Minimal, encapsulated proteomic-sample processing applied to copy-number estimation in eukaryotic cells

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

Cox, J., & Mann, M. (2008) · Nature Biotechnology · doi:10.1038/nbt.1511 · Cited by 14,855 · see citing works

Mass spectrometric sequencing of proteins silver-stained polyacrylamide gels.

Shevchenko, A., Wilm, M., Vorm, O., & Mann, M. F. (1996) · Analytical Chemistry · doi:10.1021/ac950914h · Cited by 9,047 · see citing works

Universal sample preparation method for proteome analysis

Wiśniewski, J. R., Zougman, A., Nagaraj, N., & Mann, M. (2009) · Nature Methods · doi:10.1038/nmeth.1322 · Cited by 8,352 · see citing works

Global quantification of mammalian gene expression control

Schwanhäusser, B., Busse, D., Li, N., Dittmar, G., Schuchhardt, J., Wolf, J., Chen, W., & Selbach, M. (2011) · Nature · doi:10.1038/nature10098 · Cited by 6,566 · see citing works

Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics

Ong, S.-E., Blagoev, B., Kratchmarova, I., Kristensen, D. B., Steen, H., Pandey, A., & Mann, M. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200025-mcp200 · Cited by 5,574 · see citing works

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., & Mann, M. (2011) · Journal of Proteome Research · doi:10.1021/pr101065j · Cited by 5,350 · see citing works

Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips

Rappsilber, J., Mann, M., & Ishihama, Y. (2007) · Nature Protocols · doi:10.1038/nprot.2007.261 · Cited by 4,641 · see citing works

Global analysis of protein expression in yeast

Ghaemmaghami, S., Huh, W.-K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., & Weissman, J. S. (2003) · Nature · doi:10.1038/nature02046 · Cited by 3,750 · see citing works

Lysosomal turnover, but not a cellular level, of endogenous LC3 is a marker for autophagy

Tanida, I., Minematsu-Ikeguchi, N., Ueno, T., & Kominami, E. (2005) · Autophagy · doi:10.4161/auto.1.2.1697 · Cited by 1,108 · see citing works

Deep proteome and transcriptome mapping of a human cancer cell line

Nagaraj, N., Wisniewski, J. R., Geiger, T., Cox, J., Kircher, M., Kelso, J., Pääbo, S., & Mann, M. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.81 · Cited by 979 · see citing works

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

de Godoy, L. M. F., Olsen, J. V., Cox, J., Nielsen, M. L., Hubner, N. C., Fröhlich, F., Walther, T. C., & Mann, M. (2008) · Nature · doi:10.1038/nature07341 · Cited by 873 · see citing works

Mass spectrometry-based proteomics using Q Exactive, a high-performance benchtop quadrupole Orbitrap mass spectrometer

Michalski, A., Damoc, E., Hauschild, J.-P., Lange, O., Wieghaus, A., Makarov, A., Nagaraj, N., Cox, J., Mann, M., & Horning, S. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.011015 · Cited by 832 · see citing works

The quantitative proteome of a human cell line

Beck, M., Schmidt, A., Malmstroem, J., Claassen, M., Ori, A., Szymborska, A., Herzog, F., Rinner, O., Ellenberg, J., & Aebersold, R. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.82 · Cited by 816 · see citing works

Comprehensive comparative analysis of strand-specific RNA sequencing methods

Levin, J. Z., Yassour, M., Adiconis, X., Nusbaum, C., Thompson, D. A., Friedman, N., Gnirke, A., & Regev, A. (2010) · Nature Methods · doi:10.1038/nmeth.1491 · Cited by 753 · see citing works

Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics

Picotti, P., Bodenmiller, B., Mueller, L. N., Domon, B., & Aebersold, R. (2009) · Cell · doi:10.1016/j.cell.2009.05.051 · Cited by 744 · see citing works

Phase Transfer Surfactant-Aided Trypsin Digestion for Membrane Proteome Analysis

Masuda, T., Tomita, M., & Ishihama, Y. (2008) · Journal of Proteome Research · doi:10.1021/pr700658q · Cited by 655 · see citing works

1D and 2D annotation enrichment: a statistical method integrating quantitative proteomics with complementary high-throughput data

Cox, J., & Mann, M. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-s16-s12 · Cited by 614 · see citing works

Eukaryotic MCM Proteins: Beyond Replication Initiation

Forsburg, S. L. (2004) · Microbiology and Molecular Biology Reviews · doi:10.1128/mmbr.68.1.109-131.2004 · Cited by 600 · see citing works

Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells

Marguerat, S., Schmidt, A., Codlin, S., Chen, W., Aebersold, R., & Bähler, J. (2012) · Cell · doi:10.1016/j.cell.2012.09.019 · Cited by 571 · see citing works

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

Powell, S. T., Szklarczyk, D., Trachana, K., Roth, A. C., Kuhn, M., Muller, J., Arnold, R. R., Rattei, T., Letunić, I., Doerks, T., et al. (2011) · Nucleic Acids Research · doi:10.1093/nar/gkr1060 · Cited by 564 · see citing works

Mre11–Rad50–Nbs1 is a keystone complex connecting DNA repair machinery, double-strand break signaling, and the chromatin templateThis paper is one of a selection of papers published in this Special Issue, entitled 28th International West Coast Chromatin and Chromosome Conference, and has undergone the Journal's usual peer review process.

Williams, R. S., Williams, J. S., & Tainer, J. A. (2007) · Biochemistry and Cell Biology · doi:10.1139/o07-069 · Cited by 399 · see citing works

System-wide perturbation analysis with nearly complete coverage of the yeast proteome by single-shot ultra HPLC runs on a bench top Orbitrap

Nagaraj, N., Alexander Kulak, N., Cox, J., Neuhauser, N., Mayr, K., Hoerning, O., Vorm, O., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.013722 · Cited by 392 · see citing works

Sample preparation and digestion for proteomic analyses using spin filters

Manza, L. L., Stamer, S. L., Ham, A. L., Codreanu, S. G., & Liebler, D. C. (2005) · PROTEOMICS · doi:10.1002/pmic.200401063 · Cited by 383 · see citing works

Deep and Highly Sensitive Proteome Coverage by LC-MS/MS Without Prefractionation

Thakur, S. S., Geiger, T., Chatterjee, B., Bandilla, P., Fröhlich, F., Cox, J., & Mann, M. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.003699 · Cited by 335 · see citing works

Quantitative Assessment of In-solution Digestion Efficiency Identifies Optimal Protocols for Unbiased Protein Analysis

León, I. R., Schwämmle, V., Jensen, O. N., & Sprenger, R. R. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.025585 · Cited by 258 · see citing works

Extensive quantitative remodeling of the proteome between normal colon tissue and adenocarcinoma

Wiśniewski, J. R., Ostasiewicz, P., Duś, K., Zielińska, D. F., Gnad, F., & Mann, M. (2012) · Molecular Systems Biology · doi:10.1038/msb.2012.44 · Cited by 248 · see citing works

OriDB: a DNA replication origin database

Nieduszynski, C. A., Hiraga, S., Ak, P., Benham, C. J., & Donaldson, A. D. (2006) · Nucleic Acids Research · doi:10.1093/nar/gkl758 · Cited by 168 · see citing works

A Protein Epitope Signature Tag (PrEST) Library Allows SILAC-based Absolute Quantification and Multiplexed Determination of Protein Copy Numbers in Cell Lines

Zeiler, M., Straube, W. L., Lundberg, E., Uhlen, M., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.009613 · Cited by 168 · see citing works

Analysis of High Accuracy, Quantitative Proteomics Data in the MaxQB Database

Schaab, C., Geiger, T., Stoehr, G., Cox, J., & Mann, M. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.014068 · Cited by 164 · see citing works

Ultra-High-Pressure RPLC Hyphenated to an LTQ-Orbitrap Velos Reveals a Linear Relation between Peak Capacity and Number of Identified Peptides

Köcher, T., Swart, R., & Mechtler, K. (2011) · Analytical Chemistry · doi:10.1021/ac103243t · Cited by 140 · see citing works

Trends in ultrasensitive proteomics

Altelaar, M. A. F., & Heck, A. J. R. (2012) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2011.12.011 · Cited by 139 · see citing works

PP2A impaired activity is a common event in acute myeloid leukemia and its activation by forskolin has a potent anti-leukemic effect

Cristóbal, I., García-Ortí, L., Cirauqui, C., Alonso, M. M., Calasanz, M. J., & Odero, M. D. (2011) · Leukemia · doi:10.1038/leu.2010.294 · Cited by 138 · see citing works

A novel role for MAP1 LC3 in nonautophagic cytoplasmic vacuolation death of cancer cells

Kar, R., Singha, P., Venkatachalam, M. A., & Saikumar, P. (2009) · Oncogene · doi:10.1038/onc.2009.118 · Cited by 134 · see citing works

Protease bias in absolute protein quantitation

Peng, M., Taouatas, N., Cappadona, S., van Breukelen, B., Mohammed, S., Scholten, A., & Heck, A. J. R. (2012) · Nature Methods · doi:10.1038/nmeth.2031 · Cited by 90 · see citing works

The Proteomic Reactor: A Microfluidic Device for Processing Minute Amounts of Protein Prior to Mass Spectrometry Analysis

Ethier, M., Hou, W., Duewel, H. S., & Figeys, D. (2006) · Journal of Proteome Research · doi:10.1021/pr060312m · Cited by 86 · see citing works

Detergent-Based but Gel-Free Method Allows Identification of Several Hundred Membrane Proteins in Single LC-MS Runs

Nagaraj, N., Lu, A., Mann, M., & Wiśniewski, J. R. (2008) · Journal of Proteome Research · doi:10.1021/pr800412j · Cited by 83 · see citing works

Comparisons of Mass Spectrometry Compatible Surfactants for Global Analysis of the Mammalian Brain Proteome

Chen, E. I., McClatchy, D. B., Park, S. K., & Yates, J. (2008) · Analytical Chemistry · doi:10.1021/ac800606w · Cited by 78 · see citing works

SprayQc: A Real-Time LC–MS/MS Quality Monitoring System To Maximize Uptime Using Off the Shelf Components

Scheltema, R. A., & Mann, M. (2012) · Journal of Proteome Research · doi:10.1021/pr201219e · Cited by 63 · see citing works

Rapid and Deep Profiling of Human Induced Pluripotent Stem Cell Proteome by One-shot NanoLC–MS/MS Analysis with Meter-scale Monolithic Silica Columns

Yamana, R., Iwasaki, M., Wakabayashi, M., Nakagawa, M., Yamanaka, S., & Ishihama, Y. (2012) · Journal of Proteome Research · doi:10.1021/pr300837u · Cited by 58 · see citing works

Using Guanidine-Hydrochloride for Fast and Efficient Protein Digestion and Single-step Affinity-purification Mass Spectrometry

Poulsen, J. W., Madsen, C. T., Young, C., Poulsen, F. M., & Nielsen, M. L. (2012) · Journal of Proteome Research · doi:10.1021/pr300883y · Cited by 51 · see citing works

Proteomic reactors and their applications in biology

Zhou, H., Ning, Z., Wang, F., Seebun, D., & Figeys, D. (2011) · The FEBS Journal · doi:10.1111/j.1742-4658.2011.08292.x · Cited by 34 · see citing works

Extensive Mass Spectrometry-based Analysis of the Fission Yeast Proteome

Gunaratne, J., Schmidt, A., Quandt, A., Neo, S. P., Saraç, Ö. S., Gracia, T., Loguercio, S., Ahrné, E., Xia, R. L. H., Tan, K. H., et al. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.023754 · Cited by 29 · see citing works

On the Dependency of Cellular Protein Levels on mRNA Abundance

Liu, Y., Beyer, A., & Aebersold, R. (2016) · Cell · doi:10.1016/j.cell.2016.03.014 · Cited by 3,221 · see citing works

Mass-spectrometric exploration of proteome structure and function

Aebersold, R., & Mann, M. (2016) · Nature · doi:10.1038/nature19949 · Cited by 2,334 · see citing works

Single-pot, solid-phase-enhanced sample preparation for proteomics experiments

Hughes, C. S., Moggridge, S., Müller, T., Sorensen, P. H. B., Morin, G. B., & Krijgsveld, J. (2018) · Nature Protocols · doi:10.1038/s41596-018-0082-x · Cited by 1,938 · see citing works

A Human Interactome in Three Quantitative Dimensions Organized by Stoichiometries and Abundances

Hein, M. Y., Hubner, N. C., Poser, I., Cox, J., Nagaraj, N., Toyoda, Y., Gak, I. A., Weisswange, I., Mansfeld, J., Buchholz, F., et al. (2015) · Cell · doi:10.1016/j.cell.2015.09.053 · Cited by 1,270 · see citing works

Ultrasensitive proteome analysis using paramagnetic bead technology

Hughes, C. S., Föehr, S., Garfield, D. A., Furlong, E. E. M., Steinmetz, L. M., & Krijgsveld, J. (2014) · Molecular Systems Biology · doi:10.15252/msb.20145625 · Cited by 1,194 · see citing works

Tracking cancer drugs in living cells by thermal profiling of the proteome

Savitski, M. M., Reinhard, F. B. M., Franken, H., Werner, T., Savitski, M. F., Eberhard, D., Molina, D. M., Jafari, R., Dovega, R. B., Klaeger, S., et al. (2014) · Science · doi:10.1126/science.1255784 · Cited by 1,187 · see citing works

Circular non-coding RNA ANRIL modulates ribosomal RNA maturation and atherosclerosis in humans

Holdt, L. M., Stahringer, A., Sass, K., Pichler, G., Kulak, N. A., Wilfert, W., Kohlmaier, A., Herbst, A., Northoff, B. H., Nicolaou, A., et al. (2016) · Nature Communications · doi:10.1038/ncomms12429 · Cited by 1,097 · see citing works

Mitochondrial proteins: from biogenesis to functional networks

Pfanner, N., Warscheid, B., & Wiedemann, N. (2019) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0092-0 · Cited by 1,028 · see citing works

Online Parallel Accumulation–Serial Fragmentation (PASEF) with a Novel Trapped Ion Mobility Mass Spectrometer

Meier, F., Brunner, A., Koch, S., Koch, H., Lubeck, M., Krause, M., Goedecke, N., Decker, J., Kosinski, T., Park, M. A., et al. (2018) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir118.000900 · Cited by 946 · see citing works

The Mediator complex: a central integrator of transcription

Allen, B. L., & Taatjes, D. J. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3951 · Cited by 922 · see citing works

diaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition

Meier, F., Brunner, A., Frank, M., Ha, A., Bludau, I., Voytik, E., Kaspar‐Schoenefeld, S., Lubeck, M., Raether, O., Bache, N., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-00998-0 · Cited by 902 · see citing works

SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation

Budnik, B., Levy, E., Harmange, G., & Slavov, N. (2018) · Genome Biology · doi:10.1186/s13059-018-1547-5 · Cited by 832 · see citing works

Plasma Proteome Profiling to Assess Human Health and Disease

Geyer, P. E., Kulak, N. A., Pichler, G., Holdt, L. M., Teupser, D., & Mann, M. (2016) · Cell Systems · doi:10.1016/j.cels.2016.02.015 · Cited by 734 · see citing works

An atlas of the aging lung mapped by single cell transcriptomics and deep tissue proteomics

Angelidis, I., Simon, L. M., Fernandez, I. E., Strunz, M., Mayr, C. H., Greiffo, F. R., Tsitsiridis, G., Ansari, M., Graf, E., Strom, T.-M., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-08831-9 · Cited by 637 · see citing works

Multilevel proteomics reveals host perturbations by SARS-CoV-2 and SARS-CoV

Stukalov, A., Girault, V., Grass, V., Karayel, Ö., Bergant, V., Urban, C., Haas, D. A., Huang, Y., Oubraham, L., Wang, A., et al. (2021) · Nature · doi:10.1038/s41586-021-03493-4 · Cited by 686 · see citing works

Pervasive functional translation of noncanonical human open reading frames

Chen, J., Brunner, A., Cogan, J. Z., Nuñez, J. K., Fields, A. P., Adamson, B., Itzhak, D. N., Li, J. Y., Mann, M., Leonetti, M. D., et al. (2020) · Science · doi:10.1126/science.aay0262 · Cited by 654 · see citing works

Global, quantitative and dynamic mapping of protein subcellular localization

Itzhak, D. N., Tyanova, S., Cox, J., & Borner, G. H. H. (2016) · eLife · doi:10.7554/elife.16950 · Cited by 595 · see citing works

Accessory subunits are integral for assembly and function of human mitochondrial complex I

Stroud, D. A., Surgenor, E. E., Formosa, L. E., Reljić, B., Frazier, A. E., Dibley, M. G., Osellame, L. D., Stait, T. L., Beilharz, T. H., Thorburn, D. R., et al. (2016) · Nature · doi:10.1038/nature19754 · Cited by 605 · see citing works

Genetic diagnosis of Mendelian disorders via RNA sequencing

Kremer, L. S., Bader, D. M., Mertes, C., Kopajtich, R., Pichler, G., Iuso, A., Haack, T. B., Graf, E., Schwarzmayr, T., Terrile, C., et al. (2017) · Nature Communications · doi:10.1038/ncomms15824 · Cited by 590 · see citing works

Protein Phosphorylation: A Major Switch Mechanism for Metabolic Regulation

Humphrey, S. J., James, D. E., & Mann, M. (2015) · Trends in Endocrinology and Metabolism · doi:10.1016/j.tem.2015.09.013 · Cited by 554 · see citing works

Ribosome collisions trigger general stress responses to regulate cell fate

Wu, C. C.-C., Peterson, A. F., Zinshteyn, B., Regot, S., & Green, R. (2020) · Cell · doi:10.1016/j.cell.2020.06.006 · Cited by 503 · see citing works

Technical challenges of working with extracellular vesicles

Ramirez, M. I., de Amorim, M. G., Gadelha, C., Milic, I., Welsh, J. A., Freitas, V. M., Nawaz, M., Akbar, N., Couch, Y., Makin, L., et al. (2017) · Nanoscale · doi:10.1039/c7nr08360b · Cited by 518 · see citing works

Unification of Protein Abundance Datasets Yields a Quantitative Saccharomyces cerevisiae Proteome

Ho, B., Baryshnikova, A., & Brown, G. W. (2018) · Cell Systems · doi:10.1016/j.cels.2017.12.004 · Cited by 482 · see citing works

eIF5A Functions Globally in Translation Elongation and Termination

Schuller, A. P., Wu, C. C., Dever, T. E., Buskirk, A. R., & Green, R. (2017) · Molecular Cell · doi:10.1016/j.molcel.2017.03.003 · Cited by 479 · see citing works

Definition of a High-Confidence Mitochondrial Proteome at Quantitative Scale

Morgenstern, M., Stiller, S. B., Lübbert, P., Peikert, C. D., Dannenmaier, S., Drepper, F., Weill, U., Höß, P., Feuerstein, R., Gebert, M., et al. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.06.014 · Cited by 451 · see citing works

Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry

Liu, F., Rijkers, D. T. S., Post, H., & Heck, A. J. R. (2015) · Nature Methods · doi:10.1038/nmeth.3603 · Cited by 470 · see citing works

Systematic proteomic analysis of LRRK2-mediated Rab GTPase phosphorylation establishes a connection to ciliogenesis

Steger, M., Diez, F., Dhekne, H. S., Lis, P., Nirujogi, R. S., Karayel, Ö., Tonelli, F., Martinez, T. N., Lorentzen, E., Pfeffer, S. R., et al. (2017) · eLife · doi:10.7554/elife.31012 · Cited by 465 · see citing works

A Quantitative Proteome Map of the Human Body

Jiang, L., Wang, M., Lin, S., Jian, R., Li, X., Chan, J., Dong, G., Fang, H., Robinson, A. E., Aguet, F., et al. (2020) · Cell · doi:10.1016/j.cell.2020.08.036 · Cited by 458 · see citing works

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

Savitski, M. M., Wilhelm, M., Hahne, H., Küster, B., & Bantscheff, M. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.046995 · Cited by 436 · see citing works

Systematic humanization of yeast genes reveals conserved functions and genetic modularity

Kachroo, A. H., Laurent, J. M., Yellman, C. M., Meyer, A. G., Wilke, C. O., & Marcotte, E. M. (2015) · Science · doi:10.1126/science.aaa0769 · Cited by 423 · see citing works

Physiology, ecology and industrial applications of aroma formation in yeast

Dzialo, M. C., Park, R., Steensels, J., Lievens, B., & Verstrepen, K. J. (2017) · FEMS Microbiology Reviews · doi:10.1093/femsre/fux031 · Cited by 434 · see citing works

Mass Spectrometry of Human Leukocyte Antigen Class I Peptidomes Reveals Strong Effects of Protein Abundance and Turnover on Antigen Presentation

Bassani‐Sternberg, M., Pletscher-Frankild, S., Jensen, L. J., & Mann, M. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.042812 · Cited by 428 · see citing works

A Novel LC System Embeds Analytes in Pre-formed Gradients for Rapid, Ultra-robust Proteomics

Bache, N., Geyer, P. E., Bekker‐Jensen, D. B., Hørning, O. B., Falkenby, L. G., Treit, P. V., Doll, S., Paron, I., Müller, J., Meier, F., et al. (2018) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir118.000853 · Cited by 402 · see citing works

Multidimensional proteomics for cell biology

Larance, M., & Lamond, A. I. (2015) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3970 · Cited by 407 · see citing works

Polyamines and eIF5A Hypusination Modulate Mitochondrial Respiration and Macrophage Activation

Puleston, D. J., Buck, M. D., Geltink, R. I. K., Kyle, R. L., Caputa, G., O’Sullivan, D., Cameron, A. M., Castoldi, Â., Musa, Y., Kabat, A. M., et al. (2019) · Cell Metabolism · doi:10.1016/j.cmet.2019.05.003 · Cited by 391 · see citing works

The demographics of the ubiquitin system

Clague, M. J., Heride, C., & Urbé, S. (2015) · Trends in Cell Biology · doi:10.1016/j.tcb.2015.03.002 · Cited by 365 · see citing works

High-throughput and high-sensitivity phosphoproteomics with the EasyPhos platform

Humphrey, S. J., Karayel, Ö., James, D. E., & Mann, M. (2018) · Nature Protocols · doi:10.1038/s41596-018-0014-9 · Cited by 359 · see citing works

A Critical Review of Bottom-Up Proteomics: The Good, the Bad, and the Future of This Field

Dupree, E. J., Jayathirtha, M., Yorkey, H., Mihăşan, M., Petre, B. A., & Darie, C. C. (2020) · Proteomes · doi:10.3390/proteomes8030014 · Cited by 357 · see citing works

BoxCar acquisition method enables single-shot proteomics at a depth of 10,000 proteins in 100 minutes

Meier, F., Geyer, P. E., Winter, S. V., Cox, J., & Mann, M. (2018) · Nature Methods · doi:10.1038/s41592-018-0003-5 · Cited by 341 · see citing works

Plasma Proteome Profiling to detect and avoid sample‐related biases in biomarker studies

Geyer, P. E., Voytik, E., Treit, P. V., Doll, S., Kleinhempel, A., Niu, L., Müller, J. B., Buchholtz, M., Bader, J. M., Teupser, D., et al. (2019) · EMBO Molecular Medicine · doi:10.15252/emmm.201910427 · Cited by 348 · see citing works

Protein Synthesis Initiation in Eukaryotic CellsPreprint

Merrick, W. C., & Pavitt, G. D. (2018) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a033092 · Cited by 346 · see citing works

Polar Positioning of Phase-Separated Liquid Compartments in Cells Regulated by an mRNA Competition Mechanism

Saha, S., Weber, C. A., Nousch, M., Adame-Arana, O., Hoege, C., Hein, M. Y., Nishimura, E. O., Mahamid, J., Jahnel, M., Jawerth, L. M., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.006 · Cited by 335 · see citing works

Mass-spectrometry-based proteomics: from single cells to clinical applications

Guo, T., Steen, J. A. J., & Mann, M. (2025) · Nature · doi:10.1038/s41586-025-08584-0 · Cited by 351 · see citing works

Evaluation of FASP, SP3, and iST Protocols for Proteomic Sample Preparation in the Low Microgram Range

Sielaff, M., Kuharev, J., Bohn, T., Hahlbrock, J., Bopp, T., Tenzer, S., & Distler, U. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00433 · Cited by 321 · see citing works

Recent advances in mass spectrometry based clinical proteomics: applications to cancer research

Macklin, A. M., Khan, S., & Kislinger, T. (2020) · Clinical Proteomics · doi:10.1186/s12014-020-09283-w · Cited by 320 · see citing works

Single Muscle Fiber Proteomics Reveals Fiber-Type-Specific Features of Human Muscle Aging

Murgia, M., Toniolo, L., Nagaraj, N., Ciciliot, S., Vindigni, V., Schiaffino, S., Reggiani, C., & Mann, M. (2017) · Cell Reports · doi:10.1016/j.celrep.2017.05.054 · Cited by 315 · see citing works

Stress- and ubiquitylation-dependent phase separation of the proteasome

Yasuda, S., Tsuchiya, H., Kaiho, A., Guo, Q., Ikeuchi, K., Endo, A., Arai, N., Ohtake, F., Murata, S., Inada, T., et al. (2020) · Nature · doi:10.1038/s41586-020-1982-9 · Cited by 311 · see citing works

Structure, Function, and Regulation of the Hsp90 MachineryPreprint

Biebl, M. M., & Büchner, J. (2019) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a034017 · Cited by 308 · see citing works

A genome-wide algal mutant library and functional screen identifies genes required for eukaryotic photosynthesis

Li, X., Patena, W., Fauser, F., Jinkerson, R. E., Saroussi, S., Meyer, M. T., Ivanova, N., Robertson, J. M., Yue, R., Zhang, R., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0370-6 · Cited by 302 · see citing works

Kinetic Analysis of Protein Stability Reveals Age-Dependent Degradation

McShane, E., Sin, C., Zauber, H., Wells, J. N., Donnelly, N., Wang, X., Hou, J., Chen, W., Štorchová, Z., Marsh, J. A., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.015 · Cited by 291 · see citing works

Automated sample preparation with SP3 for low‐input clinical proteomics

Müller, T., Kalxdorf, M., Longuespée, R., Kazdal, D. N., Stenzinger, A., & Krijgsveld, J. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199111 · Cited by 297 · see citing works

Extending the Compatibility of the SP3 Paramagnetic Bead Processing Approach for Proteomics

Moggridge, S., Sorensen, P. H. B., Morin, G. B., & Hughes, C. S. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00913 · Cited by 289 · see citing works

Rapid and In-Depth Coverage of the (Phospho-)Proteome With Deep Libraries and Optimal Window Design for dia-PASEF

Skowronek, P., Thielert, M., Voytik, E., Tanzer, M. C., Hansen, F. M., Willems, S., Karayel, Ö., Brunner, A., Meier, F., & Mann, M. (2022) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2022.100279 · Cited by 278 · see citing works

Plasma proteome profiling discovers novel proteins associated with non‐alcoholic fatty liver disease

Niu, L., Geyer, P. E., Albrechtsen, N. J. W., Gluud, L. L., Santos, A., Doll, S., Treit, P. V., Holst, J. J., Knop, F. K., Vilsbøll, T., et al. (2019) · Molecular Systems Biology · doi:10.15252/msb.20188793 · Cited by 278 · see citing works

Deep Proteomics of Mouse Skeletal Muscle Enables Quantitation of Protein Isoforms, Metabolic Pathways, and Transcription Factors*

Deshmukh, A. S., Murgia, M., Nagaraj, N., Treebak, J. T., Cox, J., & Mann, M. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.044222 · Cited by 275 · see citing works

Protein sequences bound to mineral surfaces persist into deep time

Demarchi, B., Hall, S., Roncal-Herrero, T., Freeman, C. L., Woolley, J., Crisp, M. K., Wilson, J., Fotakis, A., Fischer, R., Kessler, B. M., et al. (2016) · eLife · doi:10.7554/elife.17092 · Cited by 279 · see citing works

Tunable protein synthesis by transcript isoforms in human cells

Floor, S. N., & Doudna, J. A. (2016) · eLife · doi:10.7554/elife.10921 · Cited by 265 · see citing works

Single‐Cell Mass Spectrometry Approaches to Explore Cellular Heterogeneity

Zhang, L., & Vértes, Á. (2017) · Angewandte Chemie International Edition · doi:10.1002/anie.201709719 · Cited by 277 · see citing works

Yeast Proteome Dynamics from Single Cell Imaging and Automated Analysis

Chong, Y. T., Koh, J. L. Y., Friesen, H., Kaluarachchi Duffy, S., Cox, M. J., Moses, A., Moffat, J., Boone, C., & Andrews, B. J. (2015) · Cell · doi:10.1016/j.cell.2015.04.051 · Cited by 274 · see citing works

Limited Environmental Serine and Glycine Confer Brain Metastasis Sensitivity to PHGDH Inhibition

Ngo, B., Kim, E., Osorio-Vasquez, V., Doll, S., Bustraan, S., Liang, R. J., Luengo, A., Davidson, S. M., Ali, A., Ferraro, G. B., et al. (2020) · Cancer Discovery · doi:10.1158/2159-8290.cd-19-1228 · Cited by 268 · see citing works

The Organizing Principles of Eukaryotic Ribosome Recruitment

Pelletier, J., & Sonenberg, N. (2019) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-013118-111042 · Cited by 261 · see citing works

Region and cell-type resolved quantitative proteomic map of the human heart

Doll, S., Dreßen, M., Geyer, P. E., Itzhak, D. N., Braun, C., Doppler, S. A., Meier, F., Deutsch, M.-A., Lahm, H., Lange, R., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01747-2 · Cited by 265 · see citing works

Clinical Significance of Extracellular Vesicles in Plasma from Glioblastoma Patients

Osti, D., Bene, M. D., Rappa, G., Santos, M. F., Matafora, V., Richichi, C., Faletti, S., Beznoussenko, G. V., Mironov, A., Bachi, A., et al. (2018) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-18-1941 · Cited by 265 · see citing works

irCLIP platform for efficient characterization of protein–RNA interactions

Zarnegar, B. J., Flynn, R. A., Shen, Y., Do, B. T., Chang, H. Y., & Khavari, P. A. (2016) · Nature Methods · doi:10.1038/nmeth.3840 · Cited by 264 · see citing works

Circadian control of oscillations in mitochondrial rate-limiting enzymes and nutrient utilization by PERIOD proteins

Neufeld-Cohen, A., Robles, M. S., Aviram, R., Manella, G., Adamovich, Y., Ladeuix, B., Nir, D., Rousso-Noori, L., Kuperman, Y., Golik, M., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1519650113 · Cited by 262 · see citing works

Transcriptomic and proteomic landscape of mitochondrial dysfunction reveals secondary coenzyme Q deficiency in mammals

Kühl, I., Miranda, M., Atanassov, I., Kuznetsova, I., Hinze, Y., Mourier, A., Filipovska, A., & Larsson, N. (2017) · eLife · doi:10.7554/elife.30952 · Cited by 251 · see citing works

Time- and compartment-resolved proteome profiling of the extracellular niche in lung injury and repair

Schiller, H. B., Fernandez, I. E., Burgstaller, G., Schaab, C., Scheltema, R. A., Schwarzmayr, T., Strom, T. M., Eickelberg, O., & Mann, M. (2015) · Molecular Systems Biology · doi:10.15252/msb.20156123 · Cited by 261 · see citing works

Accurate Protein Complex Retrieval by Affinity Enrichment Mass Spectrometry (AE-MS) Rather than Affinity Purification Mass Spectrometry (AP-MS)

Keilhauer, E. C., Hein, M. Y., & Mann, M. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.041012 · Cited by 254 · see citing works

Performance Evaluation of the Q Exactive HF-X for Shotgun Proteomics

Kelstrup, C. D., Bekker‐Jensen, D. B., Arrey, T. N., Hogrebe, A., Harder, A., & Olsen, J. V. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00602 · Cited by 256 · see citing works

Comprehensive Proteomic Analysis of Human Erythropoiesis

Gautier, E., Ducamp, S., Leduc, M., Salnot, V., Guillonneau, F., Dussiot, M., Hale, J., Giarratana, M., Raimbault, A., Douay, L., et al. (2016) · Cell Reports · doi:10.1016/j.celrep.2016.06.085 · Cited by 248 · see citing works

Small molecule ISRIB suppresses the integrated stress response within a defined window of activation

Rabouw, H. H., Langereis, M. A., Anand, A. A., Visser, L. J., de Groot, R. J., Walter, P., & van Kuppeveld, F. J. M. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1815767116 · Cited by 242 · see citing works

Quantitative Evaluation of Filter Aided Sample Preparation (FASP) and Multienzyme Digestion FASP Protocols

Wiśniewski, J. R. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.6b00859 · Cited by 253 · see citing works

Roadblocks and resolutions in eukaryotic translation

Schuller, A. P., & Green, R. (2018) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-018-0011-4 · Cited by 245 · see citing works

Sample Preparation by Easy Extraction and Digestion (SPEED) - A Universal, Rapid, and Detergent-free Protocol for Proteomics Based on Acid Extraction

Doellinger, J., Schneider, A., Hoeller, M., & Lasch, P. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir119.001616 · Cited by 246 · see citing works

Different Material States of Pub1 Condensates Define Distinct Modes of Stress Adaptation and Recovery

Kroschwald, S., Munder, M. C., Maharana, S., Franzmann, T. M., Richter, D., Ruer, M., Hyman, A. A., & Alberti, S. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.05.041 · Cited by 244 · see citing works

Proteomics reveals the effects of sustained weight loss on the human plasma proteome

Geyer, P. E., Albrechtsen, N. J. W., Tyanova, S., Graßl, N., Iepsen, E. W., Lundgren, J. R., Madsbad, S., Holst, J. J., Torekov, S. S., & Mann, M. (2016) · Molecular Systems Biology · doi:10.15252/msb.20167357 · Cited by 235 · see citing works

Dynamic control of Hsf1 during heat shock by a chaperone switch and phosphorylation

Zheng, X., Krakowiak, J., Patel, N., Ali Beyzavi, B., Ezike, J., Khalil, A. S., & Pincus, D. (2016) · eLife · doi:10.7554/elife.18638 · Cited by 245 · see citing works

Condensation of Ded1p Promotes a Translational Switch from Housekeeping to Stress Protein Production

Iserman, C., Altamirano, C. D., Jegers, C., Friedrich, U. A., Zarin, T., Fritsch, A. W., Mittasch, M., Domingues, A. M. D. J., Hersemann, L., Jahnel, M., et al. (2020) · Cell · doi:10.1016/j.cell.2020.04.009 · Cited by 238 · see citing works

The molecular basis of translation initiation and its regulation in eukaryotes

Querido, J. B., Díaz‐López, I., & Ramakrishnan, V. (2023) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-023-00624-9 · Cited by 238 · see citing works

Mitofusin 2 is required to maintain mitochondrial coenzyme Q levels

Mourier, A., Motori, E., Brandt, T., Lagouge, M., Atanassov, I., Galinier, A., Rappl, G., Brodesser, S., Hultenby, K. R., Dieterich, C., et al. (2015) · The Journal of Cell Biology · doi:10.1083/jcb.201411100 · Cited by 234 · see citing works

Nanoliter-Scale Oil-Air-Droplet Chip-Based Single Cell Proteomic Analysis

Li, Z., Huang, M., Wang, X.-K., Zhu, Y., Li, J., Wong, C. C. L., & Fang, Q. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b00661 · Cited by 227 · see citing works

Mass Spectrometry-Based Plasma Proteomics: Considerations from Sample Collection to Achieving Translational Data

Ignjatović, V., Geyer, P. E., Palaniappan, K. K., Chaaban, J. E., Omenn, G. S., Baker, M. S., Deutsch, E. W., & Schwenk, J. M. (2019) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00503 · Cited by 226 · see citing works

Streamlined single-cell proteomics by an integrated microfluidic chip and data-independent acquisition mass spectrometry

Gebreyesus, S. T., Siyal, A. A., Kitata, R. B., Chen, E. S.-W., Enkhbayar, B., Angata, T., Lin, K., Chen, Y., & Tu, H. (2022) · Nature Communications · doi:10.1038/s41467-021-27778-4 · Cited by 231 · see citing works

pDeep: Predicting MS/MS Spectra of Peptides with Deep Learning

Zhou, X., Zeng, W., Chi, H., Luo, C., Liu, C., Zhan, J., He, S., & Zhang, Z.-F. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b02566 · Cited by 218 · see citing works

Mass spectrometry-based proteomics as an emerging tool in clinical laboratories

Birhanu, A. (2023) · Clinical Proteomics · doi:10.1186/s12014-023-09424-x · Cited by 185 · see citing works

Ultra-deep and quantitative saliva proteome reveals dynamics of the oral microbiome

Graßl, N., Kulak, N. A., Pichler, G., Geyer, P. E., Jung, J., Schubert, S., Sinitcyn, P. G., Cox, J., & Mann, M. (2016) · Genome Medicine · doi:10.1186/s13073-016-0293-0 · Cited by 222 · see citing works

Adjacent Codons Act in Concert to Modulate Translation Efficiency in Yeast

Gamble, C. E., Brule, C. E., Dean, K., Fields, S., & Grayhack, E. J. (2016) · Cell · doi:10.1016/j.cell.2016.05.070 · Cited by 222 · see citing works

The SND proteins constitute an alternative targeting route to the endoplasmic reticulum

Aviram, N., Ast, T., Boydston, E. A., Arakel, E. C., Chuartzman, S. G., Jan, C. H., Haßdenteufel, S., Dudek, J., Jung, M., Schorr, S., et al. (2016) · Nature · doi:10.1038/nature20169 · Cited by 211 · see citing works

The nucleotide exchange factors of Hsp70 molecular chaperones

Bracher, A., & Verghese, J. (2015) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2015.00010 · Cited by 212 · see citing works

Single muscle fiber proteomics reveals unexpected mitochondrial specialization

Murgia, M., Nagaraj, N., Deshmukh, A. S., Zeiler, M., Cancellara, P., Moretti, I., Reggiani, C., Schiaffino, S., & Mann, M. (2015) · EMBO Reports · doi:10.15252/embr.201439757 · Cited by 202 · see citing works

Intrinsically Disordered Proteins Drive Emergence and Inheritance of Biological Traits

Chakrabortee, S., Byers, J. S., Jones, S. K., Garcia, D. M., Bhullar, B., Chang, A., She, R., Lee, L. R., Fremin, B. J., Lindquist, S. L., et al. (2016) · Cell · doi:10.1016/j.cell.2016.09.017 · Cited by 205 · see citing works

Early Pleistocene enamel proteome from Dmanisi resolves Stephanorhinus phylogeny

Cappellini, E., Welker, F., Pandolfi, L., Ramos‐Madrigal, J., Samodova, D., Rüther, P. L., Fotakis, A. K., Lyon, D. B., Moreno-Mayar, J. V., Bukhsianidze, M., et al. (2019) · Nature · doi:10.1038/s41586-019-1555-y · Cited by 206 · see citing works

The proteome landscape of the kingdoms of life

Müller, J., Geyer, P. E., Colaço, A. R., Treit, P. V., Strauss, M. T., Oroshi, M., Doll, S., Winter, S. V., Bader, J. M., Köhler, N., et al. (2020) · Nature · doi:10.1038/s41586-020-2402-x · Cited by 199 · see citing works

Proteomics: a powerful tool to study plant responses to biotic stress

Liu, Y., Lu, S., Liu, K., Wang, S., Huang, L., & Guo, L. (2019) · Plant Methods · doi:10.1186/s13007-019-0515-8 · Cited by 206 · see citing works

A streamlined mass spectrometry–based proteomics workflow for large-scale FFPE tissue analysis

Coscia, F., Doll, S., Bech, J. M., Schweizer, L., Mund, A., Lengyel, E., Lindebjerg, J., Madsen, G. I., Moreira, J. M., & Mann, M. (2020) · The Journal of Pathology · doi:10.1002/path.5420 · Cited by 200 · see citing works

Clathrin-independent pathways do not contribute significantly to endocytic flux

Bitsikas, V., Corrêa, I. R., & Nichols, B. J. (2014) · eLife · doi:10.7554/elife.03970 · Cited by 199 · see citing works

Cytosolic Protein Vms1 Links Ribosome Quality Control to Mitochondrial and Cellular Homeostasis

Izawa, T., Park, S.-H., Zhao, L., Hartl, F. U., & Neupert, W. (2017) · Cell · doi:10.1016/j.cell.2017.10.002 · Cited by 199 · see citing works

Organellar proteomics and phospho-proteomics reveal subcellular reorganization in diet-induced hepatic steatosis

Krahmer, N., Najafi, B., Schueder, F., Quagliarini, F., Steger, M., Seitz, S., Kasper, R., Salinas, F., Cox, J., Uhlenhaut, N. H., et al. (2018) · Developmental Cell · doi:10.1016/j.devcel.2018.09.017 · Cited by 188 · see citing works

Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry

Jiang, Y., Balaya, R. D. A., Schuster, D., Neely, B. A., Rosano, G. L., Volkmar, N., Momenzadeh, A., Peters-Clarke, T. M., Egbert, S., Kreimer, S. D., et al. (2024) · ACS Measurement Science Au · doi:10.1021/acsmeasuresciau.3c00068 · Cited by 200 · see citing works

Early Events in the Endoplasmic Reticulum Unfolded Protein ResponsePreprint

Preißler, S., & Ron, D. (2018) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a033894 · Cited by 196 · see citing works

One-Tip enables comprehensive proteome coverage in minimal cells and single zygotes

Ye, Z., Sabatier, P., Gonzalez, J. M., Eguchi, A., Lechner, M. Y., Østergaard, O., Xie, J., Guo, Y., Schultz, L., Truffer, R., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-46777-9 · Cited by 86 · see citing works

Rapid, One-Step Sample Processing for Label-Free Single-Cell Proteomics

Johnston, S. M., Webber, K. G. I., Xie, X., Truong, T., Nydegger, A., Lin, H. L., Nwosu, A. J., Zhu, Y., & Kelly, R. (2023) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.3c00159 · Cited by 43 · see citing works

Proteomics for Low Cell Numbers: How to Optimize the Sample Preparation Workflow for Mass Spectrometry Analysis

Kassem, S., van der Pan, K., de Jager, A. L., Naber, B. A. E., de Laat, I. F., Louis, A., van Dongen, J. J. M., Teodósio, C., & Díez, P. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00321 · Cited by 37 · see citing works

Optimal Sample Preparation Workflow for Quantitative Mass Spectrometry-Based Studies in the Low Range

Kassem, S., & Díez, P. (2024) · Methods in molecular biology · doi:10.1007/978-1-0716-4298-6_2 · Cited by 2 · see citing works

Automated sample preparation for high-throughput single-cell proteomicsPreprint

Specht, H., Harmange, G., Perlman, D. H., Emmott, E., Niziolek, Z., Budnik, B., & Slavov, N. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/399774 · Cited by 77 · see citing works