I think it is impossible same compound have different retention times in chromatography, but different compounds could have same Rts. I think your data from the library of the GC-MS, so based on their measured MS, the software predicted the possible compound(s). For confirming the identities of the compound(s) you should compare the measured Rt and MS, with  Rt and MS of the authentic standard(s) (with same condition of GC-MS).

This can originate from different sources, e.g.

1. Among others compounds, early eluting methanol, acetonitrile can form droplets after injection, rather than distributing ideally into the capillary film, which can cause mulitple peaks. Reduce injection volume and change temperature of injection port to study the effect. Less injection may already help.

2. Stereoisomers might be separated by the GC column, often observed for sugars, derivatized by oximation into syn and anto isomers, which can give 2 or even mutliple peaks with identical spectra. Check your protocol and compounds for such potential effects.

3. To heavy sample overload can cause a contamination of your injection system (liner, port pTV sampler, etc.) so that compounds will contaminate into subsequent injections. Replace liner and inject blank sample with only solvent to check.

Best,

Christoph Wittmann

Dear Jai

Perhaps your question is more concern towards repetition of names of saturated n-alkanes (straight chain) hydrocarbons in library search results (sl no.9-11; 13-20 & 22-25 of XL file). In my opinion, the following points may be useful for you to get more clarity:

The molecular ion peak of saturated hydrocarbon is always present, though of low intensity or sometime not visible for long chain compounds.

Fragmentation pattern is characterized by clusters of peaks with m/z 14 amu units apart. The largest peak in each cluster represents a CnH2n+1 fragment accompanied by CnH2n and CnH2n-1 fragments.

The most abundant fragments are at C3 and C4.

The ion fragment abundances decrease in a smooth curve down to m/z [M - C2H5]+, [M - CH3]+ peak (weak or almost missing in recorded spectra).

Please nore that compounds with more than eight carbons show similar spectra. Thus, identification shall depend on the molecular ion peak. Since,  long chain hydrocarbons do not reveal a clear M+. This is  why you are getting same name in library search.

Moreover, due to the absence or very low abundance of parent ion or molecular ion peak in mas spectra of your sample is creating such kind of confusion. Otherwise, its impossible to see elution of same molecular wt compound at two different elution time  or RT as rightly mentioned above by learned researchers.

You may either run standards of your choice (mixture of saturated hydrocarbon, Sigma make) using same programme (EI mode) to avoid confusion or perform a fresh analysis under chemical Ionization mode to find out the pseudo-molecular ion peak for respective compounds.

I have a query regarding the type of analyzer with you spectrometer. Are you using ion trap based mass analyser or typical quadrupole? Please discuss it.

Good luck

Dr Chanotiya

Most of the time, EI mode of ionization is a near total fragmentation technique and may not provide a molecular ion. Hence it is also advisable to do a Positive Chemical Ionization (PCI)  analysis of your compounds so that you will be able to see a molecular ion and hence the confirmation by molecular weight.

Hello all,

It would be useful to have a detailed description of the analysis procedure: kind of analyser (ion trap or quadrupole), column, concentration/extraction technique (head space injection, SPME, liquid injection…), type of injection mode, manual or automated and identification procedure (library used, manual identification or automated).

In manual injection, if the run does not start inmediatly after injection, a little peak sift can be observed, but not as high as yours.

Nevertheless, it seems an identification issue (seems difficult to have a C19 compoun –peak 12– before a C17 compound –peak 14–). I agree with Dr. Chanotiya, you should inject standard compounds under the same conditions in order to have a certain identification. I am not a chemist, but I have usually found the molecular ion in EI with quadrupole detection, which helps the identification.

Good luck,

José Sánchez del Pulgar

Hi Jai:

I have seen something similar before. Not sure if this is what your are seeing but...

Isomeric connections show the same spectra while having different RT because the arrangement difference changes the phase affinity interaction with the column. This slows or does not slow the isomer which when library searched shows the same name.

If the base material has a different arrangement or a percentage of the compound is a different arrangement you will see this at different RT's as well while the spectrum is the same.

I hope this helps,

Hi,

it can be if compounds have two or more isomers. For example in analysis of monosaccharides (alpha/beta).

But in your case, there are probably alkanes. Alkanes have similar mass spectra, because parent ions of higher alkanes (correspond to their mass weights) are usually not preserved in EI ionization. I think, you identified compounds only by MS library. MS library is a good tool for preliminary identification but not for final identification. You must analyse pure standards. MS library can identify more peaks as one alkane because of similar mass spectra (only fragments) of alkanes.

You should inject mixture of alkanes and identify peaks properly.

Hi,

It is  impossible to have two peaks for a single compound in chromatography. One possibility is, if your column gets old then there will be splitting of peaks and if sample concentration is very high there will be a possibility of split peaks which gives same compound name. Other possibility are the compound contains the isomer which will be of same mass and in MS library that isomer is absent.

Hope these information will help to solve your problem. Good luck.

Regards,

Karunakara A.C

Looking at your excel file, it is rather clear that the analytes with the same name but different retention times are only isomers of he same alkanes. It is sufficient to change the position of a methyl group in the carbon chain that retention times change.

If you see two peaks in your chromatogram for a pure compound, the issues might be originated from the following: 1) Poor injection technique 2) Overloaded detector 3) Poorly installed column in the injector (

Hello Jai,

Hope you are pure form of higher alkane standard solutions.those should be more than 99.5% as they might contain excess hydrocarbon impurities which shows diff. RT's and MS library matches it to be same compound. and system cleaning and column selection is also imp step.

I am doing same analysis on mid and higher alkanes. but, as m using high quality standards and cleaning procedures we getting Standard peaks RT only and library matches it perfectly when blank subtraction is done.

f you see two peaks in your chromatogram for a pure compound, the issues might be originated from the following:

1) Poor injection technique

2) Overloaded detector

3) Poorly installed column in the injector (

I have same conditions for powder sample and I used head space SPME and GCMS, is it possible have 2 peaks with same compound? I don't use any solvent or liquid thing

Should I chose one of them or just combine the %area?

Thanks for your answers @Charles Lyle and Kami Krumah. Please can I have a reference for your submission (article or write up). I have the same issue and I am trying to back up my observation; of course with evidence. Thank you.

I also have the same problem. I have a pyrolyzed coniferyl alcohol (CFA) sample which contains a few % of unreacted CFA and its products. I get three peaks with 2-3 mins different residence time but similar mass spectra. since this compound has a long aliphatic tail, I think it should have different isomers. has anyone seen sth similar?

When I was using the essential oils in GC-MS it has happen many times and it is destructive analytical technique, CAS will be differ within the isomers/similar probability and my observation is that having compounds higher than 10% will elute 2 to 3 times after 12 to 15 min of retention time. Finally you can sum up the %. Usage of new column and theoretical plate count check regularly and minimize the similar peaks in chromatography.

Anybody is using LC-MS? because I am getting the same situation in MS1 level of LC-MS data during my global metabolomics study. Same KEGG id, same mass but different RT. Any clue?