How to deal with the less than obvious?

In environmental analysis, we often target a lot of compounds to get a detailed profile of certain pollution. However, due to different environmental process, not all of the compounds could be detected by our analysis method. For example, when I analysed PBDEs in 100 sludge samples, only a few congeners such as BDE-47, BDE-99, BDE-209 could be found in all of them. The other congerners such as BDE-28, BDE-17, BDE-153 could only be found in about 80% of them. Also some congerners such as BDE-77, BDE-53, …