I am going to do VOCs analysis using Shimadzu GCMS (it is not an accurate mass instrument). I just want to know if I will have problems with compound identification later by MSMS analysis.
Well, I will put it like this.. yes you will have problems.
However, if you have EI, MS/MS data and since your VOCs are not as complex as other molecules in metabolomics you might still have a realistic chance to identify many of the compounds. It is important to use all the information from your instrument and combine them in a propper way. EI provides arleady many structural information and cobined with MSMS you can sytematicly identify many compunds. Use the NIST library for example and try to get your own database with propper references. Use also the rentention times as importnatant citeria for identification. It will take a bit time but' you don't need a high resolution instument in this case. Nevertheless, high-res would make it much eayser and would help in complicated cases (bad fragmentation, no useful MS/MS spectrum).
The answer depends as well as from your scientific question and the characteristics of the samples. If the metabolic patterns of samples and especially their limits of variation are widely unknown and/or the number of analyses are huge I strongly recommend a two step approach. First do a screening with a common MS with nominal mass. This will ensure high stability and cheap analyses. Second use an exact mass instrument for compound identification (inclusive peak deconvolution etc.) only of interesting metabolic differences in a proper selection of the sample batch. By this way you can focus the use of the more expensive and difficult exact mass instrument on few samples.
You can use libraries such as the FiehnLib.
Anal. Chem., 2009, 81 (24), pp 10038–10048
DOI: 10.1021/ac9019522
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