I am wondering why mathane is burned to CO$_2$ for isotopic analysis, e.g with a mass spec? I have looked into several text books, they all describe how to do it but not why. Is it because of a interference on mass 16? Analysing methane it it is would give you also information about the D/H ratio. So why?
There are different types of mass spectrometers with different modes of sample introduction, analyte ionization and ion selection/focusing. You cannot generalize "with a mass spec."
In many cases of isotope ratio mass spectrometry (IRMS), compound specific isotopic analysis (CSIA), or Gas Chromatography Combustion Isotope Ratio Mass Spectrometry organic compounds (not just methane) are burned and oxidized to carbon dioxide and water and analyzed as such to determine the total ratio of carbon-13/carbon-12 and hydrogen-2/hydrogen-1. However, combustion is not the only way to introduce compounds in the mass spectrometer.
Another secondary issue is that there if often more noise at low mass ranges. Methane is a small molecule (m/z =16) and carbon dioxide is relatively large (m/z=44).