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 Abstract 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 -

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.


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G6G Abstract Number 20085

G6G Manufacturer Number 100432