pep2pro: a new tool for comprehensive proteome data analysis to reveal information about organ-specific proteomes in Arabidopsis thaliana

Large-Scale Comparative Phosphoproteomics Identifies Conserved Phosphorylation Sites in Plants

(2010) H. Nakagami et al.   PLANT PHYSIOLOGY

Deterministic protein inference for shotgun proteomics data provides new insights into Arabidopsis pollen development and function

(2009) M. A. Grobei et al.   GENOME RESEARCH

Protein Identification False Discovery Rates for Very Large Proteomics Data Sets Generated by Tandem Mass Spectrometry

(2009) Lukas Reiter et al.   MOLECULAR & CELLULAR PROTEOMICS

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

(2009) Matthias Gstaiger et al.   NATURE REVIEWS GENETICS

The Proteomics Identifications database: 2010 update

(2009) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

PhosPhAt: the Arabidopsis thaliana phosphorylation site database. An update

(2009) Pawel Durek et al.   NUCLEIC ACIDS RESEARCH

In-Depth Proteome Analysis of Arabidopsis Leaf Peroxisomes Combined with in Vivo Subcellular Targeting Verification Indicates Novel Metabolic and Regulatory Functions of Peroxisomes

(2009) S. Reumann et al.   PLANT PHYSIOLOGY

Large-Scale Arabidopsis Phosphoproteome Profiling Reveals Novel Chloroplast Kinase Substrates and Phosphorylation Networks

(2009) S. Reiland et al.   PLANT PHYSIOLOGY

Gene Expression Analysis, Proteomics, and Network Discovery

(2009) S. Baginsky et al.   PLANT PHYSIOLOGY

Comparative Functional Analysis of the Caenorhabditis elegans and Drosophila melanogaster Proteomes

(2009) Sabine P Schrimpf et al.   PLOS BIOLOGY

Phosphorylation-Specific MS/MS Scoring for Rapid and Accurate Phosphoproteome Analysis

(2008) Samuel H. Payne et al.   JOURNAL OF PROTEOME RESEARCH

Selected reaction monitoring for quantitative proteomics: a tutorial

(2008) Vinzenz Lange et al.   Molecular Systems Biology

Comprehensive mass-spectrometry-based proteome quantification of haploid versus diploid yeast

(2008) Lyris M. F. de Godoy et al.   NATURE

PPDB, the Plant Proteomics Database at Cornell

(2008) Qi Sun et al.   NUCLEIC ACIDS RESEARCH

Annotating Genes of Known and Unknown Function by Large-Scale Coexpression Analysis

(2008) K. Horan et al.   PLANT PHYSIOLOGY

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

Genome-Scale Proteomics Reveals Arabidopsis thaliana Gene Models and Proteome Dynamics

(2008) K. Baerenfaller et al.   SCIENCE