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 really appreciate your response, Paul!

I'm looking to measure hormone concentration in plant tissue using Methyl Chloroformate derivatization. I successfully detected and measured amino acids and some hormones with good sensitivity, but other hormones and some toxins are present in trace amounts (1-100 ng/g fresh weight, very variable depending on species and environment). Sinch most of these compounds have low molecular mass (C5-C10), their spectra don't make some big peaks like diterpenes (C20). I know they are usually being measured using UPLC/HPLC, but we don't have access to this equipment here. It's also very labor intensive and dangerous to use more than 200mg of tissue sample for extraction and analysis using MCF derivatization. Things I'm thinking of is to increase He pressure to 15-16 psi (and put inlet on constant pressure instead of constant flow), so that I can inject more sample without having backflush problem, use SIM instead of TIC, and in the best case, upgrade to Extractor source.

Calculate how much of each peak is being injected.

Don't increase the column flow higher than 1.2 to 1.3 ml/min, but certainly do constant flow.

How much are you injecting? What solvent is being injected? What are your other injection port parameters?  Split? Splitless  -  what splitless On time?  What splitless purge flow?  What is your initial oven temperature?   You can upload the acqmeth.txt file that exists underneath your method's ******.M subdirectory here.

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%

I mean 99.999%