Applications of targeted proteomics in systems biology and translational medicine

Mass spectrometry-based proteomics

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Targeted Data Extraction of the MS/MS Spectra Generated by Data-independent Acquisition: A New Concept for Consistent and Accurate Proteome Analysis

Gillet, L. C., Navarro, P., Tate, S., Röst, H., Selevsek, N., Reiter, L., Bonner, R., & Aebersold, R. (2012) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o111.016717 · Cited by 2,877 · see citing works

Protein biomarker discovery and validation: the long and uncertain path to clinical utility

Rifai, N., Gillette, M. A., & Carr, S. A. (2006) · Nature Biotechnology · doi:10.1038/nbt1235 · Cited by 1,867 · see citing works

Interactome Networks and Human Disease

Vidal, M., Cusick, M. E., & Barabási, A.-L. (2011) · Cell · doi:10.1016/j.cell.2011.02.016 · Cited by 1,771 · see citing works

Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise

Newman, J. R. S., Ghaemmaghami, S., Ihmels, J., Breslow, D. K., Noble, M., DeRisi, J. L., & Weissman, J. S. (2006) · Nature · doi:10.1038/nature04785 · Cited by 1,483 · see citing works

Identification and quantification of N-linked glycoproteins using hydrazide chemistry, stable isotope labeling and mass spectrometry

Zhang, H., Li, X., Martin, D. B., & Aebersold, R. H. (2003) · Nature Biotechnology · doi:10.1038/nbt827 · Cited by 1,389 · see citing works

Enzyme promiscuity: A mechanistic and evolutionary perspective

Tawfik, O. K. A. D. S. (2010) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-030409-143718 · Cited by 1,355 · see citing works

Selected reaction monitoring–based proteomics: workflows, potential, pitfalls and future directions

Picotti, P., & Aebersold, R. (2012) · Nature Methods · doi:10.1038/nmeth.2015 · Cited by 1,302 · see citing works

Extending the Limits of Quantitative Proteome Profiling with Data-Independent Acquisition and Application to Acetaminophen-Treated Three-Dimensional Liver Microtissues

Bruderer, R., Bernhardt, O. M., Gandhi, T., Miladinović, S. M., Cheng, L.-Y., Messner, S., Ehrenberger, T., Zanotelli, V., Butscheid, Y., Escher, C., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.044305 · Cited by 1,238 · see citing works

Quantitative mass spectrometric multiple reaction monitoring assays for major plasma proteins

Anderson, L., & Hunter, C. L. (2006) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m500331-mcp200 · Cited by 1,230 · see citing works

Protein 3D Structure Computed from Evolutionary Sequence Variation

Marks, D. S., Colwell, L. J., Sheridan, R., Hopf, T. A., Pagnani, A., Zecchina, R., & Sander, C. (2011) · PLoS ONE · doi:10.1371/journal.pone.0028766 · Cited by 1,144 · see citing works

Multi-site assessment of the precision and reproducibility of multiple reaction monitoring–based measurements of proteins in plasma

Addona, T. A., Abbatiello, S. E., Schilling, B., Skates, S. J., Mani, D. R., Bunk, D. M., Spiegelman, C. H., Zimmerman, L. J., Ham, A.-J. L., Keshishian, H., et al. (2009) · Nature Biotechnology · doi:10.1038/nbt.1546 · Cited by 1,037 · see citing works

Mass Spectrometric Quantitation of Peptides and Proteins Using Stable Isotope Standards and Capture by Anti-Peptide Antibodies (SISCAPA)

Anderson, N. L., Anderson, N. G., Haines, L. R., Hardie, D. B., Olafson, R. W., & Pearson, T. W. (2004) · Journal of Proteome Research · doi:10.1021/pr034086h · Cited by 806 · see citing works

Encoding and Decoding Cellular Information through Signaling Dynamics

Purvis, J. E., & Lahav, G. (2013) · Cell · doi:10.1016/j.cell.2013.02.005 · Cited by 805 · see citing works

Microparticles

Mause, S. F., & Weber, C. (2010) · Circulation Research · doi:10.1161/circresaha.110.226456 · Cited by 787 · see citing works

Differential network biology

Ideker, T., & Krogan, N. J. (2012) · Molecular Systems Biology · doi:10.1038/msb.2011.99 · Cited by 784 · 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

SAINTexpress: Improvements and additional features in Significance Analysis of INTeractome software

Teo, G., Liu, G., Zhang, J., Nesvizhskii, A. I., Gingras, A., & Choi, H. (2013) · Journal of Proteomics · doi:10.1016/j.jprot.2013.10.023 · Cited by 685 · see citing works

Quantitative, Multiplexed Assays for Low Abundance Proteins in Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution

Keshishian, H., Addona, T. A., Burgess, M. W., Kuhn, E. W., & Carr, S. A. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700354-mcp200 · Cited by 684 · see citing works

Targeted Peptide Measurements in Biology and Medicine: Best Practices for Mass Spectrometry-based Assay Development Using a Fit-for-Purpose Approach

Carr, S. A., Abbatiello, S. E., Ackermann, B. L., Borchers, C., Domon, B., Deutsch, E. W., Grant, R. P., Hoofnagle, A. N., Hüttenhain, R., Koomen, J. M., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.036095 · Cited by 561 · see citing works

ELISA and Multiplex Technologies for Cytokine Measurement in Inflammation and Aging Research

Leng, S. X., McElhaney, J. E., Walston, J. D., Xie, D., Fedarko, N. S., & Kuchel, G. A. (2008) · The Journals of Gerontology Series A · doi:10.1093/gerona/63.8.879 · Cited by 521 · see citing works

Multiple reaction monitoring-based, multiplexed, absolute quantitation of 45 proteins in human plasma

Kuzyk, M. A., Smith, D., Yang, J., Cross, T. J., Jackson, A. M., Hardie, D. B., Anderson, N. L., & Borchers, C. H. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800540-mcp200 · Cited by 515 · see citing works

Quantitative analysis of peptides and proteins in biomedicine by targeted mass spectrometry

Gillette, M. A., & Carr, S. A. (2012) · Nature Methods · doi:10.1038/nmeth.2309 · Cited by 497 · see citing works

Multiple reaction monitoring for robust quantitative proteomic analysis of cellular signaling networks

Wolf‐Yadlin, A., Hautaniemi, S., Lauffenburger, D. A., & White, F. M. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0608638104 · Cited by 494 · see citing works

Mass spectrometry in high-throughput proteomics: ready for the big time

Nilsson, T., Mann, M., Aebersold, R., Yates, J. R., Bairoch, A., & Bergeron, J. J. M. (2010) · Nature Methods · doi:10.1038/nmeth0910-681 · Cited by 470 · see citing works

Mass Spectrometry–Based Proteomics and Network Biology

Bensimon, A., Heck, A. J. R., & Aebersold, R. H. (2012) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-072909-100424 · Cited by 407 · see citing works

Quantification of C‐reactive protein in the serum of patients with rheumatoid arthritis using multiple reaction monitoring mass spectrometry and 13C‐labeled peptide standards

Kuhn, E. W., Wu, J., Karl, J., Liao, H., Zolg, W., & Guild, B. (2004) · PROTEOMICS · doi:10.1002/pmic.200300670 · Cited by 398 · see citing works

A targeted proteomics–based pipeline for verification of biomarkers in plasma

Whiteaker, J. R., Lin, C., Kennedy, J. J., Hou, L., Trute, M., Sokal, I., Yan, P., Schoenherr, R. M., Zhao, L., Voytovich, U. J., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1900 · Cited by 365 · see citing works

Cell-cycle-regulated activation of Akt kinase by phosphorylation at its carboxyl terminus

Liu, P., Begley, M., Michowski, W., Inuzuka, H., Ginzberg, M. B., Gao, D., Tsou, P., Gan, W., Papa, A., Kim, B. M., et al. (2014) · Nature · doi:10.1038/nature13079 · Cited by 364 · see citing works

Targeted Quantitation of Proteins by Mass Spectrometry

Liebler, D. C., & Zimmerman, L. J. (2013) · Biochemistry · doi:10.1021/bi400110b · Cited by 362 · see citing works

High Sensitivity Detection of Plasma Proteins by Multiple Reaction Monitoring of N-Glycosites

Stahl-Zeng, J., Lange, V., Ossola, R., Eckhardt, K., Krek, W., Aebersold, R. H., & Domon, B. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700132-mcp200 · Cited by 361 · see citing works

LC-MS/MS in the Clinical Laboratory - Where to From Here?

Grebe, S. K. G., & Singh, R. J. (2011) · Europe PMC (PubMed Central) · Cited by 356 · see citing works

Post‐translational modification: nature's escape from genetic imprisonment and the basis for dynamic information encoding

Prabakaran, S., Lippens, G., Steen, H., & Gunawardena, J. (2012) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1185 · Cited by 335 · see citing works

Quantitative variability of 342 plasma proteins in a human twin population

Liu, Y., Buil, A., Collins, B. C., Gillet, L. C., Blum, L. C., Cheng, L., Vitek, O., Mouritsen, J., Lachance, G., Spector, T. D., et al. (2015) · Molecular Systems Biology · doi:10.15252/msb.20145728 · Cited by 328 · see citing works

Stimulus‐dependent dynamics of p53 in single cells

Batchelor, E., Loewer, A., Mock, C. S., & Lahav, G. (2011) · Molecular Systems Biology · doi:10.1038/msb.2011.20 · Cited by 322 · see citing works

A complete mass-spectrometric map of the yeast proteome applied to quantitative trait analysis

Picotti, P., Clément-Ziza, M., Lam, H., Campbell, D. S., Schmidt, A., Deutsch, E. W., Röst, H., Sun, Z., Rinner, O., Reiter, L., et al. (2013) · Nature · doi:10.1038/nature11835 · Cited by 318 · cited 1× · see citing works

A Decade of Systems Biology

Chuang, H., Hofree, M., & Ideker, T. (2010) · Annual Review of Cell and Developmental Biology · doi:10.1146/annurev-cellbio-100109-104122 · Cited by 316 · see citing works

Quantification of Thyroglobulin, a Low-Abundance Serum Protein, by Immunoaffinity Peptide Enrichment and Tandem Mass Spectrometry

Hoofnagle, A. N., Becker, J. O., Wener, M. H., & Heinecke, J. W. (2008) · Clinical Chemistry · doi:10.1373/clinchem.2008.109652 · Cited by 314 · cited 2× · see citing works

Connecting Genomic Alterations to Cancer Biology with Proteomics: The NCI Clinical Proteomic Tumor Analysis Consortium

Ellis, M. J., Gillette, M. A., Carr, S. A., Paulovich, A. G., Smith, R. D., Rodland, K., Townsend, R. R., Kinsinger, C. R., Mesri, M., Rodriguez, H., et al. (2013) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0219 · Cited by 311 · see citing works

Cell type‐specific nuclear pores: a case in point for context‐dependent stoichiometry of molecular machines

Ori‬‬, A., Banterle, N., Iskar, M., Andrés‐Pons, A., Escher, C., Bui, K. H., Sparks, L., Solis‐Mezarino, V., Rinner, O., Peer Bork, B., et al. (2013) · Molecular Systems Biology · doi:10.1038/msb.2013.4 · Cited by 308 · see citing works

Solid-phase extraction of N-linked glycopeptides

Tian, Y., Zhou, Y. F., Elliott, S., Aebersold, R. H., & Zhang, H. (2007) · Nature Protocols · doi:10.1038/nprot.2007.42 · Cited by 286 · see citing works

Quantification of Cardiovascular Biomarkers in Patient Plasma by Targeted Mass Spectrometry and Stable Isotope Dilution

Keshishian, H., Addona, T. A., Burgess, M. W., Mani, D. R., Shi, X. D., Kuhn, E. W., Sabatine, M. S., Gerszten, R. E., & Carr, S. A. (2009) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900140-mcp200 · Cited by 286 · see citing works

Human cell type diversity, evolution, development, and classification with special reference to cells derived from the neural crest

Vickaryous, M. K., & Hall, B. K. (2006) · Biological reviews/Biological reviews of the Cambridge Philosophical Society · doi:10.1017/s1464793106007068 · Cited by 279 · see citing works

A pipeline that integrates the discovery and verification of plasma protein biomarkers reveals candidate markers for cardiovascular disease

Addona, T. A., Shi, X. D., Keshishian, H., Mani, D. R., Burgess, M. W., Gillette, M. A., Clauser, K. R., Shen, D., Lewis, G. D., Farrell, L. A., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.1899 · Cited by 249 · see citing works

Reproducible Quantification of Cancer-Associated Proteins in Body Fluids Using Targeted Proteomics

Hüttenhain, R., Soste, M., Selevsek, N., Röst, H. L., Sethi, A., Carapito, C., Farrah, T., Deutsch, E. W., Kusebauch, U., Moritz, R. L., et al. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3003989 · Cited by 245 · see citing works

Multilayered Genetic and Omics Dissection of Mitochondrial Activity in a Mouse Reference Population

Wu, Y., Williams, E. G., Dubuis, S., Mottis, A., Jovaisaite, V., Houten, S. M., Argmann, C. A., Faridi, P., Wolski, W., Kutalik, Z., et al. (2014) · Cell · doi:10.1016/j.cell.2014.07.039 · Cited by 244 · see citing works

The interface between biomarker discovery and clinical validation: The tar pit of the protein biomarker pipeline

Paulovich, A. G., Whiteaker, J. R., Hoofnagle, A. N., & Wang, P. (2008) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.200780174 · Cited by 229 · see citing works

Absolute Quantification of the G Protein-Coupled Receptor Rhodopsin by LC/MS/MS Using Proteolysis Product Peptides and Synthetic Peptide Standards

Barnidge, D. R., Dratz, E. A., Martin, T., Bonilla, L. E., Moran, L. B., & Lindall, A. W. (2003) · Analytical Chemistry · doi:10.1021/ac026154+ · Cited by 227 · see citing works

Selected reaction monitoring mass spectrometry reveals the dynamics of signaling through the GRB2 adaptor

Bisson, N., James, D. A., Ivosev, G., Tate, S. A., Bonner, R. F., Taylor, L., & Pawson, T. J. (2011) · Nature Biotechnology · doi:10.1038/nbt.1905 · Cited by 222 · see citing works

Antibody-free, targeted mass-spectrometric approach for quantification of proteins at low picogram per milliliter levels in human plasma/serum

Shi, T., Fillmore, T., Sun, X., Zhao, R., Schepmoes, A., Hossain, M., Xie, F., Wu, S., Kim, J., Jones, N., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1204366109 · Cited by 220 · see citing works

Large-Scale Interlaboratory Study to Develop, Analytically Validate and Apply Highly Multiplexed, Quantitative Peptide Assays to Measure Cancer-Relevant Proteins in Plasma

Abbatiello, S. E., Schilling, B., Mani, D. R., Zimmerman, L. J., Hall, S. C., MacLean, B., Albertolle, M., Allen, S., Burgess, M., Cusack, M. P., et al. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.047050 · Cited by 215 · see citing works

Comparative and Targeted Proteomic Analyses of Urinary Microparticles from Bladder Cancer and Hernia Patients

Chen, C., Lai, Y.-F., Tang, P., Chien, K., Yu, J., Tsai, C.-H., Chen, H., Wu, C., Chung, T., Hsu, C., et al. (2012) · Journal of Proteome Research · doi:10.1021/pr3008732 · Cited by 212 · see citing works

Large-Scale Targeted Proteomics Using Internal Standard Triggered-Parallel Reaction Monitoring (IS-PRM)*

Gallien, S., Kim, S.-Y., & Domon, B. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.043968 · Cited by 206 · see citing works

PASSEL : The P eptide A tlas SRM experiment library

Farrah, T., Deutsch, E. W., Kreisberg, R., Sun, Z., Campbell, D. S., Mendoza, L., Kusebauch, U., Brusniak, M., Hüttenhain, R., Schiess, R., et al. (2012) · PROTEOMICS · doi:10.1002/pmic.201100515 · Cited by 206 · see citing works

MRM ‐based multiplexed quantitation of 67 putative cardiovascular disease biomarkers in human plasma

Domański, D., Percy, A. J., Yang, J., Chambers, A. G., Hill, J. S., Freue, G. V. C., & Borchers, C. H. (2012) · PROTEOMICS · doi:10.1002/pmic.201100568 · Cited by 205 · see citing works

Targeted Quantitative Analysis of Streptococcus pyogenes Virulence Factors by Multiple Reaction Monitoring

Lange, V., Malmström, J. A., Didion, J. P., King, N. L., Johansson, B. P., Schäfer, J., Rameseder, J., Wong, C., Deutsch, E. W., Brusniak, M., et al. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800032-mcp200 · Cited by 203 · see citing works

Measurement of Thyroglobulin by Liquid Chromatography–Tandem Mass Spectrometry in Serum and Plasma in the Presence of Antithyroglobulin Autoantibodies

Kushnir, M. M., Rockwood, A. L., Roberts, W. L., Abraham, D., Hoofnagle, A. N., & Meikle, A. W. (2013) · Clinical Chemistry · doi:10.1373/clinchem.2012.195594 · Cited by 193 · see citing works

Perturbation Biology: Inferring Signaling Networks in Cellular Systems

Molinelli, E. J., Korkut, A., Wang, W., Miller, M. L., Gauthier, N. P., Jing, X., Kaushik, P., He, Q., Mills, G. B., Solit, D. B., et al. (2013) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1003290 · Cited by 191 · see citing works

Cancer genetics-guided discovery of serum biomarker signatures for diagnosis and prognosis of prostate cancer

Cima, I., Schiess, R., Wild, P. J., Kaelin, M., Schüffler, P. J., Lange, V., Picotti, P., Ossola, R., Templeton, A. J., Schubert, O. T., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1013699108 · Cited by 190 · see citing works

Glycoproteomic Analysis of Prostate Cancer Tissues by SWATH Mass Spectrometry Discovers N-acylethanolamine Acid Amidase and Protein Tyrosine Kinase 7 as Signatures for Tumor Aggressiveness

Liu, Y., Chen, J., Sethi, A., Li, Q. K., Chen, L., Collins, B. C., Gillet, L. C. J., Wollscheid, B., Zhang, H., & Aebersold, R. H. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.038273 · Cited by 187 · see citing works

Demonstrating the feasibility of large-scale development of standardized assays to quantify human proteins

Kennedy, J. J., Abbatiello, S. E., Kim, K., Yan, P., Whiteaker, J. R., Lin, C., Kim, J. S., Zhang, Y., Wang, X., Ivey, R. G., et al. (2014) · Nature Methods · doi:10.1038/nmeth.2763 · Cited by 184 · see citing works

Interlaboratory Evaluation of Automated, Multiplexed Peptide Immunoaffinity Enrichment Coupled to Multiple Reaction Monitoring Mass Spectrometry for Quantifying Proteins in Plasma

Kuhn, E. W., Whiteaker, J. R., Mani, D. R., Jackson, A., Zhao, L., Pope, M. E., SMITH, D. S. H., Rivera, K. D., Anderson, N. L., Skates, S. J., et al. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.013854 · Cited by 183 · see citing works

Clinical Quantitation of Prostate-specific Antigen Biomarker in the Low Nanogram/Milliliter Range by Conventional Bore Liquid Chromatography-Tandem Mass Spectrometry (Multiple Reaction Monitoring) Coupling and Correlation with ELISA Tests

Fortin, T., Salvador, A., Charrier, J., Lenz, C., Lacoux, X., Morla, A., Choquet‐Kastylevsky, G., & Lemoine, J. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800238-mcp200 · Cited by 177 · see citing works

The Mtb Proteome Library: A Resource of Assays to Quantify the Complete Proteome of Mycobacterium tuberculosis

Schubert, O. T., Mouritsen, J., Ludwig, C., Röst, H. L., Rosenberger, G., Arthur, P. K., Claassen, M., Campbell, D. S., Sun, Z., Farrah, T., et al. (2013) · Cell Host & Microbe · doi:10.1016/j.chom.2013.04.008 · Cited by 173 · see citing works

Multiple Reaction Monitoring of mTRAQ-Labeled Peptides Enables Absolute Quantification of Endogenous Levels of a Potential Cancer Marker in Cancerous and Normal Endometrial Tissues

DeSouza, L. V., Taylor, A. M., Li, W., Minkoff, M. S., Romaschin, A. D., Colgan, T. J., & Siu, K. W. M. (2008) · Journal of Proteome Research · doi:10.1021/pr800312m · Cited by 172 · see citing works

Detection of Mycobacterium tuberculosis Peptides in the Exosomes of Patients with Active and Latent M. tuberculosis Infection Using MRM-MS

Kruh‐Garcia, N. A., Wolfe, L. M., Chaisson, L. H., Worodria, W. O., Nahid, P., Schorey, J. S., Davis, J. L., & Dobos, K. M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0103811 · Cited by 169 · see citing works

Mutant proteins as cancer-specific biomarkers

Wang, Q., Chaerkady, R., Wu, J., Hwang, H. J., Papadopoulos, N., Kopelovich, L., Maitra, A., Matthaei, H., Eshleman, J. R., Hruban, R. H., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1019203108 · Cited by 168 · see citing works

Diabetic nephropathy induces changes in the proteome of human urinary exosomes as revealed by label-free comparative analysis

Zubiri, I., Posada-Ayala, M., Sanz‐Maroto, A., Calvo, E., Martin‐Lorenzo, M., Gonzalez‐Calero, L., de la Cuesta, F., López, J. A., Fernández‐Fernández, B., Ortíz, A., et al. (2013) · Journal of Proteomics · doi:10.1016/j.jprot.2013.10.037 · Cited by 167 · see citing works

Quantitative analysis of amyloid β peptides in cerebrospinal fluid of Alzheimer's disease patients by immunoaffinity purification and stable isotope dilution liquid chromatography/negative electrospray ionization tandem mass spectrometry

Oe, T., Ackermann, B. L., Inoue, K., Berna, M. J., Garner, C. O., Gelfanova, V., Dean, R. A., Siemers, E., Holtzman, D. M., Farlow, M. R., et al. (2006) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.2787 · Cited by 166 · see citing works

Preparation of stable isotope-incorporated peptide internal standards for field desorption mass spectrometry quantification of peptides in biologic tissue

Desiderio, D. M., & Kai, M. (1983) · Journal of Mass Spectrometry · doi:10.1002/bms.1200100806 · Cited by 158 · see citing works

The Utility of Paradoxical Components in Biological Circuits

Hart, Y., & Alon, U. (2013) · Molecular Cell · doi:10.1016/j.molcel.2013.01.004 · Cited by 151 · see citing works

Lysine 63-linked polyubiquitination is required for EGF receptor degradation

Huang, F., Zeng, X.-M., Kim, W., Balasubramani, M., Fortian, A., Gygi, S., Yates, N., & Sorkin, A. (2013) · Proceedings of the National Academy of Sciences of the United States of America · doi:10.1073/pnas.1308014110 · Cited by 141 · see citing works

Sequential Protein and Peptide Immunoaffinity Capture for Mass Spectrometry-Based Quantification of Total Human β-Nerve Growth Factor

Neubert, H., Muirhead, D., Kabir, M., Grace, C., Cleton, A., & Arends, R. (2012) · Analytical Chemistry · doi:10.1021/ac303031q · Cited by 134 · see citing works

Targeted Quantitation of Site-Specific Cysteine Oxidation in Endogenous Proteins Using a Differential Alkylation and Multiple Reaction Monitoring Mass Spectrometry Approach

Held, J. M., Danielson, S. R., Behring, J. B., Atsriku, C., Britton, D. J., Puckett, R., Schilling, B., Campisi, J., Benz, C. C., & Gibson, B. W. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900643-mcp200 · Cited by 134 · see citing works

Protein Standard Absolute Quantification (PSAQ) for improved investigation of staphylococcal food poisoning outbreaks

Dupuis, A., Hennekinne, J., Garin, J., & Brun, V. (2008) · PROTEOMICS · doi:10.1002/pmic.200800326 · Cited by 130 · see citing works

Abacus: A computational tool for extracting and pre‐processing spectral count data for label‐free quantitative proteomic analysis

Fermin, D., Basrur, V., Yocum, A. K., & Nesvizhskii, A. I. (2011) · PROTEOMICS · doi:10.1002/pmic.201000650 · Cited by 124 · see citing works

Targeted Quantitative Proteomics for the Analysis of 14 UGT1As and -2Bs in Human Liver Using NanoUPLC–MS/MS with Selected Reaction Monitoring

Fallon, J. K., Neubert, H., Hyland, R., Goosen, T. C., & Smith, P. C. (2013) · Journal of Proteome Research · doi:10.1021/pr4004213 · Cited by 123 · see citing works

Preferentially Increased Nitration of α-Synuclein at Tyrosine-39 in a Cellular Oxidative Model of Parkinson’s Disease

Danielson, S. R., Held, J. M., Schilling, B., Oo, M. L., Gibson, B. W., & Andersen, J. K. (2009) · Analytical Chemistry · doi:10.1021/ac901176t · Cited by 123 · see citing works

Use of an Immunoaffinity-Mass Spectrometry-based Approach for the Quantification of Protein Biomarkers from Serum Samples of Lung Cancer Patients

Nicol, G. R., Han, M., Kim, J., Birse, C. E., Brand, E., Nguyen, A., Mesri, M., FitzHugh, W., Kaminker, P. G., Moore, P. A., et al. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700476-mcp200 · Cited by 115 · see citing works

Rapid empirical discovery of optimal peptides for targeted proteomics

Stergachis, A. B., MacLean, B., Lee, K., Stamatoyannopoulos, J. A., & MacCoss, M. J. (2011) · Nature Methods · doi:10.1038/nmeth.1770 · Cited by 110 · see citing works

Targeted proteomics using selected reaction monitoring reveals the induction of specific terpene synthases in a multi‐level study of methyl jasmonate‐treated Norway spruce (Picea abies)

Zulak, K. G., Lippert, D. N. D., Kuzyk, M. A., Domański, D., Chou, T., Borchers, C. H., & Bohlmann, J. (2009) · The Plant Journal · doi:10.1111/j.1365-313x.2009.04020.x · Cited by 109 · see citing works

Why Are Computational Neuroscience and Systems Biology So Separate?

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Interlaboratory Agreement of Insulin-like Growth Factor 1 Concentrations Measured by Mass Spectrometry

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Translational Targeted Proteomics Profiling of Mitochondrial Energy Metabolic Pathways in Mouse and Human Samples

Wolters, J. C., Čiapaitė, J., van Eunen, K., Niezen‐Koning, K. E., Matton, A. P. M., Porte, R. J., Horvatovich, P. L., Bakker, B. M., Bischoff, R., & Permentier, H. P. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00419 · Cited by 52 · see citing works

Hydrophilic interaction chromatography – mass spectrometry for metabolomics and proteomics: state-of-the-art and current trends

Kohler, I., Verhoeven, M., Haselberg, R., & Gargano, A. (2021) · Microchemical journal (Print) · doi:10.1016/j.microc.2021.106986 · Cited by 47 · see citing works

Advances in Biomarker Studies in Autism Spectrum Disorders

Shen, L., Zhao, Y., Zhang, H., Feng, C., Gao, Y. L., Zhao, D., Xia, S., Qi, H., Iqbal, J., Liu, X., et al. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-05542-4_11 · Cited by 48 · see citing works

Clinical translation of MS-based, quantitative plasma proteomics: status, challenges, requirements, and potential

Percy, A. J., Byrns, S., Pennington, S. R., Holmes, D. T., Anderson, N. L., Agreste, T. M., & Duffy, M. A. (2016) · Expert Review of Proteomics · doi:10.1080/14789450.2016.1205950 · Cited by 47 · see citing works

Fast proteomics with dia‐PASEF and analytical flow‐rate chromatography

Szyrwiel, Ł., Gille, C., Mülleder, M., Demichev, V., & Ralser, M. (2023) · PROTEOMICS · doi:10.1002/pmic.202300100 · Cited by 50 · see citing works

Mass spectral libraries: A statistical review of the visible use

Milman, B. L., & Журкович, И. К. (2016) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2016.04.024 · Cited by 43 · see citing works

Mass Spectrometry-Based Metabolomic and Proteomic Strategies in Organic Acidemias

Imperlini, E., Santorelli, L., Orrù, S., Scolamiero, E., Ruoppolo, M., & Caterino, M. (2016) · BioMed Research International · doi:10.1155/2016/9210408 · Cited by 39 · see citing works

Mass Spectrometry Techniques: Principles and Practices for Quantitative Proteomics

Rotello, R. J., & Veenstra, T. D. (2020) · Current Protein and Peptide Science · doi:10.2174/1389203721666200921153513 · Cited by 39 · see citing works

Proteome-based systems biology in chronic pain

Gómez‐Varela, D., Barry, A. M., & Schmidt, M. (2018) · Journal of Proteomics · doi:10.1016/j.jprot.2018.04.004 · Cited by 38 · see citing works

Identification of proteinaceous binders in paintings: A targeted proteomic approach for cultural heritage

Vinciguerra, R., Illiano, A., Chiaro, A. D., Carpentieri, A., Lluveras‐Tenorio, A., Bonaduce, I., Marino, G., Pucci, P., Amoresano, A., & Birolo, L. (2018) · Microchemical Journal · doi:10.1016/j.microc.2018.09.021 · Cited by 36 · see citing works

Towards reproducible MRM based biomarker discovery using dried blood spots

Özcan, S., Cooper, J. D., Lago, S. G., Kenny, D. T., Rustogi, N., Stocki, P., & Bahn, S. (2017) · Scientific Reports · doi:10.1038/srep45178 · Cited by 37 · see citing works

BatMass: a Java Software Platform for LC–MS Data Visualization in Proteomics and Metabolomics

Avtonomov, D. M., Raskind, A. B., & Nesvizhskii, A. I. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00021 · Cited by 37 · see citing works

Proteomic Analysis of Extracellular Vesicles for Cancer Diagnostics

Wu, A. Y., Ueda, K., & Lai, C. P. (2018) · PROTEOMICS · doi:10.1002/pmic.201800162 · Cited by 35 · see citing works

Integrative analysis of human omics data using biomolecular networks

Robinson, J. L., & Nielsen, J. (2016) · Molecular BioSystems · doi:10.1039/c6mb00476h · Cited by 32 · see citing works

Selected reaction monitoring mass spectrometry of mastitis milk reveals pathogen-specific regulation of bovine host response proteins

Kusebauch, U., Hernández-Castellano, L. E., Bislev, S. L., Moritz, R. L., Røntved, C. M., & Bendixen, E. (2018) · Journal of Dairy Science · doi:10.3168/jds.2017-14312 · Cited by 31 · see citing works

Methods for the Analysis of Protein Phosphorylation–Mediated Cellular Signaling Networks

White, F. M., & Wolf‐Yadlin, A. (2016) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-071015-041542 · Cited by 31 · see citing works

Combinatorial degradomics: Precision tools to unveil proteolytic processes in biological systems.

Savickas, S., Kastl, P., & Keller, U. A. D. (2020) · Biochimica et Biophysica Acta - Proteins and Proteomics · doi:10.1016/j.bbapap.2020.140392 · Cited by 30 · see citing works

A data‐independent acquisition (DIA) assay library for quantitation of environmental effects on the kidney proteome of Oreochromis niloticus

Root, L., Campo, A., MacNiven, L. M., Con, P., Cnaani, A., & Kültz, D. (2021) · Molecular Ecology Resources · doi:10.1111/1755-0998.13445 · Cited by 30 · see citing works

Brain Metabolic Changes in Rats following Acoustic Trauma

He, J. B., Zhu, Y., Aa, J., Smith, P. F., Ridder, D. D., Wang, G., & Zheng, Y. (2017) · Frontiers in Neuroscience · doi:10.3389/fnins.2017.00148 · Cited by 30 · see citing works

Antibody-Based Proteomics

Wingren, C. (2016) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-42316-6_11 · Cited by 29 · see citing works

Development and Multiple Validation of the Protein Multi-marker Panel for Diagnosis of Pancreatic Cancer

Kim, Y., Yeo, I., Huh, I., Kim, J., Han, D., Jang, J., & Kim, Y. (2021) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-20-3929 · Cited by 29 · see citing works

Nonlinear effects of environmental salinity on the gill transcriptome versus proteome of Oreochromis niloticus modulate epithelial cell turnover

Root, L., Campo, A., MacNiven, L. M., Con, P., Cnaani, A., & Kültz, D. (2021) · Genomics · doi:10.1016/j.ygeno.2021.07.016 · Cited by 29 · see citing works

Multiplex and accurate quantification of acute kidney injury biomarker candidates in urine using Protein Standard Absolute Quantification (PSAQ) and targeted proteomics

Gilquin, B., Louwagie, M., Jaquinod, M., Cez, A., Picard, G., Kholy, L. E., Surin, B., Garin, J., Ferro, M., Kofman, T., et al. (2016) · Talanta · doi:10.1016/j.talanta.2016.11.023 · Cited by 28 · see citing works

Proteomics of Osmoregulatory Responses in Threespine Stickleback Gills

Li, J., & Kültz, D. (2020) · Integrative and Comparative Biology · doi:10.1093/icb/icaa042 · Cited by 27 · see citing works

Omics/systems biology and cancer cachexia

Gallagher, I. J., Jacobi, C., Tardif, N., Rooyackers, O., & Fearon, K. (2016) · Seminars in Cell and Developmental Biology · doi:10.1016/j.semcdb.2015.12.022 · Cited by 27 · see citing works

Multiplexed MRM‐based assays for the quantitation of proteins in mouse plasma and heart tissue

Percy, A. J., Michaud, S. A., Jardim, A., Sinclair, N. J. T., Zhang, S., Mohammed, Y., Palmer, A. L., Hardie, D. B., Yang, J., LeBlanc, A. M., et al. (2016) · PROTEOMICS · doi:10.1002/pmic.201600097 · Cited by 27 · see citing works

Analysis of Drosophila melanogaster proteome dynamics during embryonic development by a combination of label‐free proteomics approaches

Fabre, B., Korona, D., Groen, A. J., Vowinckel, J., Gatto, L., Deery, M. J., Ralser, M., Russell, S. R. H., & Lilley, K. S. (2016) · PROTEOMICS · doi:10.1002/pmic.201500482 · Cited by 26 · see citing works

piNET: a versatile web platform for downstream analysis and visualization of proteomics data

Shamsaei, B., Chojnacki, S., Pilarczyk, M., Najafabadi, M., Niu, W., Chen, C.-M., Ross, K. E., Matlock, A. D., Muhlich, J., Chutipongtanate, S., et al. (2019) · bioRxiv · doi:10.1093/nar/gkaa436 · Cited by 27 · see citing works

Region-Resolved Quantitative Proteome Profiling Reveals Molecular Dynamics Associated With Chronic Pain in the PNS and Spinal Cord

Barry, A. M., Sondermann, J. R., Sondermann, J.-H., Gómez‐Varela, D., & Schmidt, M. (2018) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2018.00259 · Cited by 23 · see citing works

Proteomics and Population Biology in the Cardiovascular Health Study (CHS): design of a study with mentored access and active data sharing

Austin, T. R., McHugh, C., Brody, J. A., Bis, J. C., Sitlani, C. M., Bartz, T. M., Biggs, M. L., Bansal, N., Bůžková, P., Carr, S. A., et al. (2022) · European Journal of Epidemiology · doi:10.1007/s10654-022-00888-z · Cited by 25 · see citing works

Comparison of targeted proteomics approaches for detecting and quantifying proteins derived from human cancer tissues

Faktor, J., Suchá, R., Páralová, V., Liu, Y., & Bouchal, P. (2016) · PROTEOMICS · doi:10.1002/pmic.201600323 · Cited by 24 · see citing works

Advances in endometrial cancer protein biomarkers for use in the clinic

Martínez-García, E., López-Gil, C., Campoy, I., Vallvé-Juanico, J., la Rubia, E. C.-D., Cabrera, S., y Cajal, S. R., Matías‐Guiu, X., van Oostrum, J., Reventós, J., et al. (2017) · Expert Review of Proteomics · doi:10.1080/14789450.2018.1410061 · Cited by 25 · see citing works

Obtaining Complete Human Proteomes

Martínez‐Val, A., Guzmán, U. H., & Olsen, J. V. (2022) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-112921-024948 · Cited by 22 · see citing works

Multiplexed MRM-based protein quantification of putative prognostic biomarkers for chronic kidney disease progression in plasma

Makridakis, M., Kontostathi, G., Petra, E., Stroggilos, R., Lygirou, V., Filip, S. K., Duranton, F., Mischak, H., Argilés, À., Zoidakis, J., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-61496-z · Cited by 23 · see citing works

Targeted degradomics in protein terminomics and protease substrate discovery

Savickas, S., & Keller, U. A. D. (2017) · Biological Chemistry · doi:10.1515/hsz-2017-0187 · Cited by 22 · see citing works

Quantitative Mass Spectrometry-Based Proteomic Profiling for Precision Medicine in Prostate Cancer

Flores‐Morales, A., & Iglesias‐Gato, D. (2017) · Frontiers in Oncology · doi:10.3389/fonc.2017.00267 · Cited by 22 · see citing works

A Critical Review of Proteomic Studies in Gestational Diabetes Mellitus

Zhou, T., Huang, L., Wang, M., Chen, D., Chen, Z., & Jiang, S. (2020) · Journal of Diabetes Research · doi:10.1155/2020/6450352 · Cited by 22 · see citing works

Quantification of molecular heterogeneity in kidney tissue by targeted proteomics

Hoyer-Allo, K. J. R., Dittrich, S., Bartram, M. P., & Rinschen, M. M. (2018) · Journal of Proteomics · doi:10.1016/j.jprot.2018.03.001 · Cited by 22 · see citing works

A Systems Biology Approach to Reveal Putative Host-Derived Biomarkers of Periodontitis by Network Topology Characterization of MMP-REDOX/NO and Apoptosis Integrated Pathways

Zeidán‐Chuliá, F., Gürsoy, M., de Oliveira, B. H. N., Özdemir, V., Könönen, E., & Gürsoy, U. K. (2016) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2015.00102 · Cited by 21 · see citing works

Proteomics: A groundbreaking development in cancer biology

Mir, M. A., Qayoom, H., Sofi, S., & Jan, N. (2023) · Elsevier eBooks · doi:10.1016/b978-0-323-95072-5.00004-3 · Cited by 21 · see citing works

Applications of multiple reaction monitoring targeted proteomics assays in human plasma

Kontostathi, G., Makridakis, M., Zoidakis, J., & Vlahou, A. (2019) · Expert Review of Molecular Diagnostics · doi:10.1080/14737159.2019.1615448 · Cited by 21 · see citing works

Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer

Ebhardt, H. A., Root, A., Liu, Y., Gauthier, N. P., Sander, C., & Aebersold, R. H. (2018) · npj Systems Biology and Applications · doi:10.1038/s41540-018-0064-1 · Cited by 20 · see citing works

In situ synthesis of a monolithic material with multi-sized pores and its chromatographic properties for the separation of intact proteins from human plasma

Lan, D., Bai, L., Pang, X., Liu, H., Yan, H., & Guo, H. (2018) · Talanta · doi:10.1016/j.talanta.2018.10.054 · Cited by 20 · see citing works

ProtRank: bypassing the imputation of missing values in differential expression analysis of proteomic data

Medo, M., Aebersold, D. M., & Medová, M. (2019) · BMC Bioinformatics · doi:10.1186/s12859-019-3144-3 · Cited by 19 · see citing works

Proteomic studies of bone and skeletal health outcomes

Nielson, C. M., Jacobs, J., & ORWOLL, E. S. (2019) · Bone · doi:10.1016/j.bone.2019.03.032 · Cited by 19 · see citing works

Quantification of surfactant protein D (SPD) in human serum by liquid chromatography-mass spectrometry (LC-MS).

Klont, F., Pouwels, S., Bults, P., van de Merbel, N. C., ten Hacken, N. T., Horvatovich, P., & Bischoff, R. (2019) · Talanta: The International Journal of Pure and Applied Analytical Chemistry · doi:10.1016/j.talanta.2019.05.028 · Cited by 14 · see citing works

High-Throughput Large-Scale Targeted Proteomics Assays for Quantifying Pathway Proteins in Pseudomonas putida KT2440

Gao, Y., Fillmore, T., Munoz, N. M., Bentley, G. J., Johnson, C. W., Kim, J., Meadows, J. A., Zucker, J., Burnet, M., Lipton, A. K., et al. (2020) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2020.603488 · Cited by 18 · see citing works

Applications of targeted proteomics in metabolic engineering: advances and opportunities

Yunus, I. S., & Lee, T. S. (2022) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2022.102709 · Cited by 18 · see citing works

Evaluation of Peripheral Blood and Cord Blood Platelet Lysates in Isolation and Expansion of Multipotent Mesenchymal Stromal Cells

Christou, I., Mallis, P., Michalopoulos, Ε., Chatzistamatiou, T. K., Mermelekas, G., Zoidakis, J., Vlahou, A., & Stavropoulos‐Giokas, C. (2018) · Bioengineering · doi:10.3390/bioengineering5010019 · Cited by 18 · see citing works

Application of immobilized ATP to the study of NLRP inflammasomes

Liao, K., Sandall, C. F., Carlson, D. A., Ulke‐Lemée, A., Platnich, J. M., Hughes, P. F., Muruve, D. A., Haystead, T., & MacDonald, J. A. (2019) · Archives of Biochemistry and Biophysics · doi:10.1016/j.abb.2018.12.031 · Cited by 18 · see citing works

Effects of pejus and pessimum zone salinity stress on gill proteome networks and energy homeostasis in Oreochromis mossambicus

Root, L., & Kültz, D. (2023) · PROTEOMICS · doi:10.1002/pmic.202300121 · Cited by 17 · see citing works

Proteomic-based approaches to cardiac development and disease

Dorr, K. M., & Conlon, F. L. (2019) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2019.01.001 · Cited by 17 · see citing works

Mass Spectrometry Analysis of Lysine Posttranslational Modifications of Tau Protein from Alzheimer’s Disease Brain

Thomas, S. N., & Yang, A. J. (2016) · Methods in molecular biology · doi:10.1007/978-1-4939-6598-4_10 · Cited by 15 · see citing works

An Overview of Mass Spectrometry-Based Methods for Functional Proteomics

O’Neill, J. R. (2018) · Methods in molecular biology · doi:10.1007/978-1-4939-8814-3_13 · Cited by 15 · see citing works

Multiplex High-Throughput Targeted Proteomic Assay To Identify Induced Pluripotent Stem Cells

Baud, A., Wessely, F., Mazzacuva, F., McCormick, J., Camuzeaux, S., Heywood, W., Little, D., Vowles, J., Tuefferd, M., Mosaku, O., et al. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.6b04368 · Cited by 16 · see citing works

Proteomic Advances in Glial Tumors through Mass Spectrometry Approaches

Pîrlog, R., Șușman, S., Iuga, C. A., & Florian, I. Ş. (2019) · Medicina · doi:10.3390/medicina55080412 · Cited by 15 · see citing works

Assessment of Cytokine-Mediated Signaling Pathway Dysregulation in Arm Skin After CO2 Laser Therapy

Rostami‐Nejad, M., Rezaei–Tavirani, M., Zadeh-Esmaeel, M.-M., Rezaei-Tavirani, S., Akbari, Z., Esmaeili, S., & Okhovatian, F. (2019) · Journal of lasers in medical sciences · doi:10.15171/jlms.2019.42 · Cited by 14 · see citing works

Fuzzy-FishNET: a highly reproducible protein complex-based approach for feature selection in comparative proteomics

Goh, W. W. B. (2016) · BMC Medical Genomics · doi:10.1186/s12920-016-0228-z · Cited by 14 · see citing works

An extra dimension in protein tagging by quantifying universal proteotypic peptides using targeted proteomics

Vandemoortele, G., Staes, A., Gonnelli, G., Samyn, N., Sutter, D. D., Vandermarliere, E., Timmerman, E., Gevaert, K., Martens, L., & Eyckerman, S. (2016) · Scientific Reports · doi:10.1038/srep27220 · Cited by 14 · see citing works

Peptide Selection for Accurate Targeted Protein Quantification via a Dimethylation High-Resolution Mass Spectrum Strategy with a Peptide Release Kinetic Model

Chen, Q., Jiang, Y., Ren, Y., Ying, M., & Lu, B. (2020) · ACS Omega · doi:10.1021/acsomega.9b02002 · Cited by 14 · see citing works

Multiple reaction monitoring assays for large-scale quantitation of proteins from 20 mouse organs and tissues

Michaud, S. A., Pětrošová, H., Sinclair, N. J. T., Kinnear, A. L., Jackson, A., McGuire, J. C., Hardie, D. B., Bhowmick, P., Ganguly, M., Flenniken, A. M., et al. (2024) · Communications Biology · doi:10.1038/s42003-023-05687-0 · Cited by 13 · see citing works

Proteomic approaches for drug discovery against tegumentary leishmaniasis

Negrão, F. N., Eberlin, M. N., & Giorgio, S. (2017) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2017.08.089 · Cited by 13 · see citing works

Optimised plasma sample preparation and LC‐MS analysis to support large‐scale proteomic analysis of clinical trial specimens: Application to the Fenofibrate Intervention and Event Lowering in Diabetes (FIELD) trial

O’Rourke, M. B., Januszewski, A. S., SULLIVAN, D. R., Lengyel, I., Stewart, A. J., Arya, S., Ronald, C. W., Galande, S., Hardikar, A. A., Joglekar, M. V., et al. (2023) · PROTEOMICS - CLINICAL APPLICATIONS · doi:10.1002/prca.202200106 · Cited by 12 · see citing works

Microwave-Assisted Protein Digestion in a Plate Well for Facile Sampling and Rapid Digestion

Kim, H., Kim, H. S., Lee, D., Shin, D., Shin, D., Kim, J., & Kim, J. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.7b02169 · Cited by 13 · see citing works

An integrated quantitative proteomics strategy reveals the dual mechanisms of celastrol against acute inflammation

Xie, G., Zhu, L., Song, Y., Huang, W., Hu, D., & Cai, Z. (2020) · Chinese Chemical Letters · doi:10.1016/j.cclet.2020.11.064 · Cited by 12 · see citing works

Current Trends and Future Perspectives of State-of-the-Art Proteomics Technologies Applied to Cardiovascular Disease Research

Singh, S. A., Aikawa, E. R., & Aikawa, M. (2016) · Circulation Journal · doi:10.1253/circj.cj-16-0499 · Cited by 12 · see citing works

Exploring novel protein-based biomarkers for advancing breast cancer diagnosis: A review

Vellan, C. J., Islam, T., Silva, S. D., Taib, N. A. M., Prasanna, G., & Jayapalan, J. J. (2024) · Clinical Biochemistry · doi:10.1016/j.clinbiochem.2024.110776 · Cited by 11 · see citing works

Delineating protein biomarkers for gastric cancers: A catalogue of mass spectrometry-based markers and assessment of their suitability for targeted proteomics applications

Ramesh, P., Nisar, M., Neha, Ammankallu, S., Babu, S., Nandakumar, R., Abhinand, C. S., Prasad, T. S. K., Codi, J. A. K., & Raju, R. (2024) · Journal of Proteomics · doi:10.1016/j.jprot.2024.105262 · Cited by 11 · see citing works

Murine cutaneous leishmaniasis investigated by MALDI mass spectrometry imaging

Negrão, F. N., Rocha, D. F. D. O., Jaeeger, C. F., Rocha, F. J. S., Eberlin, M. N., & Giorgio, S. (2017) · Molecular BioSystems · doi:10.1039/c7mb00411g · Cited by 11 · see citing works

Proteomics and the blood–brain barrier: how recent findings help drug development

Karamanos, Y., & Pottiez, G. (2016) · Expert Review of Proteomics · doi:10.1586/14789450.2016.1143780 · Cited by 11 · see citing works

Integrated and Quantitative Proteomics of Human Tumors

Yakkioui, Y., Temel, Y., Chevet, É., & Négroni, L. (2016) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.09.034 · Cited by 11 · see citing works

Evaluation and minimization of nonspecific tryptic cleavages in proteomic sample preparation

Lin, Z., Ren, Y., Shi, Z., Zhang, K., Yang, H., Liu, S., & Hao, P. (2020) · Rapid Communications in Mass Spectrometry · doi:10.1002/rcm.8733 · Cited by 11 · see citing works

Speedy-PASEF: Analytical flow rate chromatography and trapped ion mobility for deep high-throughput proteomicsPreprint

Szyrwiel, Ł., Gille, C., Mülleder, M., Demichev, V., & Ralser, M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.02.17.528968 · Cited by 11 · see citing works

A year (2014–2015) of plants in Proteomics journal. Progress in wet and dry methodologies, moving from protein catalogs, and the view of classic plant biochemists

Sánchez‐Lucas, R., Mehta, Â., Valledor, L., Cabello‐Hurtado, F., Romero-Rodríguez, M. C., Simova‐Stoilova, L., Demir, S., Rodriguez‐de‐Francisco, L. E., Maldonado-Alconada, A. M., Jorrin‐Prieto, A. L., et al. (2015) · PROTEOMICS · doi:10.1002/pmic.201500351 · Cited by 10 · see citing works

Diagnostic and Therapeutic Application of Proteomics in Infectious Disease

Yihunie, F. B., Belete, M. A., Fentahun, G., Getachew, S., & Dubie, T. (2023) · Advances in Cell and Gene Therapy · doi:10.1155/2023/5510791 · Cited by 10 · see citing works

Utilizing ion mobility to identify isobaric post-translational modifications: resolving acrolein and propionyl lysine adducts by TIMS mass spectrometry

Gomez, J. D., Ridgeway, M. E., Park, M. A., & Fritz, K. S. (2018) · International Journal for Ion Mobility Spectrometry · doi:10.1007/s12127-018-0237-z · Cited by 10 · see citing works

Targeted proteomics by selected reaction monitoring mass spectrometry: applications to systems biology and biomarker discovery

Elschenbroich, S., & Kislinger, T. (2010) · Molecular BioSystems · doi:10.1039/c0mb00159g · Cited by 81 · see citing works

Advances in targeted proteomics and applications to biomedical research

Shi, T., Song, E., Nie, S., Rodland, K., Liu, T., Qian, W., & Smith, R. D. (2016) · PROTEOMICS · doi:10.1002/pmic.201500449 · Cited by 259 · see citing works

SRM-MS Applications in Proteomics

Hossain, M. (2020) · Springer eBooks · doi:10.1007/978-3-030-53433-2_7 · Cited by 5 · see citing works

The promise of targeted proteomics for quantitative network biology

Matsumoto, M., & Nakayama, K. I. (2018) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2018.02.014 · Cited by 14 · see citing works

Mass spectrometry‐based targeted quantitative proteomics: Achieving sensitive and reproducible detection of proteins

Boja, E. S., & Rodriguez, H. (2012) · PROTEOMICS · doi:10.1002/pmic.201100387 · Cited by 165 · see citing works