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    Bioinformatics Solutions PEAKS

    Category  Proteomics>Mass Spectrometry Analysis/Tools

    Abstract  PEAKS is advanced software for the analysis of peptide
    mass spectrometry data. The PEAKS family consists of: PEAKS Studio,
    PEAKS Online, PEAKS Client, and PEAKS Viewer.

    PEAKS Studio -- A fully functional proteomics workbench, PEAKS
    Studio will perform de novo sequencing, protein identification, meta-
    protein identification (PEAKS inChorus), assisted manual sequencing
    and data manipulation, either along side PEAKS Online or
    independently. PEAKS Studio reads all supported mass-spectrometry
    data formats, and PEAKS' native ANZ files. Each copy of PEAKS Studio
    is meant to be installed on a single computer with up to 4 CPUs, and
    used by one user at a time.

    PEAKS Online -- The server version, PEAKS Online means high-
    through put on a shared resource. It is fully parallelized, with the ability
    to run on any cluster or multi-cpu machine. PEAKS Online returns auto
    de novo sequences and identifies peptides/proteins given Mass
    Spectrometry (MS)/MS tandem spectral data. The results are displayed
    in HyperText Markup Language (HTML) via a built-in web server. Links
    to the results are e-mailed to the user after analysis. This means that
    everyone in your institution, who has a browser, an e-mail address and
    access to the cluster, can submit data and view results.

    PEAKS Client -- The latest addition to the PEAKS Family, PEAKS Client,
    takes the best of PEAKS Studio and PEAKS Online and bundles them
    together. From the Studio side, multiple files can be processed and
    organized in a high throughput batch workflow. The Online influence
    allows a user to set up and process raw data on a cluster and work
    simultaneously.

    PEAKS Viewer -- This data viewing tool reads all supported mass-
    spectrometry data formats, and PEAKS' native ANZ files. It is meant for
    distributing results of PEAKS processed data. The results can be
    viewed, edited, and saved. PEAKS Viewer does Not contain the auto de
    novo or protein ID algorithms. A PEAKS Viewer license grants provided
    users with unlimited distribution capabilities.

    Products capabilities/features include:

    De Novo Sequencing -- In a process called de novo sequencing,
    peptide sequences are derived from the masses of their fragments as
    shown on a tandem mass spectrum. When performing de novo
    sequencing, No protein sequence database is used for reference.

    1) PEAKS offers an advanced accurate auto de novo algorithm.

    2) PEAKS provides confidence assignment at the amino acid level.

    3) PEAKS can find post-translational modifications on peptides when
    de novo sequencing, and position them in the sequence.

    4) PEAKS is specifically tuned to handle data from Quadrupole Time-
    Of-Flight mass spectrometer (QTOF), TOF-TOF, Ion Trap, Orbi-Trap
    and Fourier Transform MS (FTMS) instruments, while using y and b
    ions or c and z ions for fragmentation flexibility.

    Protein Identification -- The new generation of protein identification
    tools, like PEAKS, use de novo sequencing to help in the database
    search. Sequence tags are used, in conjunction with fragment ion
    mass matching, to speed up the search, remove false positive
    matches, and find peptides with interesting sequence variations or
    modifications that would prevent them from being otherwise identified.

    1) inChorus Meta Protein ID - With this feature, PEAKS Studio Not only
    performs de novo sequencing and identifies proteins, but compares
    its results with those of such MS/MS databases as Mascot (see G6G
    Product Number 20087), OMSSA, SEQUEST, X! Tandem and
    sequence tag search tool SPIDER. Furthermore, you can eliminate
    false positives and recover false negatives by comparing to de novo
    sequences -- this is automatic, at-a-glance information from PEAKS
    inChorus.

    2) SPIDER, Software Protein Identifier, is a sequence tag based
    search tool, which can be used to identify peptides that traditional
    tandem mass spectrometry ion search tools will miss. SPIDER can
    also be used to improve coverage on a protein that is already in a
    database, by seeking exact sequence matches and being plugged into
    a specialized database.

    Post Translational Modifications (PTMs) -- PEAKS provides a number
    of features designed specifically to help identify modified proteins.
    PEAKS Studio employs both de novo sequencing and database
    search technology to identify PTMs. To identify modifications, PEAKS
    provides:

    1) A library of ~30 common PTMs (e.g. carbamidomethylation,
    phosphorylation, oxidation).

    2) A user-defined system for the creation of custom PTMs.

    3) Specify the modification(s) of interest and PEAKS will consider this
    information when providing sequence candidates or identification of
    proteins from your tandem MS spectra.

    4) The PEAKS auto de novo algorithm derives sequences with PTMs.
    The PTMs are then removed and both partial and complete sequence
    matches (i.e. tags) are used to search the database to find protein
    candidates. The short list of proteins in the database is then searched
    for spectrum-sequence matches, looking for variations in mass to
    identify PTMs. When this search finds a match with a PTM, the
    algorithm evaluates the quality of the match, and provides the result
    with a final score.

    Load and Preprocess RAW data -- PEAKS provides algorithms for
    loading, refining and preprocessing RAW data. Load in RAW data from
    most instruments directly into PEAKS, or use a standard data format.
    Then choose to:

    1) Merge Scans of the same peptide - The MS instrument can MS/MS
    the same peptide several times. Merging these scans means higher
    quality data. PEAKS uses the retention time and precursor
    mass/charge (m/z) value to avoid merging the wrong scans.

    2) Recalculate correct precursor charge - RAW data often contains
    incomplete or inaccurate charge information. But PEAKS can
    recalculate it carefully by the examination of the survey scan (or in the
    case of ion-trap data, the MS/MS itself).

    3) Remove MS/MS scans that are of poor quality - A large percentage of
    MS/MS scans contain only noise. Removing these will speed up
    processing time, and reduce the risk of random false positive
    assignments.

    4) Preprocess within MS/MS scans by - a) Baseline deduction noise
    filtering; b) Centroiding; c) Deconvolution.

    System Requirements  

    PEAKS can be run on any computer that supports Sun's Java Runtime
    Environment (JRE) 1.4 (or JRE 1.5 for PEAKS Studio 4.0 or later). On
    installation, PEAKS will install a dedicated JRE for its use, so it can co-
    exist with another version of Java on our machine. The system should
    also have: 1-2Gb RAM, 1GB free space on hard drive (more for mass
    spec data and results), an AMD or Intel 2GHz CPU. The minimum
    configuration is 1GB of RAM and 1Ghz CPU.

    Manufacturer   Home office.



    Price   Contact manufacturer

    G6G Product Number  20085

    G6G Manufacturer Number 100432
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