An LC/MS-based data analysis approach which incorporates novel nonlinear retention time alignment, feature detection, and feature matching. The XCMS software reads and processes LC/MS data stored in netcdf , mzXML, mzData and mzML files. It provides methods for feature detection, non-linear retention time alignment, visualization, relative quantization and statistics. XCMS is capable of simultaneously preprocessing, analyzing, and visualizing the raw data from hundreds of samples. XCMS is freely available under an open-source license.
Provides a web-based analytical pipeline for high-throughput metabolomics studies. MetaboAnalyst aims to offer a variety of commonly used procedures for metabolomic data processing, normalization, multivariate statistical analysis, as well as data annotation. The current implementation focuses on exploratory statistical analysis, functional interpretation, and advanced statistics for translational metabolomics studies. This tool is also available as desktop version.
An industry standard mass spectrometer data system for acquiring, processing, and reporting data. Uniquely designed to meet the needs of today’s laboratory professionals in the food/flavor/fragrance, metabolomics, environmental, and petrochemical industries. ChromaTOF® offers seamless control of both the instrument and accessories, as well as an intuitive acquisition queue with built-in data processing.
Proposes a module for searching within the NIST/EPA/NIH Mass Spectral Database. NIST MS Search is an application able to query more than 100 mass spectral libraries simultaneously. It includes features to: (i) investigate the exact mass of a precursor by using its mass or exact m/z of a product ion, (ii) combine libraries in any order, (iii) do comparisons of user-generated mass spectra as well as (iv) generate user libraries to search against.
Provides an application for daily routine and emergency toxicology. AMDIS is a software developed to identify of even low-abundant peaks in the total ion chromatograms (TIC) and the reduction of the evaluation time by half. This method first deconvolutes pure component spectra and related information such as peak shape and retention time from complex chromatograms and subsequently matches the obtained spectra with those of a reference library.
Helps to process accurate mass data as nominal mass data. MetAlign is a software program for the pre-processing and comparison of full scan nominal or accurate mass Liquid chromatography-mass spectrometry (LC–MS) and Gas chromatography-mass spectrometry (GC–MS) data. It involves running multiple threads simultaneously so that a one thread per core situation is established in which memory between threads is not shared.
An open-source software tool for mass-spectrometry data processing, with the main focus on LC-MS data. It is based on the original MZmine toolbox described in the 2006 Bioinformatics publication, but has been completely redesigned and rewritten since then. Our main goal is to provide a user-friendly, flexible and easily extendable software with a complete set of modules covering the entire LC-MS data analysis workflow.