Assigning significance to peptides identified by tandem mass spectrometry using decoy databases.
By Lukas Käll, John D. Storey, Michael J. MacCoss, William Stafford Noble. Journal of Proteome Research, 2008
621 citations recorded by the source corpus.
Subfields: Molecular Biology, Spectroscopy
View Paper: https://www.semanticscholar.org/paper/1ef83b2b980b406db708adb6104533be05af9854
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In Molecular Biology
- Matthias Mann
- Alexey I. Nesvizhskii
- Jüergen Cox
- R. Aebersold
- Steven P. Gygi
- Joshua E. Elias
- Lukas Reiter
- Baozhen Shan
In Spectroscopy
- Matthias Mann
- Alexey I. Nesvizhskii
- Jüergen Cox
- R. Aebersold
- Steven P. Gygi
- Joshua E. Elias
- Lukas Reiter
- Baozhen Shan
Citations in the corpus
- Target-Decoy Search Strategy for Mass Spectrometry-Based Proteomics (2010, methodology): “Proteins— Protein shuffling is another method used for creating decoy sequences (16) in which the amino acids of each input target protein are randomly rearranged to yield a new decoy protein.”
- MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification (2008, methodology): “We use a database containing all true protein sequences, concatenated with reversed nonsense versions of these sequence”
- Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry* (2009, background): “The approach extends the well established targetdecoy strategy designed to estimate FDR at the PSM level (17, 18) to the level of protein identifications, i.”
- Accurate and Sensitive Peptide Identification with Mascot Percolator (2009, methodology): “Sample 2: Peak lists (35 236 spectra) were searched with Mascot 2.2. against the same target and decoy databases that were used by Ka¨ll et al. 14 The following parameters were used: enzyme ) trypsin; maximum missed cleavages ) 2; fixed modification ) carbamidomethylation of cysteine; peptide mass tol”
- Spectral Probabilities and Generating Functions of Tandem Mass Spectra: a Strike Against Decoy Databases (2008, neutral): “, 2008 [2] for recent reviews).”
- Untargeted metabolomics strategies – Challenges and Emerging Directions (2016, background): “In MS-based proteomic studies, targetdecoy search-based FDR calculations are widely accepted [34, 35].”
- PEAKS DB: De Novo Sequencing Assisted Database Search for Sensitive and Accurate Peptide Identification (2011, methodology): “achieved by the target decoy method (18, 19).”