your attention! The model numberd is G7080B with a diffusion oil pump.

I couldn't upload the file, so I copied the whole text here:

INSTRUMENT CONTROL PARAMETERS: GCMS
--------------------------------------

D:\EhsanKhedive\GC_AquisitionMethod\Total_Metabolome.M
Mon Mar 20 09:53:06 2023

Control Information
------- -----------

Sample Inlet : GC
Injection Source : GC ALS
Injection Location: Front
Mass Spectrometer : Enabled

No Sample Prep method has been assigned to this method.

GC
GC Summary
Run Time 36.357 min
Post Run Time 1 min

Oven
Temperature
Setpoint On
(Initial) 45 °C
Hold Time 1 min
Post Run 45 °C
Program
#1 Rate 7 °C/min
#1 Value 240 °C
#1 Hold Time 1 min
#2 Rate 20 °C/min
#2 Value 270 °C
#2 Hold Time 5 min

Equilibration Time 0.5 min
Max Temperature 325 °C
Maximum Temperature Override Disabled
Slow Fan Disabled

ALS
Front Injector
Syringe Size 10 μL
Injection Volume 2 μL
Solvent A Washes (PreInj) 2
Solvent A Washes (PostInj) 2
Solvent A Volume 8 μL
Solvent B Washes (PreInj) 2
Solvent B Washes (PostInj) 2
Solvent B Volume 8 μL
Sample Washes 0
Sample Wash Volume 2 μL
Sample Pumps 3
Dwell Time (PreInj) 0 min
Dwell Time (PostInj) 0 min
Solvent Wash Draw Speed 300 μL/min
Solvent Wash Dispense Speed 6000 μL/min
Sample Wash Draw Speed 300 μL/min
Sample Wash Dispense Speed 6000 μL/min
Injection Dispense Speed 6000 μL/min
Viscosity Delay 0 sec
Sample Depth Disabled
Injection Type Standard
L1 Airgap 0.2 μL
Solvent Wash Mode A, B

Front SSZ Inlet He
Mode Splitless
Heater On 260 °C
Pressure On 7.2892 psi
Gas Saver Off
Purge Flow to Split Vent 3 mL/min at 0.75 min

Thermal Aux 1 (MSD Transfer Line)
Temperature
Setpoint On
(Initial) 280 °C
Post Run 0 °C

Column
Column #1
Flow
Setpoint On
(Initial) 1 mL/min
Post Run 1 mL/min

Agilent 19091S-433UI
HP-5ms Ultra Inert
-60 °C—325 °C (325 °C): 30 m x 250 μm x 0.25 μm
In Front SSZ Inlet He
Out MSD
(Initial) 45 °C
Pressure 7.2892 psi
Flow 1 mL/min
Average Velocity 36.473 cm/sec
Holdup Time 1.3709 min

Column Outlet Pressure 0 psi

Signals
Signal #1: Test Plot
Description Test Plot
Details
Save Off
Data Rate 50 Hz
Dual Injection Assignment Front Sample

Signal #2: Test Plot
Description Test Plot
Details
Save Off
Data Rate 50 Hz
Dual Injection Assignment Back Sample

Signal #3: Test Plot
Description Test Plot
Details
Save Off
Data Rate 50 Hz
Dual Injection Assignment Back Sample

Signal #4: Test Plot
Description Test Plot
Details
Save Off
Data Rate 50 Hz
Dual Injection Assignment Back Sample

MS Information
-- -----------

General Information
------- -----------

Acquisition Mode : Scan
Solvent Delay (minutes) : 4.3
Tune file : D:\MassHunter\GCMS\1\5977\ATUNE.U
EM Setting mode Gain : 1.000000

Normal or Fast Scanning : Normal Scanning
Trace Ion Detection : Off
Run Time (if MS only) : 650 minutes

[Scan Parameters]
Start Time : 4.3
Low Mass : 31
High Mass : 400
Threshold : 150
A/D Samples: : 4

[MSZones]

MS Source : 230 C maximum 250 C
MS Quad : 150 C maximum 200 C

Timed Events
----- ------
Number Events= 0

END OF MS ACQUISTION PARAMETERS

TUNE PARAMETERS for SN: US1638P001
---------------------------------

Trace Ion Detection is OFF.

34.593 : EMISSION
70.007 : ENERGY
32.907 : REPELLER
90.331 : IONFOCUS
17.627 : ENTRANCE_LENS
1271.928 : EMVOLTS
1394.3 : Actual EMV
1.00 : GAIN FACTOR
2834.000 : AMUGAIN
138.500 : AMUOFFSET
1.000 : FILAMENT
0.000 : DCPOLARITY
15.482 : ENTLENSOFFSET
0.000 : Ion_Body
0.000 : EXTLENS
323.000 : MASSGAIN
-25.000 : MASSOFFSET

END OF TUNE PARAMETERS
----------------------

END OF INSTRUMENT CONTROL PARAMETERS
------------------------------------

First recommendations and some questions:

Thank you for your valuable recommendations!

• I will increase the equilibrium time.
• My solvent is Chloroform and from Vapor Volume Calculator I realized it will occupy ~82% of liner volume (~900ul) at 260C/7psi. So, I thought its feasible to inject 2ul. Chloroform boiling point is 61C, but I wasn't aware of this. Thank you!
• I will increase the delay to 1-2 sec.
• Liner is single taper.
• Thank you for the pulsed splitless injection recommendation. I will use it. What would be the optimum injection pressure and time in that case?
• I thought keeping inlet cooler than oven by ~10C prevents compound buildup and carry-over. That was the reason I keep it cooler. That's also the reason I put TL 10C higher than column.
• Purge flow: I thought it might be problematic. I try to save gas since it's grade 5 (9.9999) and expensive. I will change the split vent flow. Is it possible to put the split vent on 3ml/min in standby mode and then increase it to 50ml/min a couple of hours before the start of analysis?
• Most of the compounds of interest have very low mass (as low as 100). Even for some of them mass 27 is among the main mass peaks. I was even thinking to reduce it to 25m/z. What problem would this make? I usually put the maximum mass as my molecular weight+30Da in case they are methylated during derivatization.
• Since I keep my split vent low, sometimes I see m/z 32, especially during my blank run before the batch.

I mean 99.999%

The lower the injection port pressure, the less realistic is the vapor volume calculator. It's not perfection in there and 82% is too much.  With Chloroform you'd want the initial oven temperature to be 40° C or even lower. You say your compounds are very light, so reducing it to even 35° C might help chromatographic peak shapes.

Pulsed splitless.30×250×.25 at 1 ml/min is your normal column flow with the inlet at 7.2892 psi at 45°C.  The diffusion pump in your system has a maximum allowable flow of 2 ml/min and the gas calculator says 16.497 psi to get that, so a pulse of 16 psi until 0.5 minutes and then purge flow 50 to split vent at 1.00 minutes would be a good starting point.  Then have gas saver on 25 ml/min at 2.00 minutes. 2 µL of chloroform at 16 psi and 260° C inlet gives 52% expansion, much better, much more realistic/safe/usable.

The split splitless and multimode inlets require a minimum of at least 15 ml/min of total flow to function properly.  That 15 ml/min is not really enough to eliminate the possibility of air diffusion into the system, so I recommend 25 ml/min at all times.    If you need to save helium, Agilent sells a Helium Conservation Module that will let you switch to nitrogen whenever the system is not being used.

You can scan from 10 m/z if you'd like as long as you understand that the TIC baseline will include 18, 28, and 32. 

ANY 32 - oxygen -- in your system degrades the column and oxidizes the ion source requiring more cleaning. 

Thank you for your time and valuable information Paul! I really appreciate it! I am aware of water (18), N2 (28), and O2(32) and constantly check their presence.

Best!

Ehsan

Thank you for your time and valuable information Paul! I really appreciate it! I am aware of water (18), N2 (28), and O2(32) and constantly check their presence.

Best!

Ehsan