Selective enrichment of newly synthesized proteins for quantitative secretome analysis

Cytoscape: A software Environment for integrated models of biomolecular interaction networks

Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., & Ideker, T. (2003) · Genome Research · doi:10.1101/gr.1239303 · Cited by 51,888

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890

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

Bioconductor: open software development for computational biology and bioinformatics

Gentleman, R. C., Carey, V. J., Bates, D. M., Bolstad, B., Dettling, M., Dudoit, S., Ellis, B., Gautier, L., Ge, Y., Gentry, J., et al. (2004) · Genome biology · doi:10.1186/gb-2004-5-10-r80 · Cited by 12,082

Linear Models and Empirical Bayes Methods for Assessing Differential Expression in Microarray Experiments

Smyth, G. K. (2004) · Statistical Applications in Genetics and Molecular Biology · doi:10.2202/1544-6115.1027 · Cited by 11,829

SignalP 4.0: discriminating signal peptides from transmembrane regions

Petersen, T. N., Brunak, S., von Heijne, G., & Nielsen, H. (2011) · Nature Methods · doi:10.1038/nmeth.1701 · Cited by 8,847

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

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 5,520

The Human Plasma Proteome

Anderson, N. L., & Anderson, N. G. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r200007-mcp200 · Cited by 4,414

Widespread changes in protein synthesis induced by microRNAs

Selbach, M., Schwanhäusser, B., Thierfelder, N., Fang, Z., Khanin, R., & Rajewsky, N. (2008) · Nature · doi:10.1038/nature07228 · Cited by 3,429

Stop and Go Extraction Tips for Matrix-Assisted Laser Desorption/Ionization, Nanoelectrospray, and LC/MS Sample Pretreatment in Proteomics

Rappsilber, J., Ishihama, Y., & Mann, M. (2002) · Analytical Chemistry · doi:10.1021/ac026117i · Cited by 2,627

TRANSFORMING GROWTH FACTOR-β REGULATION OF IMMUNE RESPONSES

Li, M. O., Wan, Y. Y., Sanjabi, S., Robertson, A.-K. L., & Flavell, R. A. (2005) · Annual Review of Immunology · doi:10.1146/annurev.immunol.24.021605.090737 · Cited by 2,264

Incorporation of azides into recombinant proteins for chemoselective modification by the Staudinger ligation

Kiick, K. L., Saxon, E., Tirrell, D. A., & Bertozzi, C. R. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.012583299 · Cited by 911

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

Dieterich, D. C., Link, A. J., Graumann, J., Tirrell, D. A., & Schuman, E. M. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0601637103 · Cited by 874

Directing Transition from Innate to Acquired Immunity: Defining a Role for IL-6

Jones, S. A. (2005) · The Journal of Immunology · doi:10.4049/jimmunol.175.6.3463 · Cited by 773

PANTHER: a browsable database of gene products organized by biological function, using curated protein family and subfamily classification

Thomas, P. D. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg115 · Cited by 665

The SCX/IMAC enrichment approach for global phosphorylation analysis by mass spectrometry

Villén, J., & Gygi, S. P. (2008) · Nature Protocols · doi:10.1038/nprot.2008.150 · Cited by 637

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

Mi, H., Dong, Q., Muruganujan, A., Gaudet, P., Lewis, S., & Thomas, P. D. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp1019 · Cited by 609

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

Combination of FASP and StageTip-based fractionation allows in-depth analysis of the hippocampal membrane proteome

Wiśniewski, J. R., Zougman, A., & Mann, M. (2009) · Journal of Proteome Research · doi:10.1021/pr900748n · Cited by 545

Infrastructure for the life sciences: design and implementation of the UniProt website

Jain, E., Bairoch, A., Duvaud, S., Phan, I. Q., Redaschi, N., Süzek, B. E., Martin, M. J., McGarvey, P. B., & Gasteiger, E. (2009) · BMC Bioinformatics · doi:10.1186/1471-2105-10-136 · Cited by 485

Laminin isoforms in tumor invasion, angiogenesis and metastasis

Patarroyo, M. E., Tryggvason, K., & Virtanen, I. (2002) · Seminars in Cancer Biology · doi:10.1016/s1044-579x(02)00023-8 · Cited by 407

Global analysis of cellular protein translation by pulsed SILAC

Schwanhäusser, B., Gossen, M., Dittmar, G., & Selbach, M. (2009) · PROTEOMICS · doi:10.1002/pmic.200800275 · Cited by 356

Serum starvation: caveat emptor

Pirkmajer, S., & Chibalin, A. (2011) · American Journal of Physiology-Cell Physiology · doi:10.1152/ajpcell.00091.2011 · Cited by 301

A high-quality catalog of the Drosophila melanogaster proteome

Brunner, E., Ahrens, C. H., Mohanty, S., Baetschmann, H., Lövenich, S. N., Potthast, F., Deutsch, E. W., Panse, C., de Lichtenberg, U., Rinner, O., et al. (2007) · Nature Biotechnology · doi:10.1038/nbt1300 · Cited by 276

Secretome proteomics for discovery of cancer biomarkers

Makridakis, M., & Vlahou, A. (2010) · Journal of Proteomics · doi:10.1016/j.jprot.2010.07.001 · Cited by 250

Cytokine secretion in macrophages and other cells: Pathways and mediators

Stow, J. L., Low, P. C., Offenhäuser, C., & Sangermani, D. (2009) · Immunobiology · doi:10.1016/j.imbio.2008.11.005 · Cited by 205

Subcompartments of the macrophage recycling endosome direct the differential secretion of IL-6 and TNFα

Manderson, A. P., Kay, J. G., Hammond, L. A., Brown, D. L., & Stow, J. L. (2007) · The Journal of Cell Biology · doi:10.1083/jcb.200612131 · Cited by 198

Heme Oxygenase-1 Contributes to an Alternative Macrophage Activation Profile Induced by Apoptotic Cell Supernatants

Weis, N., Weigert, A., von Knethen, A., & Brüne, B. (2009) · Molecular Biology of the Cell · doi:10.1091/mbc.e08-10-1005 · Cited by 169

Proteomic Analysis of Conditioned Media from the PC3, LNCaP, and 22Rv1 Prostate Cancer Cell Lines: Discovery and Validation of Candidate Prostate Cancer Biomarkers

Sardana, G., Jung, K., Stephan, C., & Diamandis, E. P. (2008) · Journal of Proteome Research · doi:10.1021/pr8003216 · Cited by 159

Conditioned media from cell lines: A complementary model to clinical specimens for the discovery of disease‐specific biomarkers

Dowling, P., & CLYNES, M. M. (2010) · PROTEOMICS · doi:10.1002/pmic.201000530 · Cited by 152

Reappraisal of serum starvation, the restriction point, G0, and G1 phase arrest points

Cooper, S. (2003) · The FASEB Journal · doi:10.1096/fj.02-0352rev · Cited by 140

Quantitative Subcellular Proteome and Secretome Profiling of Influenza A Virus-Infected Human Primary Macrophages

Lietzén, N., Öhman, T., Rintahaka, J., Julkunen, I., Aittokallio, T., Matikainen, S., & Nyman, T. A. (2011) · PLoS Pathogens · doi:10.1371/journal.ppat.1001340 · Cited by 137

A novel method for generation of signature networks as biomarkers from complex high throughput data

Nikolsky, Y., Ekins, S., Nikolskaya, T., & Bugrim, A. E. (2005) · Toxicology Letters · doi:10.1016/j.toxlet.2005.02.004 · Cited by 134

Primary mouse hepatocytes for systems biology approaches: a standardized in vitro system for modelling of signal transduction pathways

Klingmüller, U., Bauer, A., Bohl, S., Nickel, P. J., Breitkopf, K., Dooley, S., Zellmer, S., Kern, C., Merfort, I., Sparna, T., et al. (2006) · IEE Proceedings - Systems Biology · doi:10.1049/ip-syb:20050067 · Cited by 127

Activation of the insulin-like growth factor-1 receptor promotes the survival of human keratinocytes following ultraviolet B irradiation

Kuhn, C., Hurwitz, S. A., Kumar, M. G., Cotton, J. P., & Spandau, D. F. (1999) · International Journal of Cancer · doi:10.1002/(sici)1097-0215(19990129)80:3 · Cited by 120

Different Changes in Protein and Phosphoprotein Levels Result from Serum Starvation of High-Grade Glioma and Adenocarcinoma Cell Lines

Levin, V. A., Panchabhai, S. C., Shen, L., Kornblau, S. M., Qiu, Y., & Baggerly, K. A. (2010) · Journal of Proteome Research · doi:10.1021/pr900392b · Cited by 86

Secretome Compartment Is a Valuable Source of Biomarkers for Cancer-Relevant Pathways

Caccia, D., Zanetti-Domingues, L. C., Miccichè, F., Bortoli, M. D., Carniti, C., Mondellini, P., & Bongarzone, I. (2011) · Journal of Proteome Research · doi:10.1021/pr200344n · Cited by 51

Metabolic Labeling and Protein Linearization Technology Allow the Study of Proteins Secreted by Cultured Cells in Serum-Containing Media

Colzani, M., Waridel, P., Laurent, J., Faes, E., Rüegg, C., & Quadroni, M. (2009) · Journal of Proteome Research · doi:10.1021/pr900476b · Cited by 50

Secretome of Human Endothelial Cells under Shear Stress

Burghoff, S., & Schrader, J. (2010) · Journal of Proteome Research · doi:10.1021/pr100937a · Cited by 50

Platelet-derived growth factor (PDGF) activates primitive hematopoietic precursors (pre-CFCmulti) by up-regulating IL-1 in PDGF receptor-expressing macrophages

Yan, X. Q., Brady, G., & Iscove, N. (1993) · The Journal of Immunology · doi:10.4049/jimmunol.150.6.2440 · Cited by 34

Extracellular proteomes of M‐CSF (CSF‐1) and GM‐CSF‐dependent macrophages

Bailey, M. J., Lacey, D. C., de Kok, B., Veith, P. D., Reynolds, E. C., & Hamilton, J. A. (2010) · Immunology and Cell Biology · doi:10.1038/icb.2010.92 · Cited by 23

Identification of low abundant secreted proteins and peptides from primary culture supernatants of human T-cells

Finoulst, I., Vink, P. M., Rovers, E., Pieterse, M., Pinkse, M. W. H., Bos, E. S., & Verhaert, P. D. E. M. (2011) · Journal of Proteomics · doi:10.1016/j.jprot.2011.03.034 · Cited by 21

Dual Ligand Stimulation of RAW 264.7 Cells Uncovers Feedback Mechanisms That Regulate TLR-Mediated Gene Expression

Zhu, X., Chang, M. S., Hsueh, R. C., Taussig, R., Smith, K. D., Simon, M. I., & Choi, S. (2006) · The Journal of Immunology · doi:10.4049/jimmunol.177.7.4299 · Cited by 20

mRNAs, proteins and the emerging principles of gene expression control

Buccitelli, C., & Selbach, M. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0258-4 · Cited by 1,243

Cellular Incorporation of Unnatural Amino Acids and Bioorthogonal Labeling of Proteins

Lang, K., & Chin, J. W. (2014) · Chemical Reviews · doi:10.1021/cr400355w · Cited by 1,051

Dynamic profiling of the protein life cycle in response to pathogens

Jovanovic, M., Rooney, M. S., Mertins, P., Przybylski, D., Chevrier, N., Satija, R., Rodriguez, E. H., Fields, A. P., Schwartz, S., Raychowdhury, R., et al. (2015) · Science · doi:10.1126/science.1259038 · Cited by 460

Protein Aggregation Capture on Microparticles Enables Multipurpose Proteomics Sample Preparation*

Batth, T. S., Tollenaere, M. A. X., Rüther, P. L., González-Franquesa, A., Prabhakar, B. S., Bekker‐Jensen, S., Deshmukh, A. S., & Olsen, J. V. (2019) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir118.001270 · Cited by 432

The Human RNA-Binding Proteome and Its Dynamics during Translational Arrest

Trendel, J., Schwarzl, T., Horos, R., Prakash, A., Bateman, A. G., Hentze, M. W., & Krijgsveld, J. (2018) · Cell · doi:10.1016/j.cell.2018.11.004 · Cited by 408

Combining Pulsed SILAC Labeling and Click-Chemistry for Quantitative Secretome Analysis

Eichelbaum, K., & Krijgsveld, J. (2014) · Methods in molecular biology · doi:10.1007/978-1-4939-0944-5_7 · Cited by 30

Quantitative Secretome Analysis of Activated Jurkat Cells Using Click Chemistry-Based Enrichment of Secreted Glycoproteins

Witzke, K. E., Rosowski, K., Müller, C. R., Ahrens, M., Eisenacher, M., Megger, D. A., Knobloch, J., Koch, A., Bracht, T., & Sitek, B. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00575 · Cited by 22

Single‐Cell Secretome Profiling Enabled by Selective Enrichment and NanoLC‐MS/MS Analysis

He, Y., Liu, X., Zhu, F., Dai, Z., Xiao, L., Li, L., Zhao, B., Yuan, H., Lu, Y., Liang, Z., et al. (2024) · Angewandte Chemie · doi:10.1002/ange.202417351

Metabolic labeling and LC-MS/MS-based identification of interleukin-1α-induced secreted proteomes from epithelial cells in the presence or absence of serum

Priester, J., Meier‐Soelch, J., Weiser, H., Heylmann, D., Weber, A., Linne, U., & Kracht, M. (2023) · STAR Protocols · doi:10.1016/j.xpro.2023.102195 · Cited by 1

In-Depth Proteomic Quantification of Cell Secretome in Serum-Containing Conditioned Medium

Weng, Y., Sui, Z., Shan, Y., Jiang, H., Zhou, Y., Zhu, X., Liang, Z., Zhang, L., & Zhang, Y. (2016) · Analytical Chemistry · doi:10.1021/acs.analchem.6b00910 · Cited by 42