QuaNCAT: quantitating proteome dynamics in primary cells

Selective enrichment of newly synthesized proteins for quantitative secretome analysis

(2012) Katrin Eichelbaum et al.   NATURE BIOTECHNOLOGY

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

(2011) Jürgen Cox et al.   JOURNAL OF PROTEOME RESEARCH

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

Use of stable isotope labeling by amino acids in cell culture as a spike-in standard in quantitative proteomics

(2011) Tamar Geiger et al.   Nature Protocols

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

Comparative Analysis of Proteome and Transcriptome Variation in Mouse

(2011) Anatole Ghazalpour et al.   PLoS Genetics

Cleavable Biotin Probes for Labeling of Biomolecules via Azide−Alkyne Cycloaddition

(2010) Janek Szychowski et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Methods for combining peptide intensities to estimate relative protein abundance

(2009) Brian Carrillo et al.   BIOINFORMATICS

Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models

(2008) Simon Rogers et al.   BIOINFORMATICS

MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification

(2008) Jürgen Cox et al.   NATURE BIOTECHNOLOGY

Global analysis of cellular protein translation by pulsed SILAC

(2008) Björn Schwanhäusser et al.   PROTEOMICS