Analysis of the Resolution Limitations of Peptide Identification Algorithms
| Autor: | Sven Degroeve, Kenny Helsens, Lennart Martens, Niklaas Colaert |
|---|---|
| Rok vydání: | 2011 |
| Předmět: |
Proteomics
False discovery rate Matching (statistics) Computer science computer.software_genre Biochemistry Mass Spectrometry Fungal Proteins 03 medical and health sciences Search algorithm Yeasts Humans Amino Acids Databases Protein 030304 developmental biology 0303 health sciences 030302 biochemistry & molecular biology Computational Biology Reproducibility of Results General Chemistry Thresholding Search Engine Identification (information) Mutation Proteome Data mining Peptides Decoy computer Algorithms |
| Zdroj: | Journal of Proteome Research |
| ISSN: | 1535-3907 1535-3893 |
| DOI: | 10.1021/pr200913a |
| Popis: | Proteome identification using peptide-centric proteomics techniques is a routinely used analysis technique. One of the most powerful and popular methods for the identification of peptides from MS/MS spectra is protein database matching using search engines. Significance thresholding through false discovery rate (FDR) estimation by target/decoy searches is used to ensure the retention of predominantly confident assignments of MS/MS spectra to peptides. However, shortcomings have become apparent when such decoy searches are used to estimate the FDR. To study these shortcomings, we here introduce a novel kind of decoy database that contains isobaric mutated versions of the peptides that were identified in the original search. Because of the supervised way in which the entrapment sequences are generated, we call this a directed decoy database. Since the peptides found in our directed decoy database are thus specifically designed to look quite similar to the forward identifications, the limitations of the existing search algorithms in making correct calls in such strongly confusing situations can be analyzed. Interestingly, for the vast majority of confidently identified peptide identifications, a directed decoy peptide-to-spectrum match can be found that has a better or equal match score than the forward match score, highlighting an important issue in the interpretation of peptide identifications in present-day high-throughput proteomics. |
| Databáze: | OpenAIRE |
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