PEAKS Online

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PEAKS Online, means high-throughput sequencing on a shared resource. This proteomics server software is fully parallelized with the ability to run on any cluster or multi-CPU machine. PEAKS users get the same detail-oriented results as PEAKS Studio with the advantage of using a shared resource. Users interested in accurate quantification results can add an optional PEAKS Q quantification module.

Users are able to run the same proven algorithms included in the PEAKS Studio solution, efficiently and on a larger scale. The interactive tool used to send/retrieve data to/from the server is called PEAKS Client, presenting results in the same intuitive manner as available in the desktop solution.

Algorithms

Industry Leading de novo Sequencing

PEAKS is the preferred de novo sequencing software for identifying novel peptides and studying unsequenced organisms. Even when the peptide sequence is in a database, de novo sequencing can greatly improve the database search identification.

PEAKS has been reported as the best-performing de novo sequencing software in multiple independent publications.

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Sensitive and Accurate Database Searching

Database searching is a standard way to identify the peptides whose sequences are in a database. It is also an important function of the PEAKS software. While database searching cannot discover new peptides, it is a great way to confirm the existence of expected peptides and PTMs. It also serves the foundation of many other proteomics analyses, such as protein quantification and deep replication.

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Advanced Post Translational Modification Searching

Post-translational modifications (PTMs) are crucial to the functions of proteins. Their accurate and sensitive characterization is of great importance to every proteomics researcher. Since the PTM information is usually absent or incomplete in today’s protein databases, the identification of PTMs poses a number of challenges to the traditional database search approach. The PEAKS software includes the advanced PEAKS PTM algorithm to meet these challenges and is the only commercial software that can identify unspecified variable PTMs.

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Sequence Tag Homology Searching

Biological samples commonly contain proteins with slightly different sequences to those protein databases. This is frequently caused by polymorphism, antibody diversity, database errors, and cross-species database searching. Ignoring those mutated peptides can potentially lead to an oversight of a potential biomarker, an error in antibody confirmation, or simply low coverage of proteins. To handle mutations, PEAKS software includes the SPIDER algorithm that is specially designed to detect peptide mutations and perform cross-species homology search.
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Launch Multiple Search Engines Together

PEAKS inChorus currently can combine results from Mascot, X!Tandem, OMSSA, and Proteome Discoverer (Sequest). It can call Mascot, X!Tandem, and OMSSA directly within PEAKS GUI and the results are automatically retrieved and combined by PEAKS inChorus.

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Label & Label Free Quantification

As researchers press further into the understanding of life sciences, quantification provides greater insight into proteomic mysteries. PEAKS Q is the optional module of PEAKS for protein quantification analysis based on mass spectrometry data. PEAKS Q has both labeling and label-free methods, including:

• LFQ (Label-Free) • ICAT • ICPL
• SILAC • N-Terminal 18O
• iTRAQ • TMT (MS2/MS3) • User Defined Labeling

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