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: 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: PyMS

Location: http://bioinformatics.bio21.unimelb.edu.au/pyms.html

Description: PyMS is a Python toolkit for processing of chromatography--mass spectrometry data. The idea behind PyMS is to decouple processing methods form visualization and the concept of interactive processing altogether, to provide a set of components for the development and testing of high-throughput processing pipeline for metabolomics. This includes development of new methods for data processing, and prototyping of advanced features such as intelligent processing layers for automated data processing and capabilities to leverage distributed and Grid computing.

Freeware

Alignments tools

Name: MultiAlign

Location: http://omics.pnl.gov/software/MultiAlign.php

Description: Aligns multiple LC-MS datasets to one another, after which LC-MS features can be matched to a database of peptides (e.g. an AMT tag database)

Freeware

Name: COMSPARI

Location: http://www.biomechanic.org/comspari/

Description: COMSPARI is the acronym for COMparison of SPectral And Retention Information. It is a software that has been written to facilitate the analysis of "paired" samples, i.e. samples that are almost identical yet present some qualitative difference. The software was originally written for the analysis of data files produced by GC/MS and LC/MS, but can be used for other techniques, too.

Freeware

Name: MetAlign

Location: http://www.metalign.wur.nl/UK/

Description: MetAlign™ has been designed to distinguish between and filter out statistically significant differences between pre-defined classes of full scan LC or GC mass spectrometry data sets. 

Freeware

Name: Pairseqsim

Location: http://www.bioconductor.org/packages/bioc/1.8/html/pairseqsim.html

Description: Pairwise sequence alignment and scoring algorithms for global,local and overlap alignement with affine gap penalty.

Freeware

Name: MSFACTs

Location: http://www.noble.org/PlantBio/MS/MSFACTs/MSFACTs.html

Description: Metabolomics spectral formatting, alignment and conversion tools, (MSFACTs) is described here for the automated import, reformatting, alignment, and export of large chromatographic data sets to allow more rapid visualization and interrogation of metabolomic data.

MSFACTs incorporates two tools: one for the alignment of integrated chromatographic peak lists and another for extracting information from raw chromatographic ASCII formatted data files. MSFACTs is illustrated in the processing of GC/MS metabolomic data from different tissues of the model legume plant, Medicago truncatula. The results document that various tissues such as roots, stems, and leaves from the same plant can be easily differentiated based on metabolite profiles. Further, similar types of tissues within the same plant, such as the first to eleventh internodes of stems, could also be differentiated based on metabolite profiles.

Shareware

Name: MathDAMP

Location: http://mathdamp.iab.keio.ac.jp/

Description: MathDAMP facilitates the visualization of differences between metabolite profiles acquired by hyphenated mass spectrometry techniques. Differences are highlighted by applying arithmetic operations to all corresponding signal intensities from whole raw (automatically preprocessed and normalized) datasets on a datapoint-by-datapoint basis.

Freeware (but mathematica is necessary)

Name: OBI-Warp

Location: http://sourceforge.net/projects/obi-warp/

Description: Ordered Bijective Interpolated Warping (OBI-Warp) aligns matrices using Dynamic Time Warping with a one-to-one (bijective) smooth warp-function. It is ideal for the chromatographic alignment of complex mass spectrometry proteomics data.

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