What is a decoy database?
The decoy sequence database contains biologically nonexistent sequences that share some statistical attributes with the target sequences. Ideally, random peptide spectrum matches (PSMs) are expected to hit both the decoy and the target sequences with the same probabilistic distributions.
What are decoy peptides?
Peptide decoys or decoy receptors are molecules specifically designed to mimic the role of a certain receptor protein, encouraging target entities to interact with them so that these interactions can be studied and analyzed, or even exploited to initiate a certain activity or response.
What is decoy sequence?
Answer: The hs38d1 decoy contains DNA viral sequences (e.g. Epstein-Barr Virus) as well human genomic sequence that could not be placed on chromosomes when the reference genome was put together. Much of the decoy consists of repeats that are difficult to assemble.
What is a decoy genome?
What are decoy sequences?
Decoy sequences are unique decoys bearing deoxyribonucleic acid viral continuities and genomic continuities in humans that were impossible to set on chromosomes while assembling the reference genome. This genome is challenging to bring together due to its repeats.
What is the target-decoy search strategy for mass spectrometry-based proteomics?
The target-decoy search strategy has emerged as a simple, effective tool for generating such estimations. This strategy is ba … Target-decoy search strategy for mass spectrometry-based proteomics Methods Mol Biol. 2010;604:55-71.doi: 10.1007/978-1-60761-444-9_5. Authors Joshua E Elias 1 , Steven P Gygi
How are incorrect PSMS distributed between target and decoy sequences?
Under the concatenated target-decoy paradigm, incorrect PSMs are distributed between target and decoy sequences according to their background frequency (i.e., 1:1 for reversed sequences).
What is the target-decoy search strategy for peptide identification?
The target-decoy search strategy has emerged as a simple, effective tool for generating such estimations. This strategy is ba … Accurate and precise methods for estimating incorrect peptide and protein identifications are crucial for effective large-scale proteome analyses by tandem mass spectrometry.
How to create a decoy database for protein databases?
In both case, once you upload your protein database containing contaminants, the decoy database is created on its own. In case of Proteome Discoverer, once you upload the database, there is a option of index the database. You have to go and choose your proteolytic enzyme (eg. trypsin) and the algorithm takes care of the decoy database.