How do you know that the two peaks are the same compound ?

Many different compounds, especially those with long alkyl chains have spectra so similar that they cannot be reliably differentiated by mass spectrometry. If you think that they are the same compound because a library search gives the same best fit then the search is probably wrong for at least one of the peaks.

Also, stereoisomers often have very similar spectra but different retention times.

Or you may have a problem with the GC that is causing retentions to shift between runs.

I would just add to Dr. Apps answer recommendation to use a standard for Your compound, individually included in the same GC-MS run, and detect its RT.

I will add that you did not mention the RI difference, remember that RT is recorded at the highest point in the peak. If there are high concentration differences you can find some sligh differences in RT such as 0.01 min for the same compound.

ok i will add RT. 

As Sandra touched on, you can use Retention Indices (RI) to confirm the MS library identification of a compound peak. So if you don't have access to a standard that you can run the using RI's will help refine your MS library matches.

Hence if you have more than one peak labelled by the MS library as the same compound then it is likely that a published RI for that compound will line up with only one of these peaks. If you run a suitable alkane mix then you can determine the RI values for the peaks run on your system and then compare these to published data identifying the compound in question run on the same column type. You will then find this helps eliminate the false identifications. As Peter mentioned earlier it maybe that these peaks have very similar structures and hence produce MS spectra that are very close hence distinguishing them using an MS search alone is difficult. Hence using RI values will help refine your MS library matches.

Regards

Jason :)

Dear Shazia Kanwal Malik 

I am agree will all so you need to refer standard to monitor your analysis.

Thank you

Marius

Dear scientists,

Thanks you for helping me. I just want to ask is there any specific web link for the search of RI for compounds.

Cant it be possible without using standards. standards are very costly.

Hi Shazia

Try www.chemspider.com it has information about retention indices under a section called "Properties - Gas Chromatography" just scroll down till you find the options. These groupings include kovats, normal alkane and linear. Make sure you can identify results that have the same column type that you are using. A published reference will be given for each retention index listed.You will find there often a number of published RIs for a given column type so pick the general consensus. Not everything can be found here so other options are www.flavornet.org and www.pherobase.com. But chemspider is the best I have found.

Regards

Jason :)

The NIST chemistry site also has retention indices, but only for a limited selection of stationary phases.

Keep in mind that a retention index that matches your MS library hit does not rigorously confirm identity, but if your peak's retention index is clearly different form the literature value for the compound that the library search returns then the library search is almost certainly wrong. If all you have is GC-MS data, the minimum confirmation that any reputable journal will accept is co-elution with an authentic standard.

You still have not told us why you think that the two peaks are the same compound.

Peter,

because of the SI number of  NIST library searching hints, i was confused. 

Thank you Shazia

Do you get two peaks with the same search hits on one chromatogram, or are they in different chromatograms ? 

Do the other peaks on the chromatogram have retention times that are the same from run to run ?

Peter I m attaching both files. Plz guide now

yes it was the same chromatogram. Secondly how to measure RetIndex, it is zero here.

Hello Shazia

You have molecules with long alkyl chains - the library searches cannot differentiate well between them. To measure a retention index you need to run a series of n-alkanes under exactly the same conditions as you ran the samples. The retention indices of the alkanes are by definition 100 times their carbon number. Find the alkanes on either side of the peak you are interested in and divide the time between them into 100 segments, then calculate how many segments after the first peak your aldehyde elutes. The retention index is 100 times the alkane carbon number plus the number of segments. If you google gas chromatography retention index you will get a lot of much clearer explanations. 

Do not be surprised if none of the library matches corresponds to the RI.

Also, you need to background subtract you spectra - that big 169 peak is probably in the background and it makes the library fit scores lower.

Peter

The same situation. Silylated carboxylic acids give two, and even three peaks with practically identical mass spectra of pentadecanoic acid. A sample was runned in two different laboratories and similar results were obtained. The spectra do not differ, except for minor non-permanent peaks. The branched hydrocarbon skeleton should give significantly different mass spectrum than that of straight chain carbonic acid.

Compare:

In this figure, two spectra are near. Compare will be much easier. One corresponds to a peak with a retention time of 21.237 min, the other corresponds to 21.325 min. How is this possible - nobody knows... :D

You column is hopelessly overloaded, causing the peaks to front tail and overlap, which gives mixed spectra for both peaks. Use splitting or dilution to reduce the amount in each peak by 10 times at least, and maybe 100 times.

I think I had same problem while using GCMS...This is one of the demerit...

I suggest you use LCMS-QToF...

For a particular compound of interest the there is always a fragmentation into Parent & daughter ions...These ions bears same chemical compounds...

A change of method will clear your doubt...

No, Peter. :D Column is not overloaded (look at Abundance scale, values are very low. Chromatogram extracted from TIC by m/z=299). Instead, look here for TIC chromatogram and it's magnified fragment:

Then you have something else distorting the peaks - they should not have that slowly rising leading edge and they should be a lot taller and narrower.

Probably, you're right concerning fronting peak. However, calculation of N (N=16*(tr/W)2) gives N=775,000 t.p. for these peaks. Not bad for 25 m capillary column. Anyway, it doesn't explain similar spectra. No more coincidings observed here. Same conclusions were made during analysis in another laboratory (500 km apart :D). It is a very rare chance of a simultaneous mistake or poor separation.

https://blog.restek.com/?p=8558

Please Go through.