Bioinformatic analysis of proteomics data

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

(2013) Paola Picotti et al.   NATURE

Consecutive Proteolytic Digestion in an Enzyme Reactor Increases Depth of Proteomic and Phosphoproteomic Analysis

(2012) Jacek R. Wiśniewski et al.   ANALYTICAL CHEMISTRY

EnrichNet: network-based gene set enrichment analysis

(2012) Enrico Glaab et al.   BIOINFORMATICS

Current algorithmic solutions for peptide-based proteomics data generation and identification

(2012) Michael R Hoopmann et al.   CURRENT OPINION IN BIOTECHNOLOGY

Trends in ultrasensitive proteomics

(2012) AF Maarten Altelaar et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Characterization of the insertase for β-barrel proteins of the outer mitochondrial membrane

(2012) Astrid Klein et al.   JOURNAL OF CELL BIOLOGY

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

(2012) Paola Picotti et al.   NATURE METHODS

Improvements in the protein identifier cross-reference service

(2012) Samuel P. Wein et al.   NUCLEIC ACIDS RESEARCH

STRING v9.1: protein-protein interaction networks, with increased coverage and integration

(2012) Andrea Franceschini et al.   NUCLEIC ACIDS RESEARCH

Global Identification of Modular Cullin-RING Ligase Substrates

(2011) Michael J. Emanuele et al.   CELL

Absolute quantification of protein and post-translational modification abundance with stable isotope–labeled synthetic peptides

(2011) Arminja N Kettenbach et al.   Nature Protocols

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

The IntAct molecular interaction database in 2012

(2011) S. Kerrien et al.   NUCLEIC ACIDS RESEARCH

SMART 7: recent updates to the protein domain annotation resource

(2011) I. Letunic et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

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

Reactome: a database of reactions, pathways and biological processes

(2010) D. Croft et al.   NUCLEIC ACIDS RESEARCH

From proteome lists to biological impact- tools and strategies for the analysis of large MS data sets

(2010) Rainer Malik et al.   PROTEOMICS

Subcellular fractionation methods and strategies for proteomics

(2010) Yie Hou Lee et al.   PROTEOMICS

NetPath: a public resource of curated signal transduction pathways

(2010) Kumaran Kandasamy et al.   GENOME BIOLOGY

SciMiner: web-based literature mining tool for target identification and functional enrichment analysis

(2009) Junguk Hur et al.   BIOINFORMATICS

Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics

(2009) Paola Picotti et al.   CELL

Bioinformatics analysis of mass spectrometry-based proteomics data sets

(2009) Chanchal Kumar et al.   FEBS LETTERS

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Proteomics data repositories

(2009) Michael Riffle et al.   PROTEOMICS

CRONOS: the cross-reference navigation server

(2008) Brigitte Waegele et al.   BIOINFORMATICS

Use and misuse of the gene ontology annotations

(2008) Seung Yon Rhee et al.   NATURE REVIEWS GENETICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH