Unbiased False Discovery Rate Estimation for Shotgun Proteomics Based on the Target-Decoy Approach.
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Lev I Levitsky | Mark V Ivanov | Mikhail V Gorshkov | Anna A Lobas | M. V. Ivanov | A. Lobas | M. Gorshkov | L. Levitsky
[1] L. Käll,et al. Quality assessments of peptide–spectrum matches in shotgun proteomics , 2011, Proteomics.
[2] Stephan M. Winkler,et al. MS Amanda, a Universal Identification Algorithm Optimized for High Accuracy Tandem Mass Spectra , 2014, Journal of proteome research.
[3] P. Pevzner,et al. Target-Decoy Approach and False Discovery Rate: When Things May Go Wrong , 2011, Journal of the American Society for Mass Spectrometry.
[4] William Stafford Noble,et al. Semi-supervised learning for peptide identification from shotgun proteomics datasets , 2007, Nature Methods.
[5] Joshua E. Elias,et al. Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome. , 2003, Journal of proteome research.
[6] Edward L Huttlin,et al. Prediction of error associated with false-positive rate determination for peptide identification in large-scale proteomics experiments using a combined reverse and forward peptide sequence database strategy. , 2007, Journal of proteome research.
[7] Pavel A. Pevzner,et al. Universal database search tool for proteomics , 2014, Nature Communications.
[8] William Stafford Noble,et al. Posterior error probabilities and false discovery rates: two sides of the same coin. , 2008, Journal of proteome research.
[9] William Stafford Noble,et al. Assigning significance to peptides identified by tandem mass spectrometry using decoy databases. , 2008, Journal of proteome research.
[10] Yudi Pawitan,et al. Estimation of false discovery proportion under general dependence , 2006, Bioinform..
[11] William Stafford Noble,et al. Non-parametric estimation of posterior error probabilities associated with peptides identified by tandem mass spectrometry , 2008, ECCB.
[12] Chao Liu,et al. A theoretical foundation of the target-decoy search strategy for false discovery rate control in proteomics , 2015, 1501.00537.
[13] Alexey I Nesvizhskii,et al. Analysis and validation of proteomic data generated by tandem mass spectrometry , 2007, Nature Methods.
[14] Nuno Bandeira,et al. False discovery rates in spectral identification , 2012, BMC Bioinformatics.
[15] Alexey I Nesvizhskii,et al. Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search. , 2002, Analytical chemistry.
[16] John D. Storey,et al. Statistical significance for genomewide studies , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[17] Steven P Gygi,et al. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry , 2007, Nature Methods.
[18] Jianqing Fan,et al. Journal of the American Statistical Association Estimating False Discovery Proportion under Arbitrary Covariance Dependence Estimating False Discovery Proportion under Arbitrary Covariance Dependence , 2022 .
[19] William Stafford Noble,et al. Determining the calibration of confidence estimation procedures for unique peptides in shotgun proteomics. , 2013, Journal of proteomics.
[20] M. Mann,et al. Andromeda: a peptide search engine integrated into the MaxQuant environment. , 2011, Journal of proteome research.
[21] Roger E. Moore,et al. Qscore: An algorithm for evaluating SEQUEST database search results , 2002, Journal of the American Society for Mass Spectrometry.
[22] Lev I Levitsky,et al. Pyteomics—a Python Framework for Exploratory Data Analysis and Rapid Software Prototyping in Proteomics , 2013, Journal of The American Society for Mass Spectrometry.
[23] M. Mann,et al. MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification , 2008, Nature Biotechnology.
[24] B. Sorić. Statistical “Discoveries” and Effect-Size Estimation , 1989 .
[25] J. Coon,et al. A proteomics search algorithm specifically designed for high-resolution tandem mass spectra. , 2013, Journal of proteome research.