| # | Title | Journal | Year | Citations |
|---|
| 1 | Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition) | Autophagy | 2016 | 4,701 |
| 2 | Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis | Molecular and Cellular Proteomics | 2012 | 2,285 |
| 3 | On the Dependency of Cellular Protein Levels on mRNA Abundance | Cell | 2016 | 2,216 |
| 4 | Mass Spectrometry and Protein Analysis | Science | 2006 | 1,787 |
| 5 | Checkpoint blockade cancer immunotherapy targets tumour-specific mutant antigens | Nature | 2014 | 1,705 |
| 6 | Mass-spectrometric exploration of proteome structure and function | Nature | 2016 | 1,573 |
| 7 | The CRAPome: a contaminant repository for affinity purification–mass spectrometry data | Nature Methods | 2013 | 1,353 |
| 8 | Selected reaction monitoring for quantitative proteomics: a tutorial | Molecular Systems Biology | 2008 | 1,215 |
| 9 | Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions | Nature Methods | 2012 | 1,177 |
| 10 | Protter: interactive protein feature visualization and integration with experimental proteomic data | Bioinformatics | 2014 | 1,090 |
| 11 | L-Arginine Modulates T Cell Metabolism and Enhances Survival and Anti-tumor Activity | Cell | 2016 | 1,077 |
| 12 | Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues | Molecular and Cellular Proteomics | 2015 | 873 |
| 13 | Mechanisms and optimization of in vivo delivery of lipophilic siRNAs | Nature Biotechnology | 2007 | 854 |
| 14 | Full Dynamic Range Proteome Analysis of S. cerevisiae by Targeted Proteomics | Cell | 2009 | 733 |
| 15 | miR-375 maintains normal pancreatic α- and β-cell mass | Proceedings of the National Academy of Sciences of the United States of America | 2009 | 710 |
| 16 | Modulation of Myelopoiesis Progenitors Is an Integral Component of Trained Immunity | Cell | 2018 | 702 |
| 17 | Data‐independent acquisition‐based SWATH ‐ MS for quantitative proteomics: a tutorial | Molecular Systems Biology | 2018 | 701 |
| 18 | OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data | Nature Biotechnology | 2014 | 692 |
| 19 | The quantitative and condition-dependent Escherichia coli proteome | Nature Biotechnology | 2016 | 655 |
| 20 | Computational prediction of proteotypic peptides for quantitative proteomics | Nature Biotechnology | 2007 | 653 |
| 21 | Systematic evaluation of objective functions for predicting intracellular fluxes in Escherichia coli | Molecular Systems Biology | 2007 | 623 |
| 22 | Multi-omics analysis identifies ATF4 as a key regulator of the mitochondrial stress response in mammals | Journal of Cell Biology | 2017 | 590 |
| 23 | Metabolic networks in motion: 13 C‐based flux analysis | Molecular Systems Biology | 2006 | 582 |
| 24 | Options and considerations when selecting a quantitative proteomics strategy | Nature Biotechnology | 2010 | 581 |
| 25 | Orm family proteins mediate sphingolipid homeostasis | Nature | 2010 | 544 |
| 26 | OpenMS: a flexible open-source software platform for mass spectrometry data analysis | Nature Methods | 2016 | 537 |
| 27 | 13C-based metabolic flux analysis | Nature Protocols | 2009 | 520 |
| 28 | Using iRT, a normalized retention time for more targeted measurement of peptides | Proteomics | 2012 | 517 |
| 29 | A roadmap for interpreting 13 C metabolite labeling patterns from cells | Current Opinion in Biotechnology | 2015 | 513 |
| 30 | Explosive cell lysis as a mechanism for the biogenesis of bacterial membrane vesicles and biofilms | Nature Communications | 2016 | 487 |
| 31 | Discovery and Characterization of Gut Microbiota Decarboxylases that Can Produce the Neurotransmitter Tryptamine | Cell Host and Microbe | 2014 | 473 |
| 32 | Metabolic control of adult neural stem cell activity by Fasn-dependent lipogenesis | Nature | 2013 | 448 |
| 33 | An Assessment of Software Solutions for the Analysis of Mass Spectrometry Based Quantitative Proteomics Data | Journal of Proteome Research | 2008 | 423 |
| 34 | Multi-laboratory assessment of reproducibility, qualitative and quantitative performance of SWATH-mass spectrometry | Nature Communications | 2017 | 423 |
| 35 | Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans | Nature | 2009 | 402 |
| 36 | diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition | Nature Methods | 2020 | 387 |
| 37 | Mass Spectrometry–Based Proteomics and Network Biology | Annual Review of Biochemistry | 2012 | 382 |
| 38 | A repository of assays to quantify 10,000 human proteins by SWATH-MS | Scientific Data | 2014 | 370 |
| 39 | Multidimensional Optimality of Microbial Metabolism | Science | 2012 | 360 |
| 40 | Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry | Science | 2012 | 357 |
| 41 | A Mass Spectrometric-Derived Cell Surface Protein Atlas | PLoS ONE | 2015 | 356 |
| 42 | A Map of Protein-Metabolite Interactions Reveals Principles of Chemical Communication | Cell | 2018 | 350 |
| 43 | The complete structure of the 55 S mammalian mitochondrial ribosome | Science | 2015 | 344 |
| 44 | Crosslinking and Mass Spectrometry: An Integrated Technology to Understand the Structure and Function of Molecular Machines | Trends in Biochemical Sciences | 2016 | 330 |
| 45 | High-Throughput, Accurate Mass Metabolome Profiling of Cellular Extracts by Flow Injection–Time-of-Flight Mass Spectrometry | Analytical Chemistry | 2011 | 324 |
| 46 | Targeted proteomic strategy for clinical biomarker discovery | Molecular Oncology | 2009 | 321 |
| 47 | Crucial HSP70 co-chaperone complex unlocks metazoan protein disaggregation | Nature | 2015 | 320 |
| 48 | Building high-quality assay libraries for targeted analysis of SWATH MS data | Nature Protocols | 2015 | 319 |
| 49 | Ultrahigh Performance Liquid Chromatography−Tandem Mass Spectrometry Method for Fast and Robust Quantification of Anionic and Aromatic Metabolites | Analytical Chemistry | 2010 | 317 |
| 50 | Cell-wide analysis of protein thermal unfolding reveals determinants of thermostability | Science | 2017 | 313 |
