Metabolomics Software and Servers
BioSpider is essentially an automated report generator designed specifically to tabulate and summarize data on biomolecules - both large and small. Specifically, BioSpider allows users to type in almost any kind of biological or chemical identifier (protein/gene name, sequence, accession number, chemical name, brand name, SMILES string, InCHI string, CAS number, etc.) and it returns an in-depth synoptic report (approximately 3-30 pages in length) about that biomolecule and any other biomolecule it may target. This summary includes physico-chemical parameters, images, models, data files, descriptions and predictions concerning the query molecule.
COLMAR query is a webserver for identifying metabolites by NMR from complex metabolite mixtures. The COLMAR web-suite screens NMR chemical shift lists or raw 1D NMR cross sections taken from covariance total correlation spectroscopy (TOCSY) spectra or other multidimensional NMR spectra against an NMR spectral database. Cross peaks are selected using local clustering to avoid ambiguities between chemical shifts and scalar J-coupling effects. With the use of three different algorithms, the corresponding chemical shift list is then screened against chemical shift lists extracted from 1D spectra of a NMR database. The resulting query scores produced by forward assignment, reverse assignment, and bipartite weighted-matching algorithms are combined into a consensus score, which provides a robust means for identifying the correct compound.
FiD (Fragment iDentificator) is a software tool for the structural identification of product ions produced with tandem mass spectrometric measurement of low molecular weight organic compounds. FiD conducts a combinatorial search over all possible fragmentation paths and outputs a ranked list of alternative structures. This gives the user an advantage in situations where the MS/MS data of compounds with less well-known fragmentation mechanisms are processed. The software has an easy-to-use graphical interface with built-in visualization capabilities for structures of product ions and fragmentation pathways.
The HORA suite (Human blOod Range vAlidator) consists of a Java application used to validate the metabolomic analysis of human blood against a database that stores the normal plasma and serum range concentrations of metabolites. The goal of HORA is to find the metabolites that are outside the normal range and to show those not present in the list provided by the user, for different thresholds of concentration. Moreover it supplies a graphical interface to manage the data. The software can also be used to compare different metabolomic techniques.
MeltDB is a web-based software platform for the analysis and annotation of datasets from metabolomics experiments. MeltDB supports open file formats (netCDF, mzXML, mzDATA) and facilitates the integration and evaluation of existing preprocessing methods. The system provides researchers with means to consistently describe and store their experimental datasets. Comprehensive analysis and visualization features of metabolomics datasets are offered to the community through a web-based user interface.
MetaboloAnalyst is a web-based metabolomic data processing tool that accepts a variety of input data (NMR peak lists, binned spectra, MS peak lists, compound/concentration data) in a wide variety of formats. It offers a number of options for metabolomic data processing, data normalization, multivariate statistical analysis (such as fold change analysis, t-tests, PCA, PLS-DA, hierarchical clustering along with a number of more sophisticated statistical or machine learning methods), graphing, metabolite identification and pathway mapping. Upon completion, the server generates a detailed report describing each method used, embedded with graphical and tabular outputs. MetaboAnalyst is capable of handling most kinds of metabolomic data and was designed to perform most of the common kinds of metabolomic data analyses.
MetaboMiner is a Java based software package that can be used to automatically or semi-automatically identify metabolites in complex biofluids from 2D NMR spectra. MetaboMiner is able to handle both 1H-1H total correlation spectroscopy (TOCSY) and 1H-13C heteronuclear single quantum correlation (HSQC) data. It identifies compounds by comparing 2D spectral patterns in the NMR spectrum of the biofluid mixture with specially constructed libraries containing reference spectra of ~500 pure compounds.
MolFind is a Java based software package for identifying unknown chemical structures in complex mixtures using HPLC/MS data. Identifying an unknown involves matching orthogonal experimental features measured for the unknown (RI, ECOM50, drift time and CID spectra) with computationally predicted values for candidate compounds contained in chemical or biochemical databases. The program, available as a free download from the Grant lab (http://metabolomics.pharm.uconn.edu/Software.html) features an easy to use graphical user interface and a highly multi threaded pipeline for identifying unknowns.
This page provides links to both commercial and non-commercial software suppliers that produce software for small molecule structure elucidation or MS data manipulation.
MVAPACK is an open-source toolkit for data handling in NMR and MS metabolic fingerprinting studies, and provides a complete set of easy-to-use, modular functions for performing all tasks required. Analysts using MVAPACK can transform their raw instrumental datasets into validated multivariate models in a single scripting environment, without the need for format conversion or proprietary software.
OpenMS is a software framework for rapid application development in mass spectrometry. OpenMS has been designed to be portable, easy-to-use and robust while offering a rich functionality ranging from basic data structures to sophisticated algorithms for data analysis.
This page contains links and brief synopses of ore than 30 different spectral alignment tools that can be used to align, bin or compare multiple GC-MS, LC-MS, LC and NMR data sets.
PolySearch is a text mining software tool that supports >50 different classes of queries against nearly a dozen different types of text, scientific abstract or bioinformatic databases. The typical query supported by PolySearch is 'Given X, find all Y's' where X or Y can be diseases, tissues, cell compartments, gene/protein names, SNPs, mutations, drugs and metabolites. PolySearch also exploits a variety of techniques in text mining and information retrieval to identify, highlight and rank informative abstracts, paragraphs or sentences.
SetupX, developed by the Fiehn laboratory at UC Davis, is a web-based metabolomics LIMS. It is XML compatible and built around a relational database management core. It is particularly oriented towards the capture and display of GC-MS metabolomic data through its metabolic annotation database called BinBase.
This software can be used to calculate molecular formulas from high resolution mass spectrometry data. It is derived from seven heuristic rules: (1) restrictions for the number of elements, (2) LEWIS and SENIOR chemical rules, (3) isotopic patterns, (4) hydrogen/carbon ratios, (5) element ratio of nitrogen, oxygen, phosphor, and sulphur versus carbon, (6) element ratio probabilities and (7) presence of trimethylsilylated compounds.
XCMS2 is an open source software package which has been developed to automatically search tandem mass spectrometry (MS/MS) data against high quality experimental MS/MS data from known metabolites contained in a reference library (METLIN). Scoring of hits is based on a "shared peak count" method that identifies masses of fragment ions shared between the analytical and reference MS/MS spectra. Another functional component of XCMS(2) is the capability of providing structural information for unknown metabolites, which are not in the METLIN database. This "similarity search" algorithm has been developed to detect possible structural motifs in the unknown metabolite which may produce characteristic fragment ions and neutral losses to related reference compounds contained in METLIN, even if the precursor masses are not the same.