A total solution to deal with not only data dependent MS/MS but also data independent MS/MS experiments for metabolomics and lipidomics. Its feature is 1) implementing de-convolution method for data independent MS/MS 2) using unified criteria for peak identification 3) supporting all data processing step from raw data import to statistical analysis 4) user-friendly graphic user interface. MS-DIAL deals with data independent acquisition MS/MS data (ex. SWATH) by means of two step algorithms (peak spotting and MS2Dec) for spectral deconvolution. Also, it supports compound identification, peak alignment, and principal component analysis on the graphical user interface. The spectrum information is outputted by MassBank, NIST, and Mascot formats. And the organized data matrix (sample vs metabolite) is exported as tab delimited text file.
Allows users to analyze and visualize liquid chromatography – mass spectrometry (LC-MS) data. PiMP is a comprehensive and integrated web enabled pipeline that consists of five tasks: (1) project administration, (2) data upload, (3) quality control, (4) analysis parameters and (5) data interpretation. Users can define the experimental design, specify metadata and share the project with collaborators with a chosen level of permission. It aims at automatization and standardization of metabolomics analysis.
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.
A software package which allows to perform quick quality control of raw LC/MS data through its fast visualization capabilities. BatMass also serves as a testbed for developers of LC/MS data processing algorithms by providing a data access library for open mass spectrometry file formats and a means of visually mapping processing results back to the original data.
Extracts metabolite information from raw. ADAP-GC is an automated computational pipeline for untargeted, gas chromatography mass spectrometry (GC/MS)-based metabolomics studies. This workflow is designed to preprocess raw, untargeted, GC/MS metabolomics data. It carries out a sequence of computational tasks that includes construction of extracted ion chromatograms (EICs), detection of peaks from EICs, spectral deconvolution, and alignment of analytes across samples.
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.
Aims to integrate and analyze metabolomics experiment data. MeltDB is a program that can be applied for the description and analysis of metabolomic experiments. This program hosts over 30 experiments predominantly from gas chromatography-mass spectrometry (GC/MS) measurements. Moreover, this tool includes an API allowing users to evaluate novel methods and algorithms for the preprocessing of metabolomic datasets.
An R package of a set of tools and functions to perform an automatic end-to-end analysis of LC/MS metabolomic data, putting special emphasis on peak annotation and metabolite identification. The goal of the MAIT package is to provide an array of tools that makes programmable metabolomic end-to-end statistical analysis possible. MAIT includes functions to improve peak annotation through the process called biotransformations and to assess the predictive power of statistically significant metabolites that quantify class separability.
Represents a complete collection of functions in the R programming language as an accessible GUI for biomarker discovery in large-scale liquid-chromatography high-resolution mass spectral datasets from acquisition through to final metabolite identification forming a backend to output from any peak-picking software such as XCMS. MetMSLine automatically creates subdirectories, data tables and relevant figures at the following steps: (i) signal smoothing, normalization, filtration and noise transformation (PreProc.QC.LSC.R); (ii) PCA and automatic outlier removal (Auto.PCA.R); (iii) automatic regression, biomarker selection, hierarchical clustering and cluster ion/artefact identification (Auto.MV.Regress.R); (iv) Biomarker-MS/MS fragmentation spectra matching and fragment/neutral loss annotation (Auto.MS.MS.match.R) and (v) semi-targeted metabolite identification based on a list of theoretical masses obtained from public databases (DBAnnotate.R).
Permits users to realize autonomous and real-time analysis of metabolomic data. SimExTargId is an open source R package that provides an autonomous workflow that can also calculate data preprocessing in real-time, thereby alerting the user to signal degradation or loss. This method also facilitates real-time monitoring of liquid chromatography-mass spectrometry (LC-MS) data acquisition.
Allows users to perform Two Dimensional Gas Chromatography-Mass Spectrometry (2D-GCMS) derived metabolite peak alignment and identification. R2DGC uses individual sample files including basic peak information to generate an alignment table which shows the peaks common to several samples and match the aligned one to a reference library. The pipeline also furnish a reference library gathering information about 298 peaks issued from over 125 metabolite standards and commonly observed background peaks.
Implements a methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML). proFIA is an R package that includes noise modelling, injection peak reconstruction, band detection and filtering then signal matching and missing value imputation. It generates the peak table. This approach also filters out the features whose intensity is not significantly higher than the solvent baseline.
Aligns and calculates pairwise similarity scores among mass spectrometry (MS)/MS spectral data. MetCirc is an open-source package to make biological sense of mass spectral similarities from metabolomics data by providing a dedicated data analysis infrastructure and visualization interface to explore small molecules that mediate functionally important phenotypes. It can be used to pinpoint and formulate first structural hypothesis on previously non-characterized metabolites associated with a given phenotype.
A software tool for the efficient and automatic analysis of GC/MS-based metabolomics data. Starting with raw MS data, MetaboliteDetector detects and subsequently identifies potential metabolites. Moreover, a comparative analysis of a large number of chromatograms can be performed in either a targeted or nontargeted approach. It automatically determines appropriate quantification ions and performs an integration of single ion peaks. The analysis results can directly be visualized with a principal component analysis. Since the manual input is limited to absolutely necessary parameters, the program is also usable for the analysis of high-throughput data. However, the intuitive graphical user interface of MetaboliteDetector additionally allows for a detailed examination of a single GC/MS chromatogram including single ion chromatograms, recorded mass spectra, and identified metabolite spectra in combination with the corresponding reference spectra obtained from a reference library. MetaboliteDetector is able to import GC/MS data in NetCDF and FastFlight format.
A current and significant limitation to metabolomics is the large-scale, high-throughput conversion of raw chromatographically coupled mass spectrometry datasets into organized data matrices necessary for further statistical processing and data visualization. MET-IDEA is a data extraction tool which surmounts this void. It is compatible with a diversity of chromatographically coupled mass spectrometry systems, generates an output similar to traditional quantification methods, utilizes the sensitivity and selectivity associated with selected ion quantification, and greatly reduces the time and effort necessary to obtain large-scale organized datasets by several orders of magnitude.
Analyzes and visualizes high-throughput metabolomics data aquired using chromatography-mass spectrometry. yamss preprocess data in a way that enables reliable and powerful differential analysis. Currently, yamss implements a preprocessing method “bakedpi”, which stands for bivariate approximate kernel density estimation for peak identification. “bakedpi” is a preprocessing algorithm for untargeted metabolomics data. The output of “bakedpi” is essentially a table with dimension peaks (adducts) by samples, containing quantified intensity measurements representing the abundance of metabolites.
Remotes interactive access to the large collections of mass spectrometry (MS) data. mzAccess is an open-source software to compute many mass spectrometry data. This tool can be used for the data with a function calls from scripts anywhere on the network or internet. mzAccess can get a chunk of data from couple of thousand raw files.
An automated tool with friendly user interfaces for quantifying metabolites in full-scan liquid chromatography-mass spectrometry (LC-MS) data. iMet-Q has a complete quantitation procedure for noise removal, peak detection and peak alignment. Furthermore, it gives the charge states and isotope ratios of detected metabolite peaks to facilitate metabolite identification.
Simplifies the analysis of "paired" samples, i.e. samples that are almost identical yet present some qualitative difference. COMSPARI allows users to display mass spectral datasets, and can present the data from a pair of gas chromatography-mass spectrometry (GC/MS) or liquid chromatography-mass spectrometry (LC/MS) runs. It has two primary modes of operation: “mass spectrum” and “selected ion chromatogram”.
An open source tool which is a flexible and accurate method for pre-processing very large numbers of GC-MS samples within hours. A novel strategy was developed to iteratively correct and update retention time indices for searching and identifying metabolites. TargetSearch includes a graphical user interface to allow easy use by those unfamiliar with R. It allows fast and accurate data pre-processing for GC-MS experiments and overcomes the sample number limitations and manual curation requirements of existing software.
A package of utilities for data extraction, quality control assessment, detection of overlapping and unique metabolites in multiple datasets, and batch annotation of metabolites. xMSanalyzer comprises of utilities that can be classified into five main modules: 1) merging apLCMS or XCMS sample processing results from multiple sets of parameter settings, 2) evaluation of sample quality, feature consistency, and batch-effect, 3) feature matching, and 4) characterization of m/z using KEGG REST; 5) Batch-effect correction using ComBat.
Assist users in processing, visualization and re-analysis of publicly-submitted raw and processed Gas Chromatography-Mass Spectrometry (GC-MS) metabolomics datasets. MetabolomeExpress performs three main functions: (i) store complete GC/MS metabolomics datasets in a way that makes them highly accessible, (ii) provide researchers with cost-free online access to a powerful raw data processing pipeline and (iii) store metabolite response statistics in a central database.
Comprises a library of functions for processing of instrument gas chromatography–mass spectrometry (GC-MS) data. PyMS currently provides a complete set of GC-MS processing functions, including reading of standard data formats (ANDI- MS/NetCDF and JCAMP-DX), noise smoothing, baseline correction, peak detection, peak deconvolution, peak integration, and peak alignment by dynamic programming. It implements parallel processing for by-row and by-column data processing tasks based on Message Passing Interface (MPI), allowing processing to scale on multiple CPUs in distributed computing environments.
Allows processing of liquid chromatography coupled to tandem mass spectrometry (LC-MSn) metabolomics data. MassCascade is a library and node-suite containing a collection of data processing algorithms and a visualization framework. MassCascade-KNIME is the software plug-in for the Konstanz Information Miner (KNIME) environment. The library can be used as a standalone or in combination with the plug-in, which provides a modular, step-by-step solution for building complex workflows with the ability to inspect the output of each method in between nodes.
Aims to compare and evaluate various publicly available open source label-free data processing workflows. msCompare is a modular framework that allows the arbitrary combination of different feature detection/quantification and alignment/matching algorithms in conjunction with a scoring method to evaluate their overall performance. msCompare was used to assess the performance of workflows built from modules of publicly available data processing packages such as SuperHirn, OpenMS, and MZmine and in-house developed modules. It was found that the quality of results varied greatly among workflows, and interestingly, heterogeneous combinations of algorithms often performed better than the homogenous workflows. This scoring method showed that the union of feature matrices of different workflows outperformed the original homogenous workflows in some cases. msCompare is available as a standalone command line program or can be used through a Graphical User Interface (GUI) into the Galaxy framework.
Assists users to analyze gas chromatography/differential mobility spectrometry (GC/DMS) metabolomics data. AIMS can also be applied for other similarly structured data sets, such as comprehensive two-dimensional gas chromatography (GC/GC) and other ion mobility spectrometry (IMS) modalities. Furthermore, this software includes a flexible code that can be adapted for new modules developed by others.
Offers library searching of data generated from any Liquid Chromatography-Mass Spectrometry (LC-MS) and Gas chromatography-mass spectrometry (GC-MS) platform. AnalyzerPro is a commercial and comprehensive post-processing utility for low and high-resolution LC-MS and GC-MS data with multi-vendor data support. It also provides optimized workflows for sample-to-sample comparison, target component analysis, quantification.
Allows fragment-level analysis of gas chromatography-mass spectrometry (GC-MS) metabolomics data. flagme is an R package for processing, visualizing and statistically analyzing sets of GC-MS samples. The software gives a complete suite of methods to go through all common stages of data processing, as well as various visualizations to ensure the methods applied are not black boxes.
Allows users to work on molecule match, mass chromatograms or molecular formulae. Mnova MS is a program permitting several functions such as: (1) computation of MS peak purity; (2) visualize user’s data; (3) predict isotope clusters; (4) or process and report MS data on user’s computer.
Assists users in analyzing metabolomics experiments using liquid chromatography coupled with mass spectrometry (LC-MS and LC-MS/MS). Elements for Metabolomics is a program that extracts features from the data, and performs a spectral library search to identify the extracted features. This tool allows users to organize, summarize and visualize the identified metabolites across a large number of biological samples. Moreover, it can support complex experiments by combining attributes (metadata) with Mass Spectrometry data.
Imports, aligns, and reformats spectral and chromatographic data. MSFACTs is an application that provides an automated, rapid, and flexible means of reducing large complex chromatographic/spectrometric data sets generated in metabolomic studies into well-organized, two-dimensional matrices. This method accepts and converts integrated peak lists, composed of chromatographic retention times and peak areas.
A web application designed to quantify numerous metabolites, simultaneously integrating LC distortions and asynchronous web technology to present a visual interface with dynamic interaction which allows checking and correction of LC-MS raw data pre-processing results. Moreover, quantified data obtained with EasyLCMS are fully compatible with numerous downstream applications, as well as for mathematical modelling in the systems biology field.
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