MQ: Tool for HR-AM Based Quantitative Analysis for Direct MS Workflow

Abstract There is an increased interest in using high-resolution mass spectrometry (HRMS) in the full scan mode (FS) for simultaneous qualitative and quantitative analysis with accurate mass based extracted ion chromatograms (HRMS-AM) for metabolomic profiling workflows. Herein, the capabilities and features of ‘MQ’, a common platform developed to support quantitative analysis from HRMS data are described. Module for qualitative annotation utilizes peak features that include mass accuracy, peak width, and relative abundance of isotopic distribution that offer reliable metabolic confirmation. Additionally, MQ provides multivariate clustering with Principal Component Analysis and a module for high-throughput database query based on user configurable annotated metabolite lists. MQ is capable of handling system-agnostic data formats from both direct HRMS and LC-HRMS analysis. Data processed using MQ for LC-HRMS-AM quantitation of amino acids benchmarked using a commercial tool is presented that validates the quantitative capabilities of the algorithm developed. Datasets representative of three different HRMS-AM based analysis scenarios have been showcased to demonstrate the utility of MQ. Availability and implementation Freely available on web at, http://www.ldims.com/services/software . MQ is implemented in Java and supported on Linux and Microsoft Windows system having Java runtime environment (JRE) pre-installed.