Retention time shifts and loss of repeatability

Question

Hi everyone, 
 Can somebody advice me on what could be possible cause of retention time shift and unstable areas (meaning poor repeatability) in GCMS? I have included picture below where day1 and day2 means that standards were run in different days. Is that a normal behaviour? Our system is INTUVO GCMS thus we are not cutting our columns or anything like that because we are using guard chips instead. 
 
 The GC method is attached as text file

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 toluene_AA_method.txt 
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 INSTRUMENT CONTROL PARAMETERS: GCMS
 --------------------------------------

 Fri May 27 14:00:29 2022

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 16 min
Post Run Time 0 min
Cycle Time Optimization Fast Cool (default)

Oven
Temperature
Setpoint On
(Initial) 70 &#176;C
Hold Time 7 min
Post Run 70 &#176;C
Program
#1 Rate 20 &#176;C/min
#1 Value 150 &#176;C
#1 Hold Time 5 min


Equilibration Time 0.25 min
Max Temperature 240 &#176;C
Maximum Temperature Override Disabled
Slow Fan Disabled

ALS
Injector
Syringe Size 10 μL
Injection Volume 0.2 μL
Solvent A Washes (PreInj) 3
Solvent A Washes (PostInj) 3
Solvent A Volume 4 μL
Solvent B Washes (PreInj) 3
Solvent B Washes (PostInj) 3
Solvent B Volume 4 μL
Sample Washes 3
Sample Wash Volume 4 μL
Sample Pumps 6
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

Sample Overlap
Mode Sample overlap is not enabled

ALS Errors Pause for user interaction

SS Inlet He
Mode Split
Heater On 250 &#176;C
Pressure On 2.0699 psi
Total Flow On 57 mL/min
Septum Purge Flow On 6 mL/min
Pre-Run Flow Test On
Pre-Run Flow Test Action on Failure Abort
Gas Saver Off
Split Ratio 50 :1
Split Flow 50 mL/min
Liner A Liner has not been selected.

Column
Column #1
Flow
Setpoint On
(Initial) 1 mL/min
Post Run 0.57353 mL/min

Column Information Agilent 123-9334UI-INT: US20400239
DB-BAC1 UI 
Temperature Range 20 &#176;C—270 &#176;C (270 &#176;C)
Dimensions 30 m x 320 μm x 1.8 μm
Column lock Locked
In SS Inlet He
Out MSD 
(Initial) 70 &#176;C
Pressure 2.0699 psi
Flow 1 mL/min
Average Velocity 30.691 cm/sec
Holdup Time 1.6291 min
Control Mode Constant Flow

Column Outlet Pressure 0 psi

Agilent Intuvo 9000 GC Components
Guard Chip
Temperature
Setpoint On
(Initial) 210 &#176;C
Post Run 100 &#176;C

Model Number G4587-60565: Intuvo SSI Guard Chip
Track Oven Off
Max Temperature 450 &#176;C

Isothermal Setpoints
Bus Temperature On 200 &#176;C
Use Default Bus Temperature On




Valve 1
Type Gas Sampling Valve
GSV Loop Volume 1 mL
Load Time 0.5 min
Inject Time 0.5 min

Signals
Signal #1: Test Plot
Description Test Plot
Save Off
Data Rate 50 Hz

Signal #2: 
Description None

Signal #3: 
Description None

Signal #4: 
Description None




MS Information
-- -----------


General Information
------- -----------


Acquisition Mode : SIM
Solvent Delay (minutes) : 4.5
Tune file : D:\MassHunter\GCMS\1\5977\ATUNE.U
EM Setting mode Gain : 5.000000

Number of SIM Groups : 2
Run Time (if MS only) : 650 minutes 

[SIM Parameters]
Group 1 Group ID : toluen
Resolution : 0
Group Start Time : 4.5
Number of Ions : 2
Ions
Dwell In Group :( Mass, Dwell) ( Mass, Dwell) ( Mass, Dwell) 
 ( 91.00,50 ) ( 92.00,50 ) 
Group 2 Group ID : amyl alcohol
Resolution : 0
Group Start Time : 5.8
Number of Ions : 2
Ions
Dwell In Group :( Mass, Dwell) ( Mass, Dwell) ( Mass, Dwell) 
 ( 55.00,50 ) ( 70.00,50 ) 


[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: US1422L218
 ---------------------------------

 Trace Ion Detection is OFF.

 34.593 : EMISSION 
 70.007 : ENERGY 
 31.712 : REPELLER 
 90.331 : IONFOCUS 
 17.627 : ENTRANCE_LENS
 1121.040 : EMVOLTS 
 1388 : Actual EMV 
 5.00 : GAIN FACTOR 
 358.000 : AMUGAIN 
 123.938 : AMUOFFSET 
 1.000 : FILAMENT 
 0.000 : DCPOLARITY 
 15.482 : ENTLENSOFFSET
 0.000 : Ion_Body 
 0.000 : EXTLENS 
 -1040.000 : MASSGAIN 
 -35.000 : MASSOFFSET 

 END OF TUNE PARAMETERS
 ----------------------



 END OF INSTRUMENT CONTROL PARAMETERS
 ------------------------------------

Best Regards, 
 Standwi

paulsalverda · Accepted Answer

Thank you for the very clear question and the uploaded acqmeth.txt file! 
 Observations: 
 ALS Solvent and sample washes with less than a full syringe, in your case you're doing 4uL washes, requires a PTFE tipped syringe plunger. 
 The Viscosity Delay should always be set to 2 or more seconds - this is proven to improve reproducibility. 
 The starting inlet pressure of 2.07 psi is less than 5ps i. It is very difficult for any GC inlet to precisely control pressures below 5psi. This low pressure is because you are using a 30m x 320uM column at only 1 ml/min flow going to vacuum. The only reason this is working at all is because of the guard chip in the Intuvo GC. In an 8890x/7890x system, without the extra restriction of the guard chip flow path, this column would result in an impossible negative inlet pressure setting! This ID column is typically run at more like 2 or 3 ml/min to a GC detector, not a Mass Spec. 
 Would it be possible for you to change to a 30m x 250uM column at the same 1 ml/min, or even 1.2 ml/min ? That would require an inlet pressure of at least 9 or 10 PSI or more - and allow for much, much better control. 
 Why is your septum purge flow set to 6ml/min instead of the typical 3ml/min? 
 You are running SIM on only two ions per SIM group at 50ms dwell time each. That results in a very fast SIM cycle time and quite a lot of data points per peak. You may see an increase in sensitivity and a decrease in noise if you would increase the dwell time to 100ms per ion. That would reduce the data points per peak by 1/2 but you'd sill have more than enough, more than eight to ten, to be able to quantitate the peaks. 50ms is fine, but 75ms to 100ms may be better. Many folks run too many SIM ions and then run very, very short dwell times and that is a problem. 
 What happens if you run this same standard in SCAN mode, 35-350, threshold 100 ? Do you have other peaks eluting at the same time as your peaks of interest? Other huge peaks, like the tail of the solvent? The ions are still in the source and going into the quad, they're just thrown away in the quad, the mass filter. Excess ions flying around that you are choosing not to look at still can cause issues. 
 Your peaks in this level standard are huge and you are already splitting 50:1 in the inlet. Why run MS Gain of 5, which turns up the electron multiplier to increase the detector output? Your smallest standard concentration's chromatographic peaks only need to be 3x to 4x the baseline noise to be useful. I would suggest to turn down the MS Gain to 1 and maybe even increase the split ratio further. 
 The retention time increase and peak height/area decrease are GC inlet/column flow related. This could be caused by the tiniest leak at the septum or liner O ring or any column connection before the head of the column. I would suggest running an inlet leak test as that's easy to do - but really you should change to a more usable column configuration. 
 
 and let us know what happens.

Retention time shifts and loss of repeatability

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