Hydrocarbon Contamination

[Ento_Joe]

Morning all,

I have been running some samples on my GC-MS over the last few days and keep running into a portion of the chromatogram that has huge quantities of hydrocarbons despite none being in my samples. The contamination also appears when running a column blank.

The contamination is also present no matter which column I use (two are installed), which leads me to think something else is up.

Does anyone have any ideas? I have baked the column at 300C overnight and the peaks are still present.

Best,

Joe

[tkubowicz]

Hello

If you see hydrocarbons (14amu) I'd check it for:
-fingerprints (GC column, MS analyser, ion source)
-foreline pump oil
If you have FID you can check if it is from GC (inlet or column) otherwise MSD is next step (ions source cleaning)

Regards

Tomasz Kubowicz

[Peter Apps]

Hi Joe

I've suffered similar problems. Being ruthlessly practical; are the hydrocarbons obscuring anything you are interested in, or do they just spoil the look of the chromatogram ?

Can you say what the MW range is more or less ? it is petrol, diesel or lubricant range ?

Is there anything that makes the peaks get bigger or smaller ?, and is their retention time always the same ? Are they sharp peaks or humps ?

What are the samples and how were they prepared ?

Try a new sample vial, new bottle of solvent, new syringe, complete inlet septum and liner swap. Inject clean solvent four of five times, do the hydrocarbons stay the same size ?

Good luck, Peter

[Rndirk]

I had a similar 'problem' and i narrowed it down to plasticizers in the septa of my sample vials (phtalates).

If the contamination also appears without injection from a vial, a similar source is the septum in the GC where the needle goes trough. It can also bleed/lose stuff (sometimes you can see parts of it in the liner).

Being ruthlessly practical; are the hydrocarbons obscuring anything you are interested in, or do they just spoil the look of the chromatogram ?

I tried to get rid of it by trying out other septa, but see the comment of Peter. If you run in SIM or MRM, there a big chance you won't even see it. The fact that you see it means it is getting off the column. So unless it interferes with your analysis, I would just ignore it.

[Ento_Joe]

Hello all,

Thanks for your replies, they have been very informative.

I had been at a conference for the last week and wasn't made aware that an undergraduate student had been given access to what is essentially my machine. A lab tech "showed" them how to use the instrument, but incorrectly and as a consequence the inlet liner was ripped to shreds and pieces of it had entered the inlet liner itself. As the inlet liner was a SPME one there was no silanized glass wool plug to prevent this entering the column.

I have since re run a blank and it is considerably better, although the baseline drifts substantially. I'm also unsure as to how the contamination from the septa would be present on an injection made via a different inlet...?

Best,

Joe

[Rndirk]

I have since re run a blank and it is considerably better, although the baseline drifts substantially. I'm also unsure as to how the contamination from the septa would be present on an injection made via a different inlet...?

I assume there's a septum on your second inlet as well?

I'm glad your problem is at least partially solved. Please remember that the magnitude of contamination is very subjective. A 'huge' contamination seen by you can be seen as normal to another user of another instrument (us). It's easier to judge and give advice if you can provide us with a chromatogram; and the more details about the analysis the better.

[Ento_Joe]

I have since re run a blank and it is considerably better, although the baseline drifts substantially. I'm also unsure as to how the contamination from the septa would be present on an injection made via a different inlet...?

I assume there's a septum on your second inlet as well?

I'm glad your problem is at least partially solved. Please remember that the magnitude of contamination is very subjective. A 'huge' contamination seen by you can be seen as normal to another user of another instrument (us). It's easier to judge and give advice if you can provide us with a chromatogram; and the more details about the analysis the better.

No septum on the second inlet as a thermal desorption unit is plumbed directly into it.

I will obtain a chromatogram and come back to you!

[Peter Apps]

Hi Joe

I trust you had a friendly word with those responsible.

It is tedious but worthwhile to check the first couple of metres of the column for septum fragments using a hand lens with a bright light behind the column - you would be surpised how far little bits of rubber manage to travel. If you find one you have to cut the column downstream of it, there is no way of getting them out.

Peter

[Ento_Joe]

I have included some chromatograms of the contaminated blank runs:








Peter,

I haven't yet managed to find the person responsible, but I will most certainly be having a word with them. I will also be taking a closer look at the column this afternoon, hopefully there won't be too much septa in there!

Best,

Joe

[Peter Apps]

Yuk, that is ugly.

I can't see the masses on the spectra but they don't look like hydrocarbons to me - more like siloxanes which makes sense with the shredded septum. From the flat tops on the peaks there is a hell of a lot of it.

Peter

[Ento_Joe]

The peaks primarily consist of siloxanes and hydrocarbons - particularly in the C24 - C32 region.

I have just finished examining the inlet end of the column under a microscope after removing a 30 cm section, and there appeared to be small septa particles present. Just baking the column out for a few hours and then I will try running another blank to see whether this improves my chromatography.

If not, I will have to think about my move...

Thanks for your input and guidance!

Joe

[Peter Apps]

If you can get the column out of the oven and have a look at the first two meters it will be better - you cannot bake away septum particles. With your two-column setup though that might be tricky.

Peter

[James_Ball]

Sounds like the unknown student made an injection with a large bore needle, probably not even one made for an autosampler and the injection sent cores right into the inlet.

Either that or the solvent/sample that was injected contained massive amounts of siloxanes or dissolves siloxanes. If the sample does dissolve siloxanes it could have damaged the stationary phase itself.

[Rndirk]

This looks pretty bad indeed. If you have the time for it, you can try to save the column by cutting 10-20 cm at a time. Worst case is a new column.

I would also perform a good inlet cleaning.

[Ento_Joe]

If you can get the column out of the oven and have a look at the first two meters it will be better - you cannot bake away septum particles. With your two-column setup though that might be tricky.

Peter

Hi Peter,

I have whipped the column out this morning and had a look along the first two meters with a microscope, it seems I have managed to clear the column of septum particles by removing 30 cm from the inlet end.

Sounds like the unknown student made an injection with a large bore needle, probably not even one made for an autosampler and the injection sent cores right into the inlet.

Either that or the solvent/sample that was injected contained massive amounts of siloxanes or dissolves siloxanes. If the sample does dissolve siloxanes it could have damaged the stationary phase itself.

Hi James,

I have caught up with the student this morning and it seems they may have used an unsuitable syringe to manually inject their samples, although this syringe has mysteriously disappeared without a trace so I cannot see for myself.

This looks pretty bad indeed. If you have the time for it, you can try to save the column by cutting 10-20 cm at a time. Worst case is a new column.

I would also perform a good inlet cleaning.

Hi Rndirk,

I have removed around 30 cm of column and that seems to have improved things somewhat:



Despite the imroved chromatogram it still doesn't look quite right, as the baseline is a bit all over the place and quite high. The run conditions of the instrument for that chromatogram are below:

INSTRUMENT CONTROL PARAMETERS: Nema1
---------------------------------------

C:\MassHunter\GCMS\1\methods\SPME Constant Flow.M
Thu Feb 23 11:48:42 2017

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

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


No Sample Prep method has been assigned to this method.


GC
Oven
Temperature
Setpoint On
(Initial) 40 °C
Hold Time 2 min
Post Run 50 °C
Program
#1 Rate 15 °C/min
#1 Value 300 °C
#1 Hold Time 5 min


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

ALS
Front Injector
Syringe Size 10 μL
Injection Volume 1 μL
Solvent A Washes (PreInj) 0
Solvent A Washes (PostInj) 0
Solvent A Volume 8 μL
Solvent B Washes (PreInj) 0
Solvent B Washes (PostInj) 0
Solvent B Volume 8 μL
Sample Washes 0
Sample Wash Volume 8 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 3000 μL/min
Sample Wash Draw Speed 300 μL/min
Sample Wash Dispense Speed 3000 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

Front SS Inlet He
Mode Splitless
Heater On 250 °C
Pressure On 22.123 psi
Total Flow On 104 mL/min
Septum Purge Flow On 3 mL/min
Gas Saver Off
Purge Flow to Split Vent 100 mL/min at 2 min
Liner Agilent 5190-2295: 870 μL (Universal, low pressure drop, ultra i)

Back SS Inlet He
Mode Splitless
Heater On 250 °C
Pressure On 16.555 psi
Total Flow On 18.2 mL/min
Septum Purge Flow On 3 mL/min
Gas Saver Off
Purge Flow to Split Vent 15 mL/min at 999.99 min

Thermal Aux 2 (MSD Transfer Line)
Temperature
Setpoint On
(Initial) 280 °C
Post Run 0 °C


Column
Column #1
Flow
Setpoint Off
(Initial) 1 mL/min
Post Run 0.78872 mL/min

Agilent 19091S-433: 1
HP-5ms
0 °C—325 °C (350 °C): 30 m x 250 μm x 0.25 μm
Column lock Unlocked
In Front SS Inlet He
Out PCM A
(Initial) 40 °C
Pressure 22.123 psi
Flow 1 mL/min
Average Velocity 15.761 cm/sec
Holdup Time 3.1723 min

Column #2
Flow
Setpoint Off
(Initial) 0.2 mL/min
Post Run 0 mL/min

Agilent 19091S-433: 2
HP-5ms
0 °C—325 °C (350 °C): 30 m x 250 μm x 0.25 μm
Column lock Unlocked
In Back SS Inlet He
Out PCM A
(Initial) 40 °C
Pressure 16.555 psi
Flow 0.2 mL/min
Average Velocity 3.4526 cm/sec
Holdup Time 14.482 min

Column #3
Pressure
Setpoint On
(Initial) 15 psi
Post Run 0 psi

Agilent
Retention Gap
0 °C—325 °C (325 °C): 2 m x 150 μm x 0 μm
Column lock Unlocked
In PCM A He
Out MSD
(Initial) 40 °C
Pressure 15 psi
Flow 3.6477 mL/min
Average Velocity 268.23 cm/sec
Holdup Time 0.012427 min

Column Outlet Pressure 0 psi

PCM A
PCM A He
PCM A He Supplies Column 3

Aux PCM A He
Pressure
Setpoint Off
(Initial) 10 psi
Post Run 0 psi

***Excluded from Affecting GC's Readiness State***


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
------- -----------

Acquisistion Mode : Scan
Solvent Delay (minutes) : 0.00
Tune file : C:\MassHunter\GCMS\1\5977\ATUNE.U
EM Setting mode Delta : 0.000000

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

[Scan Parameters]
Start Time : 0.00
Low Mass : 50.00
High Mass : 350.00
Threshold : 50
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: US1435L416
---------------------------------

Trace Ion Detection is ON.

EMISSION : 34.593
ENERGY : 70.007
REPELLER : 17.568
IONFOCUS : 90.331
ENTRANCE_LE : 25.226
EMVOLTS : 1135.323
Actual EMV : 1135.3
GAIN FACTOR : 1.58
AMUGAIN : 1504.000
AMUOFFSET : 123.750
FILAMENT : 1.000
DCPOLARITY : 1.000
ENTLENSOFFS : 12.901
MASSGAIN : -477.000
MASSOFFSET : -38.000

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



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

Any further adive would be much appreciated, particularly with regards to correctly undertaking a thorough inlet cleaning.

Sorry for the very long post.

Best wishes,

Joe