title: CASMI-The Small Molecule Identification Process from a Birmingham Perspective.
abstract: The Critical Assessment of Small Molecule Identification (CASMI) contest was developed to provide a systematic comparative evaluation of strategies applied for the annotation and identification of small molecules. The authors participated in eleven challenges in both category 1 (to deduce a molecular formula) and category 2 (to deduce a molecular structure) related to high resolution LC-MS data. For category 1 challenges, the PUTMEDID_LCMS workflows provided the correct molecular formula in nine challenges; the two incorrect submissions were related to a larger mass error in experimental data than expected or the absence of the correct molecular formula in a reference file applied in the PUTMEDID_LCMS workflows. For category 2 challenges, MetFrag was applied to construct in silico fragmentation data and compare with experimentally-derived MS/MS data. The submissions for three challenges were correct, and for eight challenges, the submissions were not correct; some submissions showed similarity to the correct structures, while others showed no similarity. The low number of correct submissions for category 2 was a result of applying the assumption that all chemicals were derived from biological samples and highlights the importance of knowing the origin of biological or chemical samples studied and the metabolites expected to be present to define the correct chemical space to search in annotation processes.
authors: School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK. j.w.allwood@bham.ac.uk.
authors: J William
authors: JW
authors: Allwood
authors: School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK. r.j.weber@bham.ac.uk.
authors: Ralf J M
authors: RJ
authors: Weber
authors: College of Biomedical Engineering and Instrument Science, Zhejiang University, Hangzhou 310027, China. jrzhou@me.com.
authors: Jiarui
authors: J
authors: Zhou
authors: School of Computer Sciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK. s.he@cs.bham.ac.uk.
authors: Shan
authors: S
authors: He
authors: School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK. m.viant@bham.ac.uk.
authors: Mark R
authors: MR
authors: Viant
authors: School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK. w.dunn@bham.ac.uk.
authors: Warwick B
authors: WB
authors: Dunn