GCMS newbie and the questions to be solved...

[nilo]

Hi All,

I just start my career in chemistry field 3 months ago. I'm assigned by lab manager to incharge for the GC-MS instrument. Our lab have other instruments like FTIR, LPC, SEM, HPA and also IC. After 1 month been working there, i realized that it's quite difficult to handle the GC-MS instrument. It's because the GC-MS is quite sensitive, extra care is needed either in samples preparation or instrument handling. For example, before run the samples, we have to auto tune / standard spectra tune the instrument, if air leak is detected, some services is needed (tighten/loosen the nut that connect column from GC to MS). After that, normally we will get a nice tune report. Below i stated some questions.


1. Why each time after a sequence finished run, after heat the column for 2 hours (at ~300 Celsius), the standard spectra tune generated will showing the air leak problem ? (my lab manager didn't let me know the reason, he just said air leak will affect the sensitivity and help me to settle it.) (Company just bought that latest GC-MS from US, compared with another one old GC-MS, the design of autosampler is abit different).

2. Why the emVolt will increase ? I still remember that we started to use at the end of december, the emVolt at that time is 990, and now after 1 month the instrument being used, the emVolt raise to 1130. My lab manager told me that emVolt if higher than 2500, the instrument can consider as useless, he is not telling me the reason behind it. From my knowledge, i knew that adjusting the emVolt can make fake sensitivity. The height of spectrum for the compound detected can be adjusted if we increase the value of emVolt (but the height of noise actually is increased actually).

3. Basically, the results generated by the library can be trusted 100 % ? For example, compound Hydrocarbon C40 that having longer retention time will showing the peak at minutes 39 (based on the proper GC-MS parameters setting), when i manually analyze the peak, it's showing others compound. Why ? The concentration for C40 standard is quite high also (100 ppm).

4. Any advise from those who are experiences in chemistry/biology field ? I'm considered as newbie to handle GC-MS instrument since my job's tasks mainly on results interpretation. I have to gain more knowledge for better future.

Sorry for my English. I'm a Chinese from Malaysia. Hope i can improve myself through this forum

[nilo]

Reserved 1

[nilo]

Reserved 2

[boris_gto]

hi nilo.
first able what kind of GC/MS you use. but for my opinion:
1. there is a several different metals used (like brass and ss) that used for MS interfase/transfer line connection - a different expansion value.

2. a things get dirty (like ion source): tune is trying to deal with it by increasing EM value. the numbers for EM runs between 1200 to 3000. if you increase EM you will increase you sensitivity as well but signal to noise ratio will doesn't changed (or even get down:)) so just clean you GC/MS occasionally.

3 you can not trust library to 99% always check! a specially for high mass compounds. maybe you don't see all spectrum try to increase scan mass range (you will pay with sensitivity for it).

[lmh]

and electron multipliers do gradually age. It's quite normal for the voltage to increase, and it can't be avoided completely no matter how clean you keep your instrument. If the voltage goes too high, eventually the instrument will fail, but all you need to do when this happens is buy a new EM horn and start again.

[littlepeaks]

Check your transfer-line nut to see if its leaking. Sometimes they need tightened a little bit every so often, but NOT TOO TIGHT.

The multiplier does go up with use and age, but eventually, when you clean your source, you'll see it go back down again, somewhat.

[Don_Hilton]

On library searches: look search throug the older posts on the forum. I believe that library searching has been discussed a few places and some suggestions and warnings for using searches have been given. I need to leave the house to go to work, or I would add more to this post...

[nilo]

>>Hi boris_gto
Model of MSD is 5975, with rectangular shape of autosampler (Have heating function).
Yup, since the oven temperature changed from 35 degree celcius to 300 degree celcius, thermal expansion of the metal will affect it. This is because before tune (standard spectral tune), the oven need to be heated at 300 degree celcius for 2 hours before bring down to 35 celcius when perform the tune.

That day my technicion just performed ion source cleaning using aluminium oxide. I saw several black dots on the surface of ion source (Bombarded by electron ?).

I have just increased mass scan range to 700 amu (Is it consider low for analysis of organic compound). For the sensitivity issue, do you mean the higher the mass scan range, the lower the sensitivity ? Sometimes i cannot figure out the reason why the MSD can not identify the hydrocarbon compounds. FYI, i am analyze it using the Mix Hydrocarbon Standard.



>>HI lmh,
Cleaning the ion source does give lower value of emVolt, last month my boss just cleaned the ion source (for the old GCMS instrument), the emVolt fall from 2000 till 1250. But true in fact as what you've answered, the emVolt goes higher for each use, now the emVolt is around 1350.



>>Hi littlepeaks,
For the leaking issue, i've learned about it, make the nut tighten abit and then bring up the GC oven temperature before bring it down agains for tuning purpose. So far the level of N2,H20 and 02 never exceed 3% after doing so. Agreed with you about the issue of emVolt.


>>Hi Don_Hilton,
Thanks for your info, i look through about it from older post

[nilo]

Hi all, few more questions waiting to be solved.

1.Recently i am facing problem on blank chromatogram. I'm using the hexane (JT Baker and Tedia with purity >99.99 %) to extract the clean beaker, and then analyzed it using GCMS. The problem is, beside having solvent peaks (In the range of RT4.5-RT10.0), few peaks are observed after RT 10-15, i just wonder what is that (Siloxane from column ?). FYI, the column is heated for few hours at 300 degree celcius before tuning. Below stated the parameter used.
Initial Temperature : 35
Initial Time : 1 min
Solvent Delay :4.5 Mins
Final Temperature :300
Injector Temperature :300
Temperature Ramp :15C/min
Sample injection :3 ul (splitless mode)

2. The height of starting peak is around 30,000, exceeded 5000 (My boss told me the lower the height of starting peaks after solvent delay, the more nice the result, is it true ? ) This few days i keep run the Mixhydrocarbon standard (C8-C40), the new GCMS is capable to detect C9-C26 (Height of compound peaks is quite high) with concentration 5ppm (ng/uL), but it failed to detected C32-C40 and the compounds C26-C30 are detected but in small amount, i think the noise has erased those peaks (The ratio of each type of hydrocarbon is same)-For example, 5% of n-Nonane, 5% of n-decane and so on until C40

[Peter Apps]

Q 1. You can use the MS to identify what compounds are causing the peaks.

Q 2. If you are injecting 3 ul of the alkane standard as you do for the hexane blank, you have 15 ng of each compound on the column, which is plenty for the MS to detect. The reason that you do not see such good peaks for the heavier compounds is that thier retnetion times are too long with the rapid and short temperature programme that you use, and/or they do not vaporize effectively from the inlet. Good chromatography with C30 - C40 hydrocarbons is usually done on columns with very thin films of stationary phase.

Regularly heating the column for hours at 300C will shorten its lifetime.

Peter

[nilo]

Hi >>Peter Apps

Well, i had recorded some of the spectra and result (analyzed by chemstation's library). One of the peak generated at RT 11.90 came with
ion 43 (Abundance=25000),
ion 71 (Abundance=47000),
ion 149 (Abundance=25000), and
ion 177 (Abundance=5000).

Beaker Blank Chromatogram and spectra (for peak at RT 11.90)



While the result obtained by matching the spectra with library showed Pentanoic acid,2,2,4-trimethyl-3-caroxyisopropyl,isobutyl ester (CAS=140775). How come the ester exists on my blank. The preparation of beaker blank is briefly explained as below :
300 mL beaker is washed with detergent and ultrasonicated for 1 hour >> Dry at oven with temperature 110 C >> Dry at oven with temperature 500 C for 5 hours to fully destroy all the contaminant inside the beaker >> Rinse with acetone for 20 times and Hexane for 20 times >> 30 mL of hexane is added and let it evaporate until 1 mL under fume hood >> 1mL is transferred to cleaned vial >>GC Direct injection

Spectra Library matching result (Probability >50%)


2. For the alkane standard with concentration 1ng/uL (ppm), i had injected it by volume 1 uL since the volume needed by my calibration is 1 uL. All the GC or MS parameters has been checked and it's same with the procedure. Vaporization maybe is 1 of the factor that contributed to low sensitivity (small peak) for heavy hydrocarbon detection since low hydrocarbons are detected in very sharp and high peak. I forgot to check the type of GC Column, it seems like HP xxx. 30 Meter in length

[nilo]

1.Several Peaks are observed after Retention Time 10 (RT>10). Solvent used : Hexane TEDIA n-hexane 95% (HPLC Grade).
Attached the chromatogram of Solvent Blank. (Result of solvent blank obtained by direct injection of the solvent into GC.

Solvent Blank Chromatogram


1 more questions, the early 1st line (called as starting peak ?) eluted at height 40,000 , any solution to bring it down to below 10,000. Monday just changed the septa (at inlet).

[Peter Apps]

I can't see the chromatogram, but 95% purity has a lot of potential for extra peaks. HPLC grade means that it is suitable for high performance LIQUID chromatography, not gas chromatography. Try to get some GC grade hexane - use the 99.99% purity that you mentioned in your 12 March post.

Peter

[willnatalie]

What ferrel type are you using for the column to the transfer line? It should be a vespel/graphite, full graphite will always leak. If they are new, once heated at the max temperature, they tend to shrink a bit and need to be tightened again.

I would not trust that library with that data.

Since you are heating before the run I would look more toward an injection problem (i.e. hexane is what you have in the clean-up solvents in your ASL turret?). How old is that needle? The liner? If this is extremely dirty you could cut an inch of so off the front of your column.

"i just wonder what is that (Siloxane from column ?)" The column will not give peaks, just bleed constantly and increase with the temperature.

The only thing that could suggest with the invisibility of C30 and up is that they are not reaching to the MS. Is the temperatures of your transfer line at 300C?

Normally when we run these types of runs we use a DB5 column and run it to 325C.


Good luck

[Peter Apps]

Hi Nilo

I still cannot see chromatograms.

A very large peak that elutes early in the chromatogram may be due to the solvent - you can check this by looking at the spectrum. In GC-MS it is normal practice to turn off the MS filament until the solvent peak has eluted, and to turn it on before the first analyte peaks elute of course. You may need to extend the time for which the filament is turned off, or it could be that the solvent peak is either eluting later than it should, or is tailing more than it should. Late elution may be due to a carrier gas flow that is too slow, or a column temperature that is too low. Tailing of a solvent peak may be becuase the inlet liner or the top of the column are dirty, or because the split vent is opening too late (or not at all) in a split/splitless injection.

About the glassware cleaning - make sure that you rinse very well with clean water after you wash with detergent, and then after you bake at 500C do not rinse with other solvents, which can only add contaminants. If you leave an open beaker of solvent to evaporate down in a fume hood it will pick up all sorts of contaminants from the air. It is better to evaporate it under a stream of clean nitrogen.

And you should not trust library matches unless you have supporting evidence for the identification.

Peter