Name: MarkerLynx

Location: http://www.waters.com/waters/nav.htm?cid=513801

Description: 3-dimensional peak integration, data set alignment and incorporates multivariate statistical tools. The Principal Components Analysis (PCA) algorithm is automatically applied to the processed data sets. This gives you multidimensional visualization of biochemical patterns so you can identify potential biomarkers responsible for variations in the data set. Direct integration with Umetrics Simca-P extends your data analysis capabilities, including Orthogonal Projection Least Squares (OPLS). Search ChemSpider, ChemFolder, or your own databases to identify potential biomarkers discovered by your analysis.

Commercial

Name: DAnTE

Location: http://ncrr.pnl.gov/software/dante.stm

Description: DAnTE helps users to perform various downstream data analysis, data reduction, and data comparison steps. DAnTE includes a graphical environment for visualizing the data during the processing steps. DAnTE can associate one or more "factors" with each dataset, which are then taken into consideration during the data processing. The statistical methods are implemented in R, and the graphical user interface is written in C#, using the R(D)COM server for connectivity.

Freeware

Name: CPM MatLab toolbox

Location: http://www.cs.toronto.edu/~jenn/CPM/

Description: This toolbox provides Matlab implementations of Continuous Profile Models (CPM) for alignment and normalization of time series data. Specifically, two models are provided (well, one so far), the EM-CPM, from the paper "Multiple Alignment of Continuous Time Series", and the HB-CPM, from the paper "Bayesian Detection of Infrequent Differences in Sets of Time Series with Shared Structure".

Freeware

Name: GASP

Location: http://www.genedrift.org/gasp.php

Description: GASP is a cross-platform software developed in C++ with wxWidgets as GUI framework, that allows the comparison of GC/MS runs, in order to determine differences in composition of samples. The program reads output files from Xcalibur, HP Chemstation and AMDIS, converts and align these files in order to make the comparisons. GASP has a direct link with R to generate statistical analysis of the alignments.

Shareware

Name: R

Location: http://www.r-project.org/

Description: Free software for multivariate analysis.

Freeware

Name: SpectConnect

Location: http://spectconnect.mit.edu/

Description: Use SpectConnect to find conserved components and biomarkers

Freeware

Name: Chenomx NMR Suite

Location: http://www.chenomx.com/products/index.html

Description: Chenomx NMR suite is an integrated suite of tools that allow you to easily identify and quantify metabolites in NMR spectra. Chenomx Profiler offers you a broad range of tools to assist in identifying and quantifying compound concentrations based on data in an NMR spectrum. Using a compound library of over 260 unique spectral signatures together with sophisticated computer-assisted fitting routines, you can accomplish in minutes what would have taken hours or days using manual analysis methods. Chenomx Compound Builder was developed to address a recurring customer request: the capability to add custom compounds to a Compound Library. Compound Builder allows a user to create a signature that models the compound of interest. This capability lets users create signatures for compounds that are not present in the standard Chenomx Compound Library, and subsequently use those proprietary compounds in an analysis within Profiler.

Commercial

Name: MS-Xelerator

Location: http://www.msmetrix.com/

Description: MS-Xelerator is a fast and comprehensive software product for processing of Liquid Chromatography – Mass Spectrometry (LC/MS) data, with expandability to other types of data such as GC/MS or CE/MS as well. Basic application areas of MS-Xelerator are:  Impurity Profiling, Degradation Profiling, Metabolite Profiling, Differential Analysis, Metabonomics, Quantitative Proteomics & Biomarker Discovery

Commercial

Name: MetaboliteTools

Location: http://www.bdal.de/uploads/media/metabolitetools_1.1.pdf

Description: MetaboliteToolsTM 1.1 is a software package designed for the prediction and rapid detection of metabolites and, more generally, small molecule differences between two samples. It comprises of two modules: MetabolitePredictTM and MetaboliteDetectTM, allowing for the detailed evaluation of individual samples as well as automated analysis of sample batches. Accurate mass data from orthogonal electrospray time-of-fl ight (ESI-oa-TOF) instruments, as well as MSn data from quadrupole ion traps can be utilized. This combination takes advantage of the particular strengths of these mass spectrometric techniques resulting in both a molecular formula and characteristic fragmentation and structural information of the analytes.

Commercial

Name: SIMCA

Location: http://www.umetrics.com/default.asp/pagename/software_simcapplus/c/4

Description: Widely used, not too expensive software for metabolomics analysis. For multivariate data analysis of biomedical data.

Commercial

Name: Prime

Location: http://prime.psc.riken.jp/

Description: PRIMe, the Platform for RIKEN Metabolomics, is a Web-based service for metabolomics and transcriptomics as systems for understanding life. This project measures standard metabolites by means of multi-dimensional NMR spectroscopy, GC/MS, LC/MS, and CE/MS. We also provide unique tools for metabolomics, transcriptomics, and integrated analysis of a range of other "-omics" data.

Freeware

Name: MetaFIND

Location: http://mlg.ucd.ie/metafind

Description: MetaFIND may be used to elucidate metabolite signatures from the set of features selected by diverse techniques over two metabolomics datasets. Importantly, we also show how MetaFIND may augment standard feature selection and aid the discovery of additional significant features, including those which represent novel class discriminating metabolites. MetaFIND also supports the discovery of higher level metabolite correlations. 
Standard feature selection techniques may fail to capture the full set of relevant features in the case of high dimensional, multi-collinear metabolomics data. We show that the MetaFIND ‘post-feature selection’ analysis tool may aid metabolite signature elucidation, feature discovery and inference of metabolic correlations.

Freeware