How searching against multiple libraries can lead to biased results in GC/MS-based metabolomics.

The main reason for biased results is that the information about the scan range is not stored in the metadata of library records. As a result, in the case of AMDIS and ChromaTOF software, some unrecorded peaks are considered as missing ones during the library search, the respective compound is penalized, and the correct answer falls outside the top 5 or even 10 hits. At the same time, the default algorithm for selecting the list of considered m/z values implemented in MS Search is free from such unexpected behavior.