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Low ion Abundances on samples, normal tune file

xianhai

We cleaned the ion source, cut the column, changed the inlet from front to back (because the front inlet has some issue). After these maintenances, the tune file looks good, the ion abundance in tune file is similar as before. However, low TIC was observed with 1uL injection of our samples, with about 0.2 relative abundance compared to before. And we tried to inject 5 uL to increase the signal, however, the TIC didn't improve significantly. The results obtained can go forward but we want to know what is the reason here. Does anyone meet similar issue? Thanks.

  • 0

    5 µL of what solvent at what inlet temperature and pressure with what liner installed?  What inlet mode - Split or Splitless?  What are the column dimensions? Configuration? Flow rate?  Check out the GC Calculators available here:   GC Calculators and Method Translator Software | Agilent    Use the Vapor Volume calculator to see if what you are injecting will fit in the liner.  Just injecting more sample does not necessarily mean you will see larger peaks. 

    if the tune is fine, then the MS is fine.  Do you run the samples in Scan or SIM?  What about the detector setting - Absolute, Relative, or Gain?  What is the EMV used in the run?  Are you sure you have pointed to the correct tune file in the method?

    In windows file explorer under the method subdirectory (e.g.  SampleRun.M) is a file   acqmeth.txt  .  That file contains the GC and MS parameters used in your method.   Please upload that file here.

  • 0

    Are you sure the inlet parameters were matched correctly from front to back? Has the back inlet ever been used before?

  • 0 in reply to paulsalverda

    Hi Paul, 

    Thanks for the response. We are using Agilent 5183-4702 liner, HP-5ms Ultra Inert Columns (Part Number:19091S-433UI, 30 m, 0.25 mm, 0.25 µm, 7 inch cage).

    We are running in Scan, absolute. I always use autotune, I didn't find a place to choose a tune file in the method setting.

    Please find attached acqmeth, now and before the maintenance

    Fullscreen frontinlet-before.txt Download 
    
                               INSTRUMENT CONTROL PARAMETERS:    GCMS#1
                               ----------------------------------------

   C:\MSDCHEM\1\METHODS\ZXH-STEROL-M6-MS-1ULIN-SPLITLESS.M
      Fri Jun 02 13:19:43 2023

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

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

Oven
Equilibration Time                           0.5 min
Oven Program                                 On
    200 �C for 1 min
    then 4 �C/min to 276 �C for 1 min
    then 2 �C/min to 290 �C for 2 min
Run Time                                     30 min





Front Injector
Syringe Size                                 10 �L
Injection Volume                             1 �L
Solvent A Washes (PreInj)                    5
Solvent A Washes (PostInj)                   5
Solvent A Volume                             8 �L
Solvent B Washes (PreInj)                    0
Solvent B Washes (PostInj)                   2
Solvent B Volume                             8 �L
Sample Washes                                0
Sample Wash Volume                           8 �L
Sample Pumps                                 6
Dwell Time (PreInj)                          0 min
Dwell Time (PostInj)                         0 min
Solvent Wash Draw Speed                      300 �L/min
Solvent Wash Dispense Speed                  6000 �L/min
Sample Wash Draw Speed                       300 �L/min
Sample Wash Dispense Speed                   6000 �L/min
Injection Dispense Speed                     6000 �L/min
Viscosity Delay                              0 sec
Sample Depth                                 Disabled



Front SS Inlet He
Mode                                         Splitless
Heater                                       On    300 �C
Pressure                                     On    16.089 psi
Total Flow                                   On    54 mL/min
Septum Purge Flow                            On    3 mL/min
Gas Saver                                    On    20 mL/min After 2 min
Purge Flow to Split Vent                     50 mL/min at 2 min


Back SS Inlet He
Mode                                         Split
Heater                                       On    125 �C
Pressure                                     On    19.417 psi
Total Flow                                   On    14 mL/min
Septum Purge Flow                            On    3 mL/min
Gas Saver                                    On    20 mL/min After 2 min
Split Ratio                                  10 :1
Split Flow                                   10 mL/min


Thermal Aux 2 {MSD Transfer Line}
Heater                                       On
Temperature Program                          On
    280 �C for 0 min
Run Time                                     30 min


Column #1

350 �C: 30 m x 250 �m x 0.25 �m
In: Front SS Inlet He
Out: Vacuum

(Initial)                                    200 �C
Pressure                                     16.089 psi
Flow                                         1 mL/min
Average Velocity                             38.737 cm/sec
Holdup Time                                  1.2907 min
Flow Program                                 On
    1 mL/min for 0 min
Run Time                                     30 min


Column #2

350 �C: 30 m x 250 �m x 0.25 �m
In: Back SS Inlet He
Out: Front Detector FID

(Initial)                                    200 �C
Pressure                                     19.417 psi
Flow                                         1 mL/min
Average Velocity                             30.944 cm/sec
Holdup Time                                  1.6158 min
Flow Program                                 On
    1 mL/min for 0 min
Run Time                                     30 min





Front Detector FID
Heater                                       Off
H2 Flow                                      Off
Air Flow                                     Off
Makeup Flow                                  On    5 mL/min
Const Col + Makeup                           Off
Flame                                        Off
Electrometer                                 On











Signals
 Test Plot                                   Save Off
                                             50 Hz
 Test Plot                                   Save Off
                                             50 Hz
 Test Plot                                   Save Off
                                             50 Hz
 Test Plot                                   Save Off
                                             50 Hz


                                MS ACQUISITION PARAMETERS


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

Tune File                : atune.u
Acquistion Mode          : Scan


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

Solvent Delay            : 10.00 min

EMV Mode                 : Gain Factor
Gain Factor              : 1.00
Resulting EM Voltage     : 1753

[Scan Parameters]

Low Mass                 : 50.0
High Mass                : 550.0
Threshold                : 150
Sample #                 : 2       A/D Samples    4
Plot 2 low mass          : 50.0
Plot 2 high mass         : 550.0

[MSZones]

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


                             END OF MS ACQUISITION PARAMETERS


                              TUNE PARAMETERS for SN: US83140737
                        -----------------------------

 Trace Ion Detection is OFF.

 EMISSION    :      34.610
 ENERGY      :      69.922
 REPELLER    :      21.914
 IONFOCUS    :      90.157
 ENTRANCE_LE :      16.000
 EMVOLTS     :    1752.941
                               Actual EMV  :    1752.94
                               GAIN FACTOR :       1.00
 AMUGAIN     :    1586.000
 AMUOFFSET   :     113.438
 FILAMENT    :       1.000
 DCPOLARITY  :       0.000
 ENTLENSOFFS :      19.325
 MASSGAIN    :    -775.000   
 MASSOFFSET  :     -42.000   

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



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

    Fullscreen backinlet-now.txt Download 
    
                               INSTRUMENT CONTROL PARAMETERS:    GCMS#1
                               ----------------------------------------

   C:\MSDCHEM\1\METHODS\ZXH-STEROL-M10-40MIN-MS-1ULIN-SPLITLESS-BACK.M
      Thu Aug 31 13:15:54 2023

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

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

Oven
Equilibration Time                           0.5 min
Oven Program                                 On
    200 �C for 1 min
    then 4 �C/min to 270 �C for 1 min
    then 1 �C/min to 290 �C for 0.5 min
Run Time                                     40 min





Back Injector
Syringe Size                                 10 �L
Injection Volume                             1 �L
Solvent A Washes (PreInj)                    2
Solvent A Washes (PostInj)                   0
Solvent A Volume                             5 �L
Solvent B Washes (PreInj)                    0
Solvent B Washes (PostInj)                   2
Solvent B Volume                             5 �L
Sample Washes                                0
Sample Wash Volume                           1 �L
Sample Pumps                                 6
Dwell Time (PreInj)                          0 min
Dwell Time (PostInj)                         0 min
Solvent Wash Draw Speed                      300 �L/min
Solvent Wash Dispense Speed                  6000 �L/min
Sample Wash Draw Speed                       300 �L/min
Sample Wash Dispense Speed                   6000 �L/min
Injection Dispense Speed                     6000 �L/min
Viscosity Delay                              0 sec
Sample Depth                                 Disabled



Front SS Inlet He
Mode                                         Splitless
Heater                                       Off
Pressure                                     Off
Total Flow                                   Off
Septum Purge Flow                            Off
Gas Saver                                    On    20 mL/min After 2 min
Purge Flow to Split Vent                     50 mL/min at 2 min


Back SS Inlet He
Mode                                         Splitless
Heater                                       On    300 �C
Pressure                                     On    19.417 psi
Total Flow                                   On    19 mL/min
Septum Purge Flow                            On    3 mL/min
Gas Saver                                    On    20 mL/min After 2 min
Purge Flow to Split Vent                     15 mL/min at 0.75 min


Thermal Aux 2 {MSD Transfer Line}
Heater                                       On
Temperature Program                          On
    230 �C for 0 min
Run Time                                     40 min


Column #1

350 �C: 30 m x 250 �m x 0.25 �m
In: Back SS Inlet He
Out: Vacuum

(Initial)                                    200 �C
Pressure                                     16.089 psi
Flow                                         1 mL/min
Average Velocity                             38.737 cm/sec
Holdup Time                                  1.2907 min
Flow Program                                 Off
    1 mL/min for 0 min
Run Time                                     40 min


Column #2

350 �C: 30 m x 250 �m x 0.25 �m
In: Back SS Inlet He
Out: Front Detector FID

(Initial)                                    200 �C
Pressure                                     19.417 psi
Flow                                         1 mL/min
Average Velocity                             30.944 cm/sec
Holdup Time                                  1.6158 min
Flow Program                                 Off
    1 mL/min for 0 min
Run Time                                     40 min





Front Detector FID
Heater                                       Off
H2 Flow                                      Off
Air Flow                                     Off
Makeup Flow                                  On    3 mL/min
Const Col + Makeup                           Off
Flame                                        Off
Electrometer                                 On











Signals
 Test Plot                                   Save Off
                                             50 Hz
 Test Plot                                   Save Off
                                             50 Hz
 Test Plot                                   Save Off
                                             50 Hz
 Test Plot                                   Save Off
                                             50 Hz


                                MS ACQUISITION PARAMETERS


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

Tune File                : atune.u
Acquistion Mode          : Scan


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

Solvent Delay            : 10.00 min

EMV Mode                 : Gain Factor
Gain Factor              : 1.00
Resulting EM Voltage     : 2165

[Scan Parameters]

Low Mass                 : 50.0
High Mass                : 550.0
Threshold                : 150
Sample #                 : 2       A/D Samples    4
Plot 2 low mass          : 50.0
Plot 2 high mass         : 550.0

[MSZones]

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


                             END OF MS ACQUISITION PARAMETERS


                              TUNE PARAMETERS for SN: US83140737
                        -----------------------------

 Trace Ion Detection is OFF.

 EMISSION    :      34.610
 ENERGY      :      69.922
 REPELLER    :      33.641
 IONFOCUS    :      90.157
 ENTRANCE_LE :       3.000
 EMVOLTS     :    2188.235
                               Actual EMV  :    2164.71
                               GAIN FACTOR :       0.99
 AMUGAIN     :    1604.000
 AMUOFFSET   :     104.938
 FILAMENT    :       1.000
 DCPOLARITY  :       0.000
 ENTLENSOFFS :      19.827
 MASSGAIN    :    -767.000   
 MASSOFFSET  :     -47.000   

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



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

  • 0 in reply to garyb007

    Hey thank you. Yes, both the two inlets are using. We changed the parameters accordingly. Please find the attached files above.

  • 0

    Looking at this gave me a headache knowing you swapped inlets but I'm not sure every parameter matches. I'll let Paul take this one, but I noticed your MSD transfer line temps are different. The first one is at 280 (typical) and the 2nd one is 230.

  • 0

    I see your EMV went up from1753 to 2165 but you say you lost 80% response, yes something is wrong. Your flows from col #1 don't match the new col #2. In the first one your flow programs are on and now they are off and pressures don't match either.

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