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Error-Tolerant Identification of Peptides in Sequence Databases by Peptide Sequence Tags

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Proteolytic 18O Labeling for Comparative Proteomics: Model Studies with Two Serotypes of Adenovirus

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Dedifferentiation of Mammalian Myotubes Induced by msx1

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18 O Labeling: a tool for proteomics

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Targeted Down-regulation of Caveolin-3 Is Sufficient to Inhibit Myotube Formation in Differentiating C2C12 Myoblasts

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Use of Mass Spectrometry to Study Signaling Pathways

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c-Cbl Binding and Ubiquitin-dependent Lysosomal Degradation of Membrane-associated Notch1

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Comparative proteomics based on stable isotope labeling and affinity selection

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Extracellular matrix is required for skeletal muscle differentiation but not myogenin expression

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Mass spectrometry allows direct identification of proteins in large genomes

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Bcl-2 Expression Identifies an Early Stage of Myogenesis and Promotes Clonal Expansion of Muscle Cells

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Automatic Poisson peak harvesting for high throughput protein identification

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What place for polyacrylamide in proteomics?

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Matrix-assisted laser desorption/ionization Fourier transform ion cyclotron resonance mass spectrometry with pulsed in-source collision gas and in-source ion accumulation

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Rainbow's end: the quest for multiplexed fluorescence quantitative analysis in proteomics

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A combination of chemical derivatisation and improved bioinformatic tools optimises protein identification for proteomics

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An in Vitro Assay to Study Regulated mRNA Stability

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Kinetic equivalence of stable-isotope-labeled and unlabeled phenytoin

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Dendritic cells presenting pyruvate kinase M1/M2 isozyme peptide can induce experimental allergic myositis in BALB/c mice

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

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Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction, termed MaxLFQ

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Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents

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Insights into the regulation of protein abundance from proteomic and transcriptomic analyses

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Lysine acetylation targets protein complexes and co-regulates major cellular functions

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The impact of microRNAs on protein output

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Towards a knowledge-based Human Protein Atlas

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Global Survey of Phosphotyrosine Signaling Identifies Oncogenic Kinases in Lung Cancer

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Exponentially Modified Protein Abundance Index (emPAI) for Estimation of Absolute Protein Amount in Proteomics by the Number of Sequenced Peptides per Protein

Ishihama, Y., Oda, Y., Tabata, T., Sato, T., Nagasu, T., Rappsilber, J., & Mann, M. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500061-mcp200 · Cited by 2,055 · see citing works

Correlation of mRNA and protein in complex biological samples

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

Kulak, N. A., Pichler, G., Paron, I., Nagaraj, N., & Mann, M. (2014) · Nature Methods · doi:10.1038/nmeth.2834 · Cited by 1,719 · see citing works

Absolute Quantification of Proteins by LCMSE

Silva, J. C., Gorenstein, M. V., Li, G.-Z., Vissers, J. P. C., & Geromanos, S. J. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500230-mcp200 · Cited by 1,529 · see citing works

Mass spectrometry–based proteomics turns quantitative

Ong, S.-E., & Mann, M. (2005) · Nature Chemical Biology · doi:10.1038/nchembio736 · Cited by 1,572 · see citing works

Protein Analysis by Shotgun/Bottom-up Proteomics

Zhang, Y., Fonslow, B. R., Shan, B., Baek, M.-C., & Yates, J. R. (2013) · Chemical Reviews · doi:10.1021/cr3003533 · Cited by 1,491 · see citing works

MultiNotch MS3 Enables Accurate, Sensitive, and Multiplexed Detection of Differential Expression across Cancer Cell Line Proteomes

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The growing landscape of lysine acetylation links metabolism and cell signalling

Choudhary, C., Weinert, B. T., Nishida, Y., Verdin, E., & Mann, M. (2014) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm3841 · Cited by 1,324 · see citing works

Parallel reaction monitoring for high resolution and high mass accuracy quantitative, targeted proteomics

Peterson, A. C., Russell, J. D., Bailey, D. J., Westphall, M. S., & Coon, J. J. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o112.020131 · Cited by 1,288 · see citing works

The nucleolus under stress

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Absolute protein expression profiling estimates the relative contributions of transcriptional and translational regulation

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Proteomics by Mass Spectrometry: Approaches, Advances, and Applications

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Broad activation of the ubiquitin–proteasome system by Parkin is critical for mitophagy

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

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Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT)

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Lenalidomide induces ubiquitination and degradation of CK1α in del(5q) MDS

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Quantitative interaction proteomics and genome-wide profiling of epigenetic histone marks and their readers

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Dynamic reprogramming of the kinome in response to targeted MEK inhibition in triple-negative breast cancer

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Quantitative, High-Resolution Proteomics for Data-Driven Systems Biology

Cox, J., & Mann, M. (2011) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-061308-093216 · Cited by 685 · see citing works

SILAC mouse for quantitative proteomics uncovers kindlin-3 as an essential factor for red blood cell function

Krüger, M., Moser, M., Ussar, S., Thievessen, I., Luber, C. A., Forner, F., Schmidt, S., Zanivan, S., Fässler, R., & Mann, M. (2008) · Cell · doi:10.1016/j.cell.2008.05.033 · Cited by 680 · see citing works

Increasing the Multiplexing Capacity of TMTs Using Reporter Ion Isotopologues with Isobaric Masses

McAlister, G. C., Huttlin, E. L., Haas, W., Ting, L., Jedrychowski, M. P., Rogers, J. C., Kuhn, K., Pike, I., Grothe, R. A., Blethrow, J. D., et al. (2012) · Analytical Chemistry · doi:10.1021/ac301572t · Cited by 605 · see citing works

Widespread Proteome Remodeling and Aggregation in Aging C. elegans

Walther, D. M., Kasturi, P., Zheng, M., Pinkert, S., Vecchi, G., Ciryam, P., Morimoto, R. I., Dobson, C. M., Vendruscolo, M., Mann, M., et al. (2015) · Cell · doi:10.1016/j.cell.2015.03.032 · Cited by 569 · see citing works

Progress in Top-Down Proteomics and the Analysis of Proteoforms

Toby, T. K., Fornelli, L., & Kelleher, N. L. (2016) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-071015-041550 · Cited by 576 · see citing works

Kinase-selective enrichment enables quantitative phosphoproteomics of the kinome across the cell cycle

Daub, H., Olsen, J. V., Bairlein, M., Gnad, F., Oppermann, F. S., Körner, R., Greff, Z., Kéri, G., Stemmann, O., & Mann, M. (2008) · Molecular Cell · doi:10.1016/j.molcel.2008.07.007 · Cited by 594 · see citing works

Quantitative proteomics reveals subset-specific viral recognition in dendritic cells

Luber, C. A., Cox, J., Lauterbach, H., Fancke, B., Selbach, M., Tschopp, J., Akira, S., Wiegand, M., Hochrein, H., O'Keeffe, M., et al. (2010) · Immunity · doi:10.1016/j.immuni.2010.01.013 · Cited by 576 · see citing works

mProphet: automated data processing and statistical validation for large-scale SRM experiments

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Comparative proteomic phenotyping of cell lines and primary cells to assess preservation of cell type-specific functions

Pan, C., Kumar, C., Bohl, S., Klingmueller, U., & Mann, M. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800258-mcp200 · Cited by 561 · see citing works

Super-SILAC mix for quantitative proteomics of human tumor tissue

Geiger, T., Cox, J., Ostasiewicz, P., Wisniewski, J. R., & Mann, M. (2010) · Nature Methods · doi:10.1038/nmeth.1446 · Cited by 538 · see citing works

Quantitative Phosphoproteomics Reveal mTORC1 Activates de Novo Pyrimidine Synthesis

Robitaille, A. M., Christen, S., Shimobayashi, M., Cornu, M., Fava, L. L., Moes, S., Prescianotto-Baschong, C., Sauer, U., Jenoe, P., & Hall, M. N. (2013) · Science · doi:10.1126/science.1228771 · Cited by 525 · see citing works

A Multidimensional Chromatography Technology for In-depth Phosphoproteome Analysis

Albuquerque, C. P., Smolka, M. B., Payne, S. H., Bafna, V., Eng, J., & Zhou, H. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700468-mcp200 · Cited by 504 · see citing works

Proteomic Mapping of the Human Mitochondrial Intermembrane Space in Live Cells via Ratiometric APEX Tagging

Hung, V., Zou, P., Rhee, H.-W., Udeshi, N. D., Cracan, V., Svinkina, T., Carr, S. A., Mootha, V. K., & Ting, A. Y. (2014) · Molecular Cell · doi:10.1016/j.molcel.2014.06.003 · Cited by 517 · see citing works

Global profiling of lysine reactivity and ligandability in the human proteome

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Impact of regulatory variation from RNA to protein

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A dual pressure linear ion trap orbitrap instrument with very high sequencing speed

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System-wide temporal characterization of the proteome and phosphoproteome of human embryonic stem cell differentiation

Rigbolt, K. T. G., Prokhorova, T. A., Akimov, V., Henningsen, J., Johansen, P. T., Kratchmarova, I., Kassem, M., Mann, M., Olsen, J. V., & Blagoev, B. (2011) · Science Signaling · doi:10.1126/scisignal.2001570 · Cited by 451 · see citing works

Precision proteomics: The case for high resolution and high mass accuracy

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Quantitative proteomics combined with BAC TransgeneOmics reveals in vivo protein interactions

Hubner, N. C., Bird, A. W., Cox, J., Splettstoesser, B., Bandilla, P., Poser, I., Hyman, A., & Mann, M. (2010) · Journal of Cell Biology · doi:10.1083/jcb.200911091 · Cited by 440 · see citing works

Acetylation of Smc3 by Eco1 Is Required for S Phase Sister Chromatid Cohesion in Both Human and Yeast

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A Quantitative Spatial Proteomics Analysis of Proteome Turnover in Human Cells

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Trans‐Proteomic Pipeline, a standardized data processing pipeline for large‐scale reproducible proteomics informatics

Deutsch, E. W., Mendoza, L., Shteynberg, D., Slagel, J., Sun, Z., & Moritz, R. L. (2015) · PROTEOMICS – Clinical Applications · doi:10.1002/prca.201400164 · Cited by 342 · see citing works

Defining the transcriptome and proteome in three functionally different human cell lines

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