Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry
By Joshua E. Elias, Steven P. Gygi. Nature Methods, 2007
3,933 citations recorded by the source corpus.
Subfields: Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/6798f8080d5a675a5ff091847bb39ceac6198a79
How researchers see this paper
The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.
In Molecular Biology
- Alexey I. Nesvizhskii
- Matthias Mann
- Jüergen Cox
- R. Aebersold
- John R. Yates III
- Steven P. Gygi
- Chunaram Choudhary
- Jesper V. Olsen
In Spectroscopy
- Alexey I. Nesvizhskii
- Matthias Mann
- Jüergen Cox
- R. Aebersold
- John R. Yates III
- Steven P. Gygi
- Jesper V. Olsen
- Chunaram Choudhary
Citations in the corpus
- A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics (2010, methodology): “The plausibility of these assumption was discussed in [174].”
- Untargeted metabolomics strategies – Challenges and Emerging Directions (2016, background): “In MS-based proteomic studies, targetdecoy search-based FDR calculations are widely accepted [34, 35].”
- The functional landscape of the human phosphoproteome (2019, result): “This ratio of phosphoproteins, similarly to previous findings 4 , remained constant regardless of the reported protein abundance in PaxDb (Supplementary Fig.”
- Deep Proteomics of the Xenopus laevis Egg using an mRNA-derived Reference Database (2014, positive): “5% false discovery rate (FDR) by using the target decoy strategy [1, 19, 20].”
- Proteomics by mass spectrometry: approaches, advances, and applications. (2009, methodology): “As with any database search, the decoy database is used to filter out false-positive identification (218).”
- PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2011, methodology): “Currently, this validation is typically achieved by the target decoy method (18, 19).”
- Lysine succinylation is a frequently occurring modification in prokaryotes and eukaryotes and extensively overlaps with acetylation. (2013, methodology): “Peptides were identified by a target-decoy based strategy (Elias and Gygi, 2007), allowing a maximum false discovery rate of <1%.”
- Inaugural Article: The protein expression landscape of the Arabidopsis root (2012, positive): “thaliana reference protein database TAIR9 (TAIR, release 9), concatenated with a decoy database (the reversed TAIR9 database) to estimate the overall FDR (62, 63), plus roughly 260 additional known contaminants (i.”
- Comet: An open‐source MS/MS sequence database search tool (2013, methodology): “A q-value is defined as the minimum false discovery rate (FDR) [18] for which a PSM is accepted; it is calculated as a simple correction to the standard target-decoy FDR calculation.”
- The BioPlex Network: A Systematic Exploration of the Human Interactome (2015, positive): “The target-decoy method (Elias and Gygi, 2007) was used to filter each LC-MS dataset to a preliminary 1% protein FDR.”
- Universal database search tool for proteomics (2014, methodology): “MS-GF þ estimates FDRs using the target decoy approach 38,39 .”