Successes and pitfalls in automated dereplication strategy using liquid chromatography coupled to mass spectrometry data: A CASMI 2016 experience

Publication date: Available online 15 January 2017 Source:Phytochemistry Letters Author(s): Samuel Bertrand, Yann Guitton, Catherine Roullier Automated annotation of data, originating from liquid chromatography coupled to high-resolution mass spectrometry profiles (LC–HRMS), remains a highly challenging task. Therefore, the Critical Assessment of Small Molecule Identification (CASMI) Contest (http://casmi-contest.org/) represents a unique opportunity to blindly evaluate annotation workflows. The 2016 CASMI contest consisted of 16 LC–HRMS/MS profiles with 18 detected peaks to annotate. Those peaks corresponded to compounds from natural origin. An R script based on the XCMS, IPO, RMassBank, CAMERA and MeHaloCoA packages was devised. Two other external tools: SIRIUS3 and CFM-ID were also integrated for molecular formulae and in silico fragmentation calculation, respectively. This script was used to perform peak picking, spectral interpretation, molecular formula determination and database search for structural determination. Finally, the structures were further discriminated based on in silico fragmentation. After the release of the CASMI contest solutions, successes and failures of the proposed script were investigated. In most cases, no differences were observed in the rank of the correct structure when using raw LC–HRMS data or manually obtained MS and MS/MS spectra. However, the study of the few cases where differences were detected tends to show that automatic de...
Source: Phytochemistry Letters - Category: Chemistry Source Type: research