Negative mode is responsive for the presence of electronegative moity detection at the detector.

For -enal type molecules you may not get ionisation, rest of the spectrum  is perhaps due to decomposition products / other impurities at detector

Ramesh.

Dear Delhousie

The short answer to your question is that your compound may not he 100% pure. However, the negative mode signal is very weak at 266 which mean that there are either very little contamination or that the contaminant only have a weak negative mode signal. Your compound may not have a good negative mode signal. The group of compounds around m/z 353-297 contain aliphatic character (14 of CH2 differences)  and could be either lipids or contaminant from the extraction (detergent of plasticisers). The other compounds are any one's guess, but you will have to consider the plastic ware, solvents and glassware you use, as many contaminants can be carried into your pure preparation. Plastic ware can leach phthalates and slippage agents and your glass ware may contain residual detergent if it is not properly washed and/or pyrolised.

The long answer is that you may have a more complex molecule than dodec-2-enal. I have quickly analysed your two spectra and think that you positive mode spectrum could be a fragment spectrum of a larger molecule containing the dodec-2-enal as moiety. You will need to consider the 274.3 (possibly the molecular ion)  and 109.3 ions also, as it seem that they are related to the 183. 2 ion. You must also consider doing NMR on your purified compound.

Hope it helped. Good luck with your structure elucidation.

Regards

Marina

Are you running ESI because that is the only mass spec you have access too?  I would think that GCMS would give a much more definitive identification of dodecenal.

Thanks for the reply everyone. During my isolation and purification steps, I managed to optimize the protocol to get the pure compound. In the process, I used acetonitrile to dissolve my crude extract and the pure compound. Therefore, as suggested by my supervisor and the MS operator, I can proceed with ESI-TOF-MS using either aqueous methanol or aqueous acetonitrile as the mobile phase. I will consider doing NMR and GCMS.

Are you using the same mobile phase for both positive and negative mode lc/ms analysis? A good way to analyze unknowns is to alternate between positive and negative modes in the same run. As you will be comparing the positive and negative spectra at the same retention time, it is easier to interpret the results.  

Yes. I've used the same mobile phase for both runs and the runs (positive and negative) were performed at the same time.

Ideally one would see (M+H)+ ions in positive mode and (M-H)- ion in negative mode as same compound is presented to the mass spectrometer (same retention time, alternate +/- mode scanning). But other factors can contribute to what is actually observed: ionization efficiency, mobile phase composition, instrument tuning for greater transmission of the produced ions. Other types of ions observed in positive mode are (M+Na)+, (M+NH4)+, etc, though their intensities are expected to be lower than that of (M+H)+ ion. Negative mode is less predictable: one might see (M+acetate)-, (M+Cl)-, etc. 

Based on the figures you have attached (still not clear if the data is coming from the same file), the signal in positive mode is huge (9E5) even for a single scan. I do not know, why you would exclude 274.2 ion from consideration. The negative mode signal is extremely weak (266 even after summing many scans). You may be seeing lot of background ions rather than signal from your compound eluting at that time and your compound is not ionizing as well in negative mode (not to overlook the instrument tuning).

The positive ion spectrum and the negative ion spectrum appear to have been acquired (or at least processed) on different instruments. The negative ion data appears to be from a Masslynx system but the positive ion appears to be from (possibly) a Thermo?  Are you sure the positive and negative data was acquired on the same instrument? The data is quoted to 4 decimal places is it accurate mass?

The process seems too complicated. Have you found a large, clean GC or GC-MS peak that appears to be correct, with a reasonable retention time at about 14 carbon equivalents? It used to be the easy  thing to collect that peak by preparative GC with a splitter, followed immediately by GC-MS.  Worrying about complex LCMS solvents in a mass spec is complicated, whereas the GC peak should be obvious.  

Microscale chemistry is easily done with DimethylDisulfide in diethyl ether plus a crystal of iodine, as you need only a few micrograms of your peak.  Addition of dimethyl disulfide (CH3S-SCH3 molec. wt 94) to the double bond of your aldehyde gives a heat-stable adduct that survives GC- and GC-MS, and elutes at about 7 carbons later than the starting unsaturated aldehyde.  This adduct should then fragment at the location of the double bond, yielding a large fragment of C10 + SCH3  (141+47=188).   There should be examples in the literature of conjugated aldehydes and their derivatives if it misbehaves with DMDS.

see:  Carlson, D.A, C-S. Roan, R.A. Yost and J. Hector. Dimethyl Disulfide Derivatives of Long Chain Alkenes, Alkadienes, and Alkatrienes for Gas Chromatography/Mass Spectrometry. Analyt. Chem. 61:1564-1571. 1989.

Hi all. I've uploaded the wrong chromatogram for the negative mode. Attached are my latest runs using the same equipment.

What do you see in positive mode above m/z 500 and what is the signal intensity of each the peak in the two spectra? Is it a different extract from the previous one or is it just "'older"?

There are no significant peaks observed above m/z 500. The intensities of the peaks are about the same as the ones at 380-390. The chromatograms that I've attached recently were obtained during my latest analysis using the same batch of purified compound.

Okay, I suggest that you do the following to rule out artifacts: Do a blank extraction and chromatographic run, collect the fraction at the same Rt , treat it the same as your sample and analyse it in positive and negative mode as before. Alternatively for a quick check, you can just (and must always) analyse the sample solvent in the same set of runs as your sample. You must also take care that there is no sample carry-over via a contaminated source, so it helps to do more than one injection until you get repeatability in the spectra.  

On you positive mode spectrum - it seems now that you have a dimer of the 183 ion at 365, which is  possible depending on the compound and instrument settings.  Strange that the 274 disappeared, but and 109 is still there, so was it real or is it an artifact? Was the instrument settings the same in the second run? . I suggest that you also do a experiment where you fragment the 365 and 183 ions to see if you get the 109, and maybe 274. These are all things you need to consider when planning you MS experiments.