Systematic Comparison of False-Discovery-Rate-Controlling Strategies for Proteogenomic Search Using Spike-in Experiments.
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Kyu-Baek Hwang | Eunok Paek | Hyunwoo Kim | Honglan Li | Jonghun Park | Kyu-Baek Hwang | Eunok Paek | Honglan Li | Jonghun Park | Hyunwoo J. Kim
[1] Yixue Li,et al. Identification of gene fusions from human lung cancer mass spectrometry data , 2013, BMC Genomics.
[2] 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.
[3] Jacob D. Jaffe,et al. Proteogenomic mapping as a complementary method to perform genome annotation , 2004, Proteomics.
[4] Patrick G. A. Pedrioli. Trans-Proteomic Pipeline: A Pipeline for Proteomic Analysis , 2010, Proteome Bioinformatics.
[5] B. Maček,et al. Deep Coverage of the Escherichia coli Proteome Enables the Assessment of False Discovery Rates in Simple Proteogenomic Experiments* , 2013, Molecular & Cellular Proteomics.
[6] Yohann Couté,et al. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods , 2015, Data in brief.
[7] Pavel A. Pevzner,et al. Universal database search tool for proteomics , 2014, Nature Communications.
[8] Steven P Gygi,et al. Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry , 2007, Nature Methods.
[9] California Jack Cassidy,et al. An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes in Zea mays* , 2013, Molecular & Cellular Proteomics.
[10] W. Pao,et al. A Bioinformatics Workflow for Variant Peptide Detection in Shotgun Proteomics* , 2011, Molecular & Cellular Proteomics.
[11] Gennifer E. Merrihew,et al. Proteogenomic database construction driven from large scale RNA-seq data. , 2014, Journal of proteome research.
[12] Robertson Craig,et al. TANDEM: matching proteins with tandem mass spectra. , 2004, Bioinformatics.
[13] A. Nesvizhskii. Proteogenomics: concepts, applications and computational strategies , 2014, Nature Methods.
[14] Kyu-Baek Hwang,et al. Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification , 2016, BMC Genomics.
[15] Robert J. Chalkley,et al. The Effect of Using an Inappropriate Protein Database for Proteomic Data Analysis , 2011, PloS one.
[16] Chao Liu,et al. A note on the false discovery rate of novel peptides in proteogenomics , 2015, Bioinform..
[17] Samuel H. Payne,et al. Proteogenomic strategies for identification of aberrant cancer peptides using large‐scale next‐generation sequencing data , 2014, Proteomics.
[18] S. Hubbard,et al. Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies , 2012, Journal of proteome research.
[19] Hokeun Kim,et al. Compact variant‐rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses , 2014, Proteomics.
[20] M. Mann,et al. Comparative Proteomic Analysis of Eleven Common Cell Lines Reveals Ubiquitous but Varying Expression of Most Proteins* , 2012, Molecular & Cellular Proteomics.
[21] Vineet Bafna,et al. Advanced Proteogenomic Analysis Reveals Multiple Peptide Mutations and Complex Immunoglobulin Peptides in Colon Cancer. , 2015, Journal of proteome research.
[22] J. Eng,et al. Comet: An open‐source MS/MS sequence database search tool , 2013, Proteomics.