LC-MS analysis gives one peak and the molecular weight of this peak corresponds to my desire product. However, my sample gives three spots on TLC with EtOH:CH2Cl2 1:3. Do you have an explanation for this? Can this sample be considered as pure?
I assume you are using silica TLC plates and C18 on your LC-MS? What is your LC-MS mobile phase? What is the nature of your compound? Depending on the number of basic or acidic sites and their pKa's a pure compound may show multiple spots depending on the stationary and mobile phases. Also, remember the selectivity of silica and C18 will be different. I wouldn't consider the sample as pure yet because of the 3 spots on the TLC, but you will need to prove these are the same compound.
if you can, scrape some of the material from the TLC, dissolve, filter, and inject it to see if each of the spots show the same spectrum. Also consider changing the mobile phase on the LC-MS system to see of there are different spots that can be resolved (change the selectivity of the mobile phase).
dear first you assured that you have used isocratic or gradient mode in LC-MS system for the analysis of your sample. As in isocratic mode separation was not good and you may trigger with such problem. if you used gradient mode for analysis you may get the fine results along with proper combination of solvents.
hello Eleni . beside to what Jack silver says .you know the LC.Mass analysis process depends on the amount of your product ( concentation) to detect .so you may have more than one isomers in you sample ( geomerical isomers,.....etc). to be sure check the H-NMR for your sample to see exactly what you have. I think that help you to now the chemical structure of your sample.
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