| # | Title | Journal | Year | Citations |
|---|
| 1 | Mass spectrometry-based proteomics | Nature | 2003 | 6,282 |
| 2 | Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) | Autophagy | 2016 | 4,701 |
| 3 | Global, In Vivo, and Site-Specific Phosphorylation Dynamics in Signaling Networks | Cell | 2006 | 3,201 |
| 4 | Stop and Go Extraction Tips for Matrix-Assisted Laser Desorption/Ionization, Nanoelectrospray, and LC/MS Sample Pretreatment in Proteomics | Analytical Chemistry | 2003 | 2,337 |
| 5 | Proteomic analysis of post-translational modifications | Nature Biotechnology | 2003 | 1,809 |
| 6 | Parts per Million Mass Accuracy on an Orbitrap Mass Spectrometer via Lock Mass Injection into a C-trap | Molecular and Cellular Proteomics | 2005 | 1,395 |
| 7 | Highly Selective Enrichment of Phosphorylated Peptides from Peptide Mixtures Using Titanium Dioxide Microcolumns | Molecular and Cellular Proteomics | 2005 | 1,356 |
| 8 | Proteomic characterization of the human centrosome by protein correlation profiling | Nature | 2003 | 1,204 |
| 9 | Mammalian Sir2 Homolog SIRT3 Regulates Global Mitochondrial Lysine Acetylation | Molecular and Cellular Biology | 2007 | 1,097 |
| 10 | Analysis of Proteins and Proteomes by Mass Spectrometry | Annual Review of Biochemistry | 2001 | 1,044 |
| 11 | Methylation of tRNAAsp by the DNA Methyltransferase Homolog Dnmt2 | Science | 2006 | 967 |
| 12 | Directed Proteomic Analysis of the Human Nucleolus | Current Biology | 2002 | 962 |
| 13 | Trypsin Cleaves Exclusively C-terminal to Arginine and Lysine Residues | Molecular and Cellular Proteomics | 2004 | 957 |
| 14 | Prokaryotic toxin–antitoxin stress response loci | Nature Reviews Microbiology | 2005 | 950 |
| 15 | The abc's (and xyz's) of peptide sequencing | Nature Reviews Molecular Cell Biology | 2004 | 948 |
| 16 | From genomics to proteomics | Nature | 2003 | 886 |
| 17 | Specificity in Toll-like receptor signalling through distinct effector functions of TRAF3 and TRAF6 | Nature | 2006 | 836 |
| 18 | The diploid genome sequence of an Asian individual | Nature | 2008 | 834 |
| 19 | Large-Scale Proteomic Analysis of the Human Spliceosome | Genome Research | 2002 | 808 |
| 20 | Unbiased quantitative proteomics of lipid rafts reveals high specificity for signaling factors | Proceedings of the National Academy of Sciences of the United States of America | 2003 | 783 |
| 21 | Quantitative Phosphoproteomics Applied to the Yeast Pheromone Signaling Pathway | Molecular and Cellular Proteomics | 2005 | 708 |
| 22 | A proteomics strategy to elucidate functional protein-protein interactions applied to EGF signaling | Nature Biotechnology | 2003 | 702 |
| 23 | Temporal analysis of phosphotyrosine-dependent signaling networks by quantitative proteomics | Nature Biotechnology | 2004 | 680 |
| 24 | LNA (Locked Nucleic Acid): High-Affinity Targeting of Complementary RNA and DNA† | Biochemistry | 2004 | 644 |
| 25 | Reversible lysine acetylation controls the activity of the mitochondrial enzyme acetyl-CoA synthetase 2 | Proceedings of the National Academy of Sciences of the United States of America | 2006 | 642 |
| 26 | The emergence of cold-induced brown adipocytes in mouse white fat depots is determined predominantly by white to brown adipocyte transdifferentiation | American Journal of Physiology - Endocrinology and Metabolism | 2010 | 614 |
| 27 | The Cfr rRNA Methyltransferase Confers Resistance to Phenicols, Lincosamides, Oxazolidinones, Pleuromutilins, and Streptogramin A Antibiotics | Antimicrobial Agents and Chemotherapy | 2006 | 613 |
| 28 | Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry | Nature | 2002 | 596 |
| 29 | Protein Composition of Catalytically Active Human Telomerase from Immortal Cells | Science | 2007 | 595 |
| 30 | How many human proteoforms are there? | Nature Chemical Biology | 2018 | 580 |
| 31 | Highly selective enrichment of phosphorylated peptides using titanium dioxide | Nature Protocols | 2006 | 565 |
| 32 | Orm family proteins mediate sphingolipid homeostasis | Nature | 2010 | 544 |
| 33 | A Mammalian Organelle Map by Protein Correlation Profiling | Cell | 2006 | 538 |
| 34 | Mechanism of Divergent Growth Factor Effects in Mesenchymal Stem Cell Differentiation | Science | 2005 | 531 |
| 35 | Large-scale Analysis of in Vivo Phosphorylated Membrane Proteins by Immobilized Metal Ion Affinity Chromatography and Mass Spectrometry | Molecular and Cellular Proteomics | 2003 | 523 |
| 36 | The Bacterial Toxin RelE Displays Codon-Specific Cleavage of mRNAs in the Ribosomal A Site | Cell | 2003 | 500 |
| 37 | The bacterial ribosome as a target for antibiotics | Nature Reviews Microbiology | 2005 | 486 |
| 38 | Genome-wide profiling of PPARγ:RXR and RNA polymerase II occupancy reveals temporal activation of distinct metabolic pathways and changes in RXR dimer composition during adipogenesis | Genes and Development | 2008 | 475 |
| 39 | PPARγ and the global map of adipogenesis and beyond | Trends in Endocrinology and Metabolism | 2014 | 469 |
| 40 | Phosphotyrosine interactome of the ErbB‐receptor kinase family | Molecular Systems Biology | 2005 | 468 |
| 41 | Paraspeckles | Current Biology | 2002 | 455 |
| 42 | Matrix Protein 2 of Influenza A Virus Blocks Autophagosome Fusion with Lysosomes | Cell Host and Microbe | 2009 | 454 |
| 43 | A New Strategy for Identification of N-Glycosylated Proteins and Unambiguous Assignment of Their Glycosylation Sites Using HILIC Enrichment and Partial Deglycosylation | Journal of Proteome Research | 2004 | 452 |
| 44 | Recommendations for performing, interpreting and reporting hydrogen deuterium exchange mass spectrometry (HDX-MS) experiments | Nature Methods | 2019 | 452 |
| 45 | Bacterial persistence by RNA endonucleases | Proceedings of the National Academy of Sciences of the United States of America | 2011 | 450 |
| 46 | Interpreting the protein language using proteomics | Nature Reviews Molecular Cell Biology | 2006 | 448 |
| 47 | The bacterial Sm-like protein Hfq: a key player in RNA transactions | Molecular Microbiology | 2004 | 444 |
| 48 | Phosphoproteomics of the Arabidopsis Plasma Membrane and a New Phosphorylation Site Database[W] | Plant Cell | 2004 | 443 |
| 49 | Properties of13C-Substituted Arginine in Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC) | Journal of Proteome Research | 2003 | 439 |
| 50 | Spermidine and resveratrol induce autophagy by distinct pathways converging on the acetylproteome | Journal of Cell Biology | 2011 | 439 |
