Retention time shifts and loss of repeatability

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

                        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 Summary
Run Time                                     16 min
Post Run Time                                0 min
Cycle Time Optimization                      Fast Cool (default)

Setpoint                                     On
(Initial)                                    70 °C
Hold Time                                    7 min
Post Run                                     70 °C
#1 Rate                                      20 °C/min
#1 Value                                     150 °C
#1 Hold Time                                 5 min

Equilibration Time                           0.25 min
Max Temperature                              240 °C
Maximum Temperature Override                 Disabled
Slow Fan                                     Disabled

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 °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 #1
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 °C—270 °C (270 °C)
Dimensions                                   30 m x 320 μm x 1.8 μm
Column lock                                  Locked
In                                           SS Inlet He
Out                                          MSD 
(Initial)                                    70 °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
Setpoint                                     On
(Initial)                                    210 °C
Post Run                                     100 °C

Model Number                                 G4587-60565: Intuvo SSI Guard Chip
Track Oven                                   Off
Max Temperature                              450 °C

Isothermal Setpoints
Bus Temperature                              On    200 °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

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
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
Dwell In Group            :(  Mass,  Dwell) (  Mass,  Dwell)  (  Mass,  Dwell) 
                           (  55.00,50  )  (  70.00,50  ) 


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

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


                        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


Best Regards,


  • Thank you for the very clear question and the uploaded acqmeth.txt file!


    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 5psi.   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.

  • Hi Paul,

    Thank you very much for your comprehensive and very helpful comments.

    To answer your questions in brief, some of the settings and parameters were selected due to lack of experience and knowledge thus your comments are very appreciated.

    Regarding the inlet pressure I was wondering why the pressure is so low since we did not detect any leaks in the performance test. Your explanation with column dimensions makes sense and changing the column to a different column ID is worth consideration. As I understood, it-is not recommended to use higher flowrates 2 – 3 ml/ min for the MS detector but instead opt to a column with different ID?

    Regarding the parameters for the SIM, I could see that I do not get increase in sensitivity compared to SCAN mode which was unexpected. Increasing the dwell time makes sense and yes we dont need that many datapoints to describe peaks. Thank you!

    Regarding interferences I have run the standard and blanks with a scan and no interferences are in the retention time of the peaks of the interest. Solvent peak is well within solvent delay.

    I have run a leak test and no leaks were detected do you think it is possible when the leaks are so tiny that leak test could be still negative? 

    Thank you again!


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