what about the split conditions? and are you sure the FID is on? what's the H2 flow? sometimes it happens that it turns off spontaneously if the there are problems with the hydrogen flow (or any of the other gases). Just place a piece of clean steel (like the blade of a scalpel) on top of the FID and check whether there is condensation on the blade. 

Thank you very much for a response. I think FID flame is working properly as it gives baseline and the base line rises up at time 5 minutes but the peak is like a big hump and comes back at 12 minutes. I can see the response changing in mV as well. Anyhow I will again use the tip you have mentioned  in your response.

Dear Dr. Murtaza,

Are you using perkin elmer GC ? It has two sensitivity levels Range-1 and range -20 if you inject keeping range as 1 response will be higher and if select range as 20 it will decrease 20 times. Sensitivity can be further optimised based on your requirement with the parameter attenuation with 6 levels 0,1,2,3,4,5,6 in the increasing order of response.

And what about concentration? Is it over the detection limit?

What is the injection modality, syringe?

Also, you could try to increase the injector temperature, up to 250 ºC, in order to be sure that the whole hexane and acetone amount become gas immediately, so you have no delays during the chromatography which could make the peak lower and wider.

At last, I suggest you to check the response for other compounds with higher molecular weight (and therefore higher RT). If you have the standards, you could inject a n-alkane series.

Good luck!

I was forgetting: Is it a new column or is it old? this also makes the peaks lower and wider.

It sounds to me like you have a problem with the injector, a solvent peak should be extremely sharp and have a retention time of 1 to 2 minutes. If there is flow problems or a leak you can get a large broad peak. The other possibility is the detector, you listed an air flow, helium flow which I assume is the makeup gas associated with the detector, but no hydrogen flow. Is your column correctly installed in the injector and detector ? Sometimes if the column is to high in the injector or to low in the detector peaks will become broad. Check that your injector seals and septum are not leaking.

Agree with Mr. Reed, massive leak is a possibility (you can't detect N2 leaks as agilely as you can using He, with a thermal conductivity detector "sniffer"; you might consider mounting He as carrier temporarily as you check for leaks). Another possibility: column is clogged with graphite ferrule material; always scribe and break column end *after* placing ferrule on! Then mount on injector, and bubble-check (water!) the flow on the FID end before mounting in the detector (follow the same as above for this ferrule mounting, too!). Follow proper technique for mounting in the detector, or you may splinter the column end; you should be able to *gently* feel it bottoming, then retract 3 mm or so before cinching the nut (allows the column to move without bottoming and breaking). Improper column position in the injector might give you massive tailing, but not no peak. Also: are you using a silanized glass wool plug as the vaporization surface in the injector? Also: manually confirm syringe is ejecting straight!

your choice of  gases seems a little odd to me. N2 as carrier gas in capillary GC will give you very poor performance especially if you are using very thin films of just 0.1 µm. Change that to He or H2. Furthermore where is your "burning" gas? You only wrote about  He and "synthetic air". if it is a typo and you meant H2 it should be ok.

another reason may be an overload on the column. if you inject pure hexane/acetone you have to apply a split ratio of at least 1:100 in order not to exeed the capacity of your column.  

Oh yes, nitrogen as a carrier gas does not work well. I missed that point. Peter is correct, helium or hydrogen are the correct carrier gases for a GC column. Nitrogen can be used as makeup gas in a detector but you need at least hydrogen and air for the detector flame. I think the big clue is a solvent peak at 5 to 12 minutes.  As I said before it should start at 1 to 2 minutes and have a peak width of seconds and not minutes, even if the column is overloaded from a low split ratio, as Peter mentioned. So it could be the nitrogen or a flow problem from the injector side or both. Definitely get rid of the nitrogen carrier gas.

I have used N2 as a carrier gas to separate hydrocarbons and common solvents with no problems.  When I have seen broad peaks coming out at much later than expected times, the problem was almost always bad connections in the plumbing causing either leaks or restrictions to flow.  I would check the column fittings to the injector and detector and replace with new ferrules.  If that seems okay, I would disassemble and reassemble the injector followed by detector.

As I can see you are using N2 as carrier and He for FID. I think you should use H2 and zero air for FID. please try carrier at flow rate 1 ml/min. 

oven temperature is important here. set your column flow rate to give the optimum velocity through the column. check the column manufacture's Web site, they typically have guidelines for setting column flow. there may be an example chromatogram using a similar column and a mixture that would be sufficiently similar to what you want to do that you could try the conditions used for the example. 

Your most likely problems either no flow or no flame. Test flow by demounting detector end of column and doing bubble check; (remount column) and test flame by briefly setting a shiny metal object over the detector exit vent and looking for condensation of water. After that worry about major leaks, splits, etc.

By the way Murtaza, if you have flow and condensation, you still may have problems with your FID jet. Inspect by cooling, removing, and sighting up the barrel towards a light, with your finger wrapped tightly around the jet head (to block the surrounding light). You should be able to see the orifice; it should look round (and bright!). When you insert your column, you may need to gently manipulate it with the ferrule and nut not too tight, until you find the barrel and slide it up to the top (gently!), then retract 3 mm or so before tightening the nut (to avoid smashing the column into the jet head).

Check the pressure in your system and change septum in case you haven't.

***********The first step is defining the problem before trying fixes . ***************

From your observations, it appears that the detector sees peaks, but the resolution is terrible. Working to optimize or fix the detector most likely will not address that fundamental issue.  I don't see an indication of the column diameter or length, so there is no clear calculable notion of when the peaks might emerge from the column.   I would first calculate/estimate a retention volume for the peaks, based on published chromatogram/chromatograms of the materials under similar conditions of column and temperature. This would give an indication if the peaks you see are not artifacts of some kind.  Another  related approach is to introduce the materials individually and see if the  peaks come out at the two different places you have seen.

   If the peaks are a result of the materials injected, then the problem is one of resolution and conditions. These arise from many  things. It could be a large dead volume issue, a leak, a bad column, a faulty injection arrangement, or simply overloading the column.