Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification

Database Construction and Peptide Identification Strategies for Proteogenomic Studies on Sequenced Genomes

(2014) Celine Hernandez et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data

(2014) Sunghee Woo et al.   PROTEOMICS

Identification of gene fusions from human lung cancer mass spectrometry data

(2013) Han Sun et al.   BMC GENOMICS

Whole human genome proteogenomic mapping for ENCODE cell line data: identifying protein-coding regions

(2013) Jainab Khatun et al.   BMC GENOMICS

Proteogenomic Database Construction Driven from Large Scale RNA-seq Data

(2013) Sunghee Woo et al.   JOURNAL OF PROTEOME RESEARCH

Deep Coverage of theEscherichia coliProteome Enables the Assessment of False Discovery Rates in Simple Proteogenomic Experiments

(2013) Karsten Krug et al.   MOLECULAR & CELLULAR PROTEOMICS

An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes inZea mays

(2013) Natalie E. Castellana et al.   MOLECULAR & CELLULAR PROTEOMICS

Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq

(2013) Gloria M. Sheynkman et al.   MOLECULAR & CELLULAR PROTEOMICS

A statistical model-building perspective to identification of MS/MS spectra with PeptideProphet

(2012) Kelvin Ma et al.   BMC BIOINFORMATICS

Improving X!Tandem on Peptide Identification from Mass Spectrometry by Self-Boosted Percolator

(2012) Pengyi Yang et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies

(2012) Paul Blakeley et al.   JOURNAL OF PROTEOME RESEARCH

Comet: An open-source MS/MS sequence database search tool

(2012) Jimmy K. Eng et al.   PROTEOMICS

NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

(2011) K. D. Pruitt et al.   NUCLEIC ACIDS RESEARCH

Proteogenomics to discover the full coding content of genomes: A computational perspective

(2010) Natalie Castellana et al.   Journal of Proteomics

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

Proteogenomics

(2010) Santosh Renuse et al.   PROTEOMICS

Target-Decoy with Mass Binning: A Simple and Effective Validation Method for Shotgun Proteomics Using High Resolution Mass Spectrometry

(2009) Jong Wha J. Joo et al.   JOURNAL OF PROTEOME RESEARCH

The UniProtKB/Swiss-Prot knowledgebase and its Plant Proteome Annotation Program

(2008) Michel Schneider et al.   Journal of Proteomics

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assigning Significance to Peptides Identified by Tandem Mass Spectrometry Using Decoy Databases

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH