Peak alignment software tools | Mass spectrometry-based untargeted metabolomics
Peak alignment procedures for samples from LC-MS and GC-MS (also CE-MS, MS, FT-MS, UV, NMR, MALDI) measurements play an important role during biomarker detection and metabolomic studies in general. As there is always a difference in the samples due to machine drift, samples need accurate correction to point to the same metabolite or component. Several packages have emerged since several years, some of them commercial, some of them free, some of them simple, some of them complex.
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.
Allows alignment of homogeneous data. mSPA is especially designed for two-dimensional gas chromatography mass spectrometry (GC × GC–MS). It employs the peak distance and the spectra similarity sequentially in parallel to proceed. This tool was tested on two sets of GC × GC–MS data. The results show that the Canberra distance is able to make good performances and the proposed mixture similarity peak alignment algorithm prevailed against all literature reported methods.
Allows intensity drift correction in Liquid chromatography coupled to mass spectrometry (LC/MS) data. intCor is an R package that implements five methods: common principal component analysis (CPCA), component correction CC, median fold change, ComBat and the CPCA+ median fold change. This tool permits to normalize the LC/MC metabolomic data to control the quality of the acquisition data step.
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.
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.
Permits simultaneous processing, inspection, and correction of large numbers of gas chromatography-mass spectrometry (GC–MS) samples. Maui-VIA is based on a NetBeans Rich Client Platform-based GC–MS processing software. It contains modules for: retention index (RI) calculation, a targeted library search for metabolite identification, metabolite quantification, and the export of the final datamatrix which contains the user-validated metabolite abundances for every sample in the project. The software can be used by both experts and non-experts.
Aims to formalize the analysis of gas chromatography-mass spectrometry (GC/MS) data. PYQUAN uses the AMDIS data to align the individual samples against the personal retention time (RT) library. It offers the possibility to backfill expected peaks in samples where AMDIS did not recognize those peaks. Moreover, this program utilizes AMDIS for producing for each peak a list of all possible identifications, based on a personally managed mass spectra library.
Allows Next Generation Sequencing (NGS), microarray analysis, mass spectrometry, and gene ontology. Bioinformatics Toolbox deals with genomic and proteomic information and furnishes functions to explore and display this data with sequence browsers, spatial heatmaps, and clustergrams. It can find peaks, impute values for missing data, and select features using statistical techniques.
0 - 0 of 0
1 - 3 of 3
Filters / Sort by
0 - 0 of 0