Spectral deconvolution software tools | Mass spectrometry-based untargeted metabolomics
For GC-MS data, deconvolution is the process of computationally separating co-eluting components and creating a pure spectrum for each component. Specifically, for each observed EIC that results from two or more components, deconvolution calculates the contribution of each component to the EIC depicts the necessity of deconvolution.
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.
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.
Deconvolutes complete electrospray spectra of protein mixtures. MaxEnt is a program that can produce zero-charge mass spectra on a molecular mass scale. It automatically connects data peaks of different charge state, with no need for explicit identification. Furthermore, quantitative relative intensity data can be derived from the areas under the peaks in the MaxEnt output.
Facilitates improved compound identification using mass spectrometry (MS). RANSY/RAMSY is an application that reduces spectral interference and facilitates the identification of individual molecules in overlapped MS spectra. This method is designed to work using datasets that contain multiple MS spectra for the same metabolite. It can be applied for compound identification using different analytical platforms.
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.
Performs quantitative deconvolution and charge separation of complex spectra. UniDec consists of an approach for studying intact protein complexes with both native mass spectrometry (MS) and two-dimensional ion mobility-mass spectra (IM-MS). It also allows users to observe the biophysics of heterogeneous systems such as membrane proteins, small heat shock protein assemblies, and Nanodisc lipoprotein complexes. It includes MetaUniDec, a high-throughput derivative of UniDec.
An R package for high-throughput processing of metabolomics data analysed by the Automated Mass Spectral Deconvolution and Identification System (AMDIS). In addition, it performs statistical hypothesis test (t-test) and analysis of variance (ANOVA). Doing so, Metab considerably speed up the data mining process in metabolomics and produces better quality results. Metab was developed using interactive features, allowing users with lack of R knowledge to appreciate its functionalities.
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.
A two-part approach for performing metabolomic identifications. First, MS(2) scans are collected with less stringent isolation settings to obtain improved sensitivity at the expense of specificity. Then, by evaluating MS(2) fragment intensities as a function of retention time and precursor mass targeted for MS(2) analysis, deconvolved MS(2) spectra are obtained that are consistent with pure standards and can therefore be used for metabolite identification.
Offers a platform which automates the deconvolution of combined spectra data. GAGdecon is a standalone software that is built around an isotopic pattern database approach. This program is able to perform structural assignment at the mass spectrometry (MS) level and to map the isotopic distribution of theoretical species. Its analysis can be performed on both centroid or profile data.
Adjoins the modeling of the MS2-isolation step into a deconvolution algorithm. TMTc+ intends to improve the accuracy of the complement reporter ion approach. This method is generalizable and can accommodate isolation windows of arbitrary shapes. It can identify real signal from background in a complex sample where many peptides can be co-isolated along with the peptide of interest.
Solves multiple peptide candidates that may match to a tandem mass spectrometry (MS) scan. Protalizer estimates if a substantial proportion of the modifications that it had found could represent false identifications. It is based on the premise that modifications introduce retention time shifts from their unmodified peptide counterparts. This tool is able to recognize modified peptides and to minimize false quantification results for proteins measured by a single peptide.
Consists of a parsimonious charge deconvolution algorithm that produces fewer artifacts. This algorithm is well-suited to high-resolution native mass spectrometry of intact glycoproteins and protein complexes. It simplifies the utilization of native mass spectrometry for the quantitative analysis of protein and protein assemblies, and can deconvolve monomer and dimer simultaneously.
Offers a platform dedicated to the study of top-down tandem mass spectrometry (MS/MS) spectra. BUPID-Top-Down is a web application that can be used for a wide range of functionalities including deconvolution, sequence variant analysis or fragment ion assignment. This program is able to investigate data derived from several fragmentation approaches such as electron capture dissociation (ECD) or electron transfer dissociation (ETD).
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.
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.
Supplies an algorithm for peak deconvolution for linear matrix-assisted laser desorption/ionization time of-flight (MALDI-ToF MS) spectra data. This approach provides a software, able to jointly performs baseline computation and peak deconvolution, which includes a two-steps process involving peak support followed by peak height debiasing. The method was implemented into a C++ program and was suited only to spectrum up to 1000 channels.