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

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

(2011) M. Brosch et al.   GENOME RESEARCH

A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry

(2011) R. Chaerkady et al.   GENOME RESEARCH

Proteomic Characterization of Novel Alternative Splice Variant Proteins in Human Epidermal Growth Factor Receptor 2/neu–Induced Breast Cancers

(2010) Rajasree Menon et al.   CANCER RESEARCH

Genome remodelling in a basal-like breast cancer metastasis and xenograft

(2010) Li Ding et al.   NATURE

An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome

(2010) Danny A. Bitton et al.   PLoS One

Proteogenomics

(2010) Santosh Renuse et al.   PROTEOMICS

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Gel-Eluted Liquid Fraction Entrapment Electrophoresis:  An Electrophoretic Method for Broad Molecular Weight Range Proteome Separation

(2008) John C. Tran et al.   ANALYTICAL CHEMISTRY

Incorporating sequence information into the scoring function: a hidden Markov model for improved peptide identification

(2008) Jainab Khatun et al.   BIOINFORMATICS

Identification of Novel Alternative Splice Isoforms of Circulating Proteins in a Mouse Model of Human Pancreatic Cancer

(2008) R. Menon et al.   CANCER RESEARCH

uORFs, reinitiation and alternative translation start sites in human mRNAs

(2008) Alex V. Kochetov et al.   FEBS LETTERS

Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations

(2008) G. E. Merrihew et al.   GENOME RESEARCH

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

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