TNO IMPRESS

Description: An in-house developed software package to generate peak tables of all files.

TNO EXPRESS

Description: An in-house developed software package to show the significant changes on top of the biochemical pathways

TNO EQUEST

Description: An in-house developed software package to align retention times.

TNO DECO(nvolution)

Description: The TNO-DECO tool uses curve resolution to separate overlapping peaks and corrects for retention time shifts.

LCQUAN

Description: A quantitative software package for importing sequence information from external systems, method development, data review, data processing, data reporting and exporting results to external systems in a 21 CFR Part 11 compliant environment.

CHEMSTATION

Description: A data system, handling all applications including UV-Vis, LC, LC/MS, GC, CE , GC/MS and CE/MS. A graphical user interface for laboratory tasks, including instrument control, data acquisition and automation, analysis and reporting of two- and three-dimensional data, as well as system suitability testing and diagnostics.

Name:  MZmine
Location: http://mzmine.sourceforge.net/
Description: MZmine is a platform-independent software for data processing needed in differential analysis of LC/MS data, with applications in metabolomics and proteomics. MZmine2 can read and process both unit mass resolution and exact mass resolution (e.g. FTMS) data in both continuous and centroided modes, including fragmentation scans. Supported data formats are: mxML (v1.0), mzXML (v2.0, 2.1 and 3.0) mzData (v 1.04 and 1.05), NetCDF, ThermoRaw (on Windows with Thermo Xcalibur installed).The software package enables easy integration of new algorithms and applications into the data processing pipeline. MZmine 2 can visualize your raw data, detect peaks and can report the quantification results in table form or using charts.
Freeware 

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: Genedata Expressionist/ Analyst

Location: http://www.genedata.com/products/expressionist/omics/metabolomics/index_eng.html

Description: Expressionist standardizes and automates high-throughput mass spectrometry and NMR analysis tasks. The platform guarantees reliable and reproducible results from metabolite profiling data.

Expressionist supports metabolomics with the modules Refiner MS and Analyst. Refiner MS performs objective technology-specific quality assessments, process monitoring and uploading of MS processed data to the database. There it can be accessed by the Analyst module for integrated analysis and interpretation. Based on the large number of different NMR setups and data formats we recommend data pre-processing with specialized tools and further integrated data analysis and interpretation in Analyst.

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: XCMS

Location: http://bioconductor.org/packages/bioc/html/xcms.html

Description: XCMS is a framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, and mzData files. Preprocesses data for high-throughput, untargeted analyte profiling.  XCMS can handle both LC-MS (1D GC-MS as well) and Direct-Infusion (e.g. FTICR) data and has several peak picking algorithms. Alignment is done using its own algorithm as well as Obiwarp.
Freeware