PEAKS (software)

PEAKS is a popular tandem mass spectrometry software designed for peptide sequencing and protein identification.

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Other than being used for search engine protein identification (Protein ID), it is one of the earliest adaptors for de novo sequencing (both automated and manual) and peptide sequence tag based searching. (SPIDER).^{[citation needed]}

In short, de novo sequencing is peptide sequencing performed without prior knowledge of the amino acid sequence.[1] The PEAKS website describes this as "the ability to provide the sequence of a peptide without the aid of a protein sequence database..." [2].

PEAKS provides a complete sequence for each peptide, confidence scores on individual amino acid assignments, simple reporting for high-throughput analysis, and other information intended for in depth investigations.

One of the most useful tools in any form of research is the ability to compare results. Whether this is with colleagues or in the "measure twice cut once" theory of carpentry. 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, and provide the highest possible level of confidence.