Chromatography Forum

Greetings,

I am a newbie here.
Help! I have a great difficulty and frustration in identifying some of major compounds in my sample of Capsicum frutescens. It would greatly relieve me from confusion if I can know how to identify the esters compounds. Would you kindly help me in this topic?

I used NIST 08 as my library database but the spectra doesn't match.
Is there any free library or reference I can look up.

However these researchers :Adrián Rodríguez-Burruezo, Hubert Kollmannsberger, M. Carmen González-Mas, Siegfried Nitz and Nuez Fernando.
(HS-SPME Comparative Analysis of Genotypic Diversity in the Volatile Fraction and Aroma-Contributing Compounds of Capsicum Fruits from the annuum−chinense−frutescens Complex) can identified the compounds.

I don't know where to start and a bit panicking.

Welcome to the forum.

Presuming that you are using GC-MS with electron ionization at 70 eV - the default on nearly all bench top MSs - for a given compound the mass spectrum is closely similar in all the MS libraries, so if the spectrum from your peak does not match the spectrum from NIST it will not match that compound's spectrum in any other library.

When you say that the spectrum does not match do you mean that it does not match the NIST spectrum of the compound you expect the peak to be, or that it does not match any spectrum in the library ? If it does not match the spectrum of your expected compound, what does it match ?. If there are no matches the peak probably contains more than one compound.

More details of what you are trying to do, and how you are doing it would be helpful. Is your background in analytical chemistry or in some other field ?

Peter

Welcome to the forum.

Presuming that you are using GC-MS with electron ionization at 70 eV - the default on nearly all bench top MSs - for a given compound the mass spectrum is closely similar in all the MS libraries, so if the spectrum from your peak does not match the spectrum from NIST it will not match that compound's spectrum in any other library.

When you say that the spectrum does not match do you mean that it does not match the NIST spectrum of the compound you expect the peak to be, or that it does not match any spectrum in the library ? If it does not match the spectrum of your expected compound, what does it match ?. If there are no matches the peak probably contains more than one compound.

More details of what you are trying to do, and how you are doing it would be helpful. Is your background in analytical chemistry or in some other field ?

Peter

Dear Peter,

Thank you for the warm welcome!
I felt really happy that I got instant response. My background is in Food Science.
Yes your assumption was correct, GC-MS with 70 eV, mass range = m/z 29–450

I have been doing analysis on volatile compounds of chili pepper (C. frutescens) and I wanted to identify the major peaks of the volatiles that I measured using GC-HS-SPME method. I used GC 7890 N (Agilent).

So it was unknown peaks I wanted to identify. I have been using Chemstation equipped with NIST 2008 library. But yes, the spectra of the peaks did not match. I tried to check the possibility of overlapping compounds by checking the major m/z signals but it looked just fine. It didn't seem to overlap.

Hello

You need to provide more information about your method:

-MS parameters (scan setting - threshold etc.)
-please paste some chromatograms/spectra

Otherwise is swimming in the ocean

Regards

Tomasz Kubowicz

Welcome to the forum.

Presuming that you are using GC-MS with electron ionization at 70 eV - the default on nearly all bench top MSs - for a given compound the mass spectrum is closely similar in all the MS libraries, so if the spectrum from your peak does not match the spectrum from NIST it will not match that compound's spectrum in any other library.

When you say that the spectrum does not match do you mean that it does not match the NIST spectrum of the compound you expect the peak to be, or that it does not match any spectrum in the library ? If it does not match the spectrum of your expected compound, what does it match ?. If there are no matches the peak probably contains more than one compound.

More details of what you are trying to do, and how you are doing it would be helpful. Is your background in analytical chemistry or in some other field ?

Peter

Dear Peter,

Thank you for the warm welcome!
I felt really happy that I got instant response. My background is in Food Science.
Yes your assumption was correct, GC-MS with 70 eV, mass range = m/z 29–450

I have been doing analysis on volatile compounds of chili pepper (C. frutescens) and I wanted to identify the major peaks of the volatiles that I measured using GC-HS-SPME method. I used GC 7890 N (Agilent).

So it was unknown peaks I wanted to identify. I have been using Chemstation equipped with NIST 2008 library. But yes, the spectra of the peaks did not match. I tried to check the possibility of overlapping compounds by checking the major m/z signals but it looked just fine. It didn't seem to overlap.

Is there anyone at your institution who can advise you on GC-MS ?

Peter

Have you read:

J. Agric. Food Chem., 2010, 58(7), pp 4388-4400

?

It might be helpful to you if you haven't. It looks to me like they did some things that you're trying to do.

Hello

You need to provide more information about your method:

-MS parameters (scan setting - threshold etc.)
-please paste some chromatograms/spectra

Otherwise is swimming in the ocean

Regards

Tomasz Kubowicz

Hello Tomasz,
Thank you for your response.
Honestly which parameter I have to specify, I don't really know.
Here is the settings
GC-MS analyzes were performed on a GC 7890N (Agilent Technologies, USA) linked to a 5975C inert XL Mass Selective Detector and the separations were performed with a DB-wax (60 m × 0.25 mm × 0.25 μm) column. The carrier gas (helium) flow rate was 32 cm/s, the injector and transfer line temperatures were set at 250°C, the detector was operated in EI mode (70 eV, mass range = m/z 29–450), and the temperature for electron ion source and the interface were set at 230°C. The compounds were identified by matching the mass spectra fragmentation pattern with the NIST 2008 library, and by comparing the linear retention indices (RIs) of n-alkanes (C7-C28) with literature data.

Should I put the spectra of unknown peaks picture?

Have you read:

J. Agric. Food Chem., 2010, 58(7), pp 4388-4400

?

It might be helpful to you if you haven't. It looks to me like they did some things that you're trying to do.

This paper was the one I was referring in my first post. I wonder how did they identify the compounds.

Is there anyone at your institution who can advise you on GC-MS ?

Peter

I have tried asking around.


Best regards,

Adrah

I am sorry if I sounds rude. Yes it's a bit frustrating for me not be able to find the compounds identification. I will come up with the spectra tomorrow (yet I will try to figure out how to make it into image.)

Adrah--

In the paper I referenced, doesn't it say (should be in the experimental section) how they identified the components in their samples?

I have an excellent book by Silverstein, Basler and Morrill called "Spectrometric Identification of Organic Compounds". If your databases don't give you good matches, perhaps interpreting your spectra yourself is the way to go. You need to have really pure peaks (no coeluters) to go this route.

Rb6

How poor are the matches you're getting?

One thing we do is take a second spectrum at the base of the peak and then use the subtract function. This can sometimes clean up the spectrum and improve the match.

Hi, with Agilent MSD pay attention to use STANDARD calibration to tune MSD. It's not set as default (atune is default mode). With S-tune your matches must be perfect compared to library. Try and let me know.

Regards.

Robertino Barcarolo