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    Agilent GeneSpring MS

    Category  Proteomics>Mass Spectrometry Analysis/Tools

    Abstract  GeneSpring MS software enables the rapid discovery of
    protein and metabolite biomarkers through the analysis of mass
    spectrometry (MS) data. Researchers can import, analyze and visualize
    gas chromatography/mass spectrometry (GC/MS) and liquid
    chromatography/mass spectrometry (LC/MS) data from large sample
    sets and complex experimental designs. Using a comprehensive array
    of powerful statistical analyses, GeneSpring MS can profile proteins or
    small molecules associated with changes in cellular function,
    enabling the rapid discovery of biomarkers that can detect disease or
    drug toxicity.

    Features/Capabilities include:

    Intuitive and informative display of data -
    GeneSpring MS contains a variety of graphical displays to clearly and
    intuitively visualize data. These displays are useful for assessing data
    quality and finding mass entities of interest. The Spectrum Viewer
    allows access to the acquired total ion chromatogram (TIC) and
    associated mass spectra for each LC/MS sample. The Mass Details
    window provides access to LC/MS raw data information, such as the
    reconstructed mass spectrum and the associated abundance values
    of each ion species for the mass entity of interest. The Volcano Plot
    view facilitates rapid identification of mass entities with a statistically
    significant fold-change between two experimental conditions. Other
    types of graphical displays in GeneSpring MS include:
    1) 2D and 3D Scatter plots; 2) Mass vs. Ratio of Two Conditions Plot;
    3) 2D dendrograms; 4) retention time (RT) vs. Mass Plot; 5)
    Compound Viewer.

    Detecting differential abundance of mass entities -
    Isolating mass entities with differential abundance between a set of
    experimental conditions is a key step in identifying biomarkers,
    proteins or metabolites that mediate the underlying mechanism of a
    biological process, and new potential therapeutic drug targets.
    To enable identification of these mass entities of interest in a
    statistically rigorous fashion, GeneSpring MS provides a broad set of
    tests that include: 1) Parametric and non-parametric one-way tests; 2)
    Parametric and non-parametric two-way analysis of variance (ANOVA);
    3) Family-wise error rate and false discovery rate multiple testing
    corrections; 4) Tukey and Student-Newman-Keuls
    post-hoc tests.

    Grouping mass entities with similar abundance profiles -
    Clustering analysis groups mass entities based on the similarity of
    their abundance profiles to uncover the most prominent patterns in the
    data. In addition, clustering analysis may reveal interesting biological
    relationships, as mass entities that exhibit similar behavior across a
    set of experimental conditions may share similar biological functions.
    GeneSpring MS provides a broad choice of clustering algorithms that
    include: 1) Hierarchical clustering; 2) k-means clustering; 3) Quality
    Threshold (QT) clustering; 4) Self-organizing maps (SOM).

    Comparing sample abundance profiles -
    Comparing sample abundance profiles can provide information on the
    quality of replicate samples within an experimental condition and give
    insight into similarities in biological responses. For example, if a
    compound is known to induce a mass abundance signature
    associated with liver toxicity, compounds that induce a similar profile
    may also possess toxic effects. Principal Component Analysis (PCA)
    and hierarchical clustering are two advanced methods for comparing
    sample abundance in GeneSpring MS.

    Supervised classification of abundance profiles -
    Class prediction analysis using metabolomic and proteomic data is
    becoming an increasingly valuable tool in toxicometabolomics,
    toxicoproteomics, and for early diagnosis, prognosis, and prediction of
    clinical treatment outcomes. Compound classification and predicting
    toxic effects of potential therapeutics is essential to the process of
    prioritizing compound pipelines and eliminating costly failures in drug
    development. In class prediction analysis, altered metabolite and
    protein expression patterns reflecting biological responses to well
    characterized toxicants can be used to predict toxicological
    classification of unknown compounds. For such supervised
    classification analyses, GeneSpring MS provides two (2) class
    prediction algorithms: 1) k-nearest neighbors and 2) Support Vector
    Machines (SVM).

    Protein and metabolite identification of mass entities of interest -
    Frequently, the identity of mass entities of interest from mass
    spectrometry data is unknown. A key step in placing statistically
    significant findings into a biological context is to identify the proteins or
    metabolites represented by these mass entities of interest.
    GeneSpring MS provides several tools to address common
    methodologies for protein or metabolite identification, protein and
    metabolite database searching, and tandem mass spectrometry
    analysis. Specifically, these tools include:

    1) A direct link to perform metabolite identification through Metlin
    Metabolite Database search.
    2) A direct link to perform protein identification using Protein Mass
    Fingerprinting in Agilent Spectrum Mill database.
    3) Direct export of the MS/MS inclusion list containing mass entities to
    be targeted during MS/MS acquisition for peptide/protein identification.

    System Requirements  

    PC Version

    Windows 2000/XP or Server 2003
    Pentium IV or faster
    1 GB RAM (2 GB recommended)
    100 MB disk space (application only, more required for data)
    1024 x 768 display

    Mac Version
    GeneSpring MS is NOT supported on the Mac at this time.

    Manufacturer   Home office; see web site for international locations.

    Agilent Technologies, Inc.
    Life Sciences and Chemical Analysis Group
    5301 Stevens Creek Boulevard
    Santa Clara, CA 95051-7201
    USA
    800-227-9770
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