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. Well demonstrated with a popular software compared with PEAKS protein ID on high mass accuracy data.

Using mass spectrometry, masses of peptides or fragments of peptides, can be compared against the theoretical masses of the protein subsequences to identify the peptides. By inference, proteins can be identified in this manner. Traditional database search tools designed for this purpose struggle with the balance between false positive peptide assignments and low sensitivity.

PEAKS inChorus meta-search tool allows PEAKS to integrate with your existing tools for more coverage and confidence. The most powerful solution involves a hybrid search approach like PEAKS and a more traditional tool for the best coverage. No software is perfect: all researchers are encouraged to use two or more protein identification tools to validate results and increase coverage!

With its easy to use, easy to read graphical user interface, PEAKS shows reliable and easy to read confidence scores. The user can find the most pertinent information at a glance. Yet, all the information needed for in depth analysis is provided, without cluttering up the display.

PEAKS will handle data from QTOF, TOF-TOF, Ion Trap, and FTMS instruments. It provides a reliable central processing tool for all instrument types.

Since proteins are often modified after translation, the identification of post-translational modifications (PTM), is an essential function of any protein ID tool. PEAKS provides the most flexible handling of post-translational modifications. Users are free to search for any number of PTM at once. Modifications can be selected from a pre-defined list, edited, or created from scratch. The position of a PTM is displayed in sequence, and confidence scores assigned.

Next Page => Learn more about the powerful and flexible PTM finding tools.