Can Mass Spectrometry be a difficult technique?

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maceng7
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I'm just wondering if there are any difficulties that must be overcome to use mass spectrometry. For example if you were to use it with the three isotopes of Carbon ( C12, C13, and C14) where C12 has an abundance of 99%, C13 1% and C14 0.0000000001%. Based on the abundances how would mass spectrometry be difficult? I'm just curious and I couldn't find anything on the internet. Thanks
 
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What kinds of problems are you thinking about? Misattributing a [itex]^{13}C[/itex] to [itex]^{12}CH[/itex]? How do you think that such low abundances would affect the spectrum?