Joint structural annotation of small molecules using liquid chromatography retention order and tandem mass spectrometry data

E Bach, E Schymanski, J Rousu
bioRxiv, 2022
Science Published: (Feb/2023)

We present LC-MS 2 Struct, a machine learning framework for structural annotation of small molecule data arising from liquid chromatography-tandem mass spectrometry (LC-MS 2) measurements. LC-MS 2 Struct predicts the annotations for a set of mass spectrometry features in a sample, using the ions9 observed retention orders and the output of state-of-the-art MS 2 scorers. LC-MS 2 Struct is based on a novel structured prediction model trained to benefit from dependencies between …

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