Noise filtering software tools | Mass spectrometry-based untargeted metabolomics
Smoothing aims to remove noise in the measured spectra, which facilitates further peak detection. Smoothing is an optional stage in data processing and can also be left out if the data is not noisy or if the input data is already available as centroids.
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 automatically integrates, precisely quantifies and interprets capillary electrophoresis-mass spectrometry (CE-MS) data. MasterHands is a metabolome analysis software that can also be used for comprehensive peak picking of capillary electrophoresis time-of-flight mass spectrometry (CE-TOF-MS) data. Users annotate whole peaks interactively through a graphical user interface. This data analysis application includes noise-filtering, baseline correction, peak detection and integration of the peak area from sliced electropherograms.
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.
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.
Assists users to select the mass chromatograms with a minimal amount of high-frequency noise and a minimal background. CODA detects several correlated mass chromatograms for each component, depending on the amount of fragmentation, or cluster peaks. This algorithm can choose high-quality mass chromatograms by selecting only mass chromatograms above a certain mass chromatographic quality (MCQ) level. It is able to compute the similarity index (cJ) between the length-scaled mass chromatogram and the smoothed standardized mass 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.
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.