PEAKS is a proteomics software program for tandem
mass spectrometry
Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used ...
designed for
peptide
Peptides are short chains of amino acids linked by peptide bonds. A polypeptide is a longer, continuous, unbranched peptide chain. Polypeptides that have a molecular mass of 10,000 Da or more are called proteins. Chains of fewer than twenty am ...
sequencing,
protein
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residue (biochemistry), residues. Proteins perform a vast array of functions within organisms, including Enzyme catalysis, catalysing metab ...
identification and quantification.
Description
PEAKS is commonly used for peptide identification (Protein ID) through
de novo peptide sequencing In mass spectrometry, de novo peptide sequencing is the method in which a peptide amino acid sequence is determined from tandem mass spectrometry.
Knowing the amino acid sequence of peptides from a protein digest is essential for studying the biolo ...
assisted
search engine
A search engine is a software system that provides hyperlinks to web pages, and other relevant information on World Wide Web, the Web in response to a user's web query, query. The user enters a query in a web browser or a mobile app, and the sea ...
database searching. PEAKS has also integrated PTM and mutation characterization through automatic
peptide sequence tag A peptide sequence tag is a piece of information about a peptide obtained by tandem mass spectrometry that can be used to identify this peptide in a protein database.
Mass spectrometry
In general, peptides can be identified by fragmenting them in ...
based searching (SPIDER)
[Ma B, Johnson. De Novo sequencing and homology searching Molecular & Cellular Proteomics. 10.1074/mcp.O111.014902 (2011).] and PTM Identification.
PEAKS provides a complete sequence for each peptide, confidence scores on individual amino acid assignments, simple reporting for high-throughput analysis, amongst other information.
The software has the ability to compare results of multiple search engines. PEAKS inChorus will cross check test results automatically with other protein ID search engines, like Sequest, OMSSA, X!Tandem and Mascot. This approach guards against false positive peptide assignments.
PEAKS Q is an add-on tool for protein quantification, supporting label (
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,
iTRAQ,
SILAC
Stable isotope labeling by/with amino acids in cell culture (SILAC) is a technique based on mass spectrometry that detects differences in protein abundance among samples using non-radioactive isotopic labeling. It is a popular method for quantitat ...
,
TMT,
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, etc.) and
label free techniques.
SPIDER is a sequence tag based search tool within PEAKS, which deals with the possible overlaps between the de novo sequencing errors and the homology mutations. It reconstructs the real peptide sequence by combining both the de novo sequence tag and the homolog, automatically and efficiently.
[
A collection of algorithms used within the PEAKS software have been adapted and configured into a specialized project, PEAKS AB, which has proven to be the first method for automatic monoclonal antibody sequencing.]
Notes
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Mass spectrometry software
Proteomic sequencing