PEAKS DB: Database Searching

Database searching is a standard method of identifying proteins. One thing to note is that databases are getting larger and larger. Larger databases translate to a higher possibility of false positives and longer search times. Given this, PEAKS has a unique two step approach to database searching where the initial de novo tags are first used to search the database creating a much smaller and more manageable database. Using spectral information from the data, this smaller database is then searched against for potential protein candidates. What makes this strategy unique is that it increases the efficiency of the search process, maintains speed and ultimately maintains a low false positive rate no matter the size of the database.

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 identified.

Basics of Protein ID Database Searching

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 Score Description

Advanced Protein ID Database Searching

Many experts recommend using multiple search engines to ensure confident results, rather then relying on an individual engine. While some researchers continue to manually collect results and load them into separate software for organization, PEAKS' users can launch a single set (or batch sets) of data through multiple search engines (PEAKS, Mascot, Sequest, X!Tandem and OMSSA) and automatically populate confidence scores for individual engines as well as inChorus (all together) all within one software. Click here to read more about the inChorus tool and multi-engine protein ID.

Post Translational Modifications

The PTM Finder searches (multiple) modification candidates within the PEAKS database search results. By applying considered PTMs post-database search, high quality database results can reserved from this process, thus being more efficient (not bottle necking the process with unmodified peptides) and allowing potential modification sites to be meticulously investigated. Click here for further details of the PTM Finder.