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

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

Quantitative analysis of complex protein mixtures using isotope-coded affinity tags

Gygi, S. P., Rist, B., Gerber, S. A., Turecek, F., Gelb, M. H., & Aebersold, R. (1999) · Nature Biotechnology · doi:10.1038/13690 · Cited by 4,683 · cited 1× · see citing works

Correlation between Protein and mRNA Abundance in Yeast

Gygi, S. P., Rochon, Y., Franza, B. R., & Aebersold, R. (1999) · Molecular and Cellular Biology · doi:10.1128/mcb.19.3.1720 · Cited by 3,819 · see citing works

Tandem Mass Tags: A Novel Quantification Strategy for Comparative Analysis of Complex Protein Mixtures by MS/MS

Thompson, A., Schäfer, J., Kuhn, K., Kienle, S., Schwarz, J., Schmidt, G., Neumann, T., & Hamon, C. (2003) · Analytical Chemistry · doi:10.1021/ac0262560 · Cited by 2,386 · see citing works

Absolute quantification of proteins and phosphoproteins from cell lysates by tandem MS

Gerber, S. A., Rush, J., Stemman, O., Kirschner, M. W., & Gygi, S. P. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0832254100 · Cited by 1,733 · see citing works

FatiGO: a web tool for finding significant associations of Gene Ontology terms with groups of genes

Al‐Shahrour, F., Díaz‐Uriarte, R., & Dopazo, J. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg455 · Cited by 1,118 · see citing works

Quantitative profiling of differentiation-induced microsomal proteins using isotope-coded affinity tags and mass spectrometry

Han, D. K. M., Eng, J. K., Zhou, H., & Aebersold, R. H. (2001) · Nature Biotechnology · doi:10.1038/nbt1001-946 · Cited by 876 · see citing works

A Perfect Message

Hentze, M. W., & Kulozik, A. E. (1999) · Cell · doi:10.1016/s0092-8674(00)80542-5 · Cited by 809 · see citing works

Complementary Profiling of Gene Expression at the Transcriptome and Proteome Levels in Saccharomyces cerevisiae

Griffin, T. J., Gygi, S. P., Ideker, T. E., Rist, B., Eng, J. K., Hood, L., & Aebersold, R. H. (2002) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m200001-mcp200 · Cited by 663 · see citing works

Characterization of the yeast SWI1, SWI2, and SWI3 genes, which encode a global activator of transcription

Peterson, C. L., & Herskowitz, I. (1992) · Cell · doi:10.1016/0092-8674(92)90192-f · Cited by 601 · see citing works

Making ribosomes

Fatica, A., & Tollervey, D. W. (2002) · Current Opinion in Cell Biology · doi:10.1016/s0955-0674(02)00336-8 · Cited by 446 · see citing works

Properties of 13C-Substituted Arginine in Stable Isotope Labeling by Amino Acids in Cell Culture (SILAC)

Ong, S., Kratchmarova, I., & Mann, M. (2002) · Journal of Proteome Research · doi:10.1021/pr0255708 · Cited by 434 · see citing works

Genome-Wide Analysis of mRNAs Regulated by the Nonsense-Mediated and 5′ to 3′ mRNA Decay Pathways in Yeast

He, F., Li, X., Spatrick, P., Casillo, R., Dong, S., & Jacobson, A. (2003) · Molecular Cell · doi:10.1016/s1097-2765(03)00446-5 · Cited by 419 · see citing works

Yeast cells lacking 5'-->3' exoribonuclease 1 contain mRNA species that are poly(A) deficient and partially lack the 5' cap structure.

HSU, C. L., & Stevens, A. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.8.4826 · Cited by 374 · see citing works

A yeast gene important for protein assembly into the endoplasmic reticulum and the nucleus has homology to DnaJ, an Escherichia coli heat shock protein.

Sadler, I., Chiang, A., Kurihara, T., Rothblatt, J. A., Way, J. C., & Silver, P. A. (1989) · The Journal of Cell Biology · doi:10.1083/jcb.109.6.2665 · Cited by 287 · see citing works

Advances in quantitative proteomics via stable isotope tagging and mass spectrometry

Tao, W. A., & Aebersold, R. H. (2003) · Current Opinion in Biotechnology · doi:10.1016/s0958-1669(02)00018-6 · Cited by 262 · see citing works

Molecular Characterization of a Human DNA Kinase

Karimi‐Busheri, F., Daly, G., Robins, P., Cañas, B., Pappin, D., SGOUROS, J. G., Miller, G. G., Fakhrai, H., Davis, E. M., Beau, M. M. L., et al. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.34.24187 · Cited by 235 · see citing works

Yeast Cells Lacking 5'→3' Exoribonuclease 1 Contain mRNA Species That are Poly(A) Deficient and Partially Lack the 5' Cap Structure

HSU, C. L., & Stevens, A. (1993) · Molecular and Cellular Biology · doi:10.1128/mcb.13.8.4826-4835.1993 · Cited by 205 · see citing works

A single amino acid substitution in yeast eIF‐5A results in mRNA stabilization

Zuk, D., & Jacobson, A. (1998) · The EMBO Journal · doi:10.1093/emboj/17.10.2914 · Cited by 197 · see citing works

Pbp1p, a Factor Interacting withSaccharomyces cerevisiaePoly(A)-Binding Protein, Regulates Polyadenylation

Mangus, D. A., Amrani, N., & Jacobson, A. (1998) · Molecular and Cellular Biology · doi:10.1128/mcb.18.12.7383 · Cited by 190 · see citing works

Stable isotope-coded proteomic mass spectrometry

Goshe, M. B., & Smith, R. D. (2003) · Current Opinion in Biotechnology · doi:10.1016/s0958-1669(02)00014-9 · Cited by 175 · see citing works

A human DNA editing enzyme homologous to the Escherichia coli DnaQ/MutD protein

Höss, M., Robins, P., Naven, T. J. P., Pappin, D., SGOUROS, J. G., & Lindahl, T. L. (1999) · The EMBO Journal · doi:10.1093/emboj/18.13.3868 · Cited by 170 · see citing works

The yeast SIS1 protein, a DnaJ homolog, is required for the initiation of translation

Zhong, T., & Arndt, K. T. (1993) · Cell · doi:10.1016/0092-8674(93)90646-8 · Cited by 151 · see citing works

SAM2 encodes the second methionine S-adenosyl transferase in Saccharomyces cerevisiae: physiology and regulation of both enzymes.

Thomas, D., Rothstein, R. J., Rosenberg, N., et al. (1988) · Molecular and Cellular Biology · doi:10.1128/mcb.8.12.5132 · Cited by 138 · see citing works

REB1, a Yeast DNA-Binding Protein with Many Targets, Is Essential for Cell Growth and Bears Some Resemblance to the Oncogene myb

Ju, Q., Morrow, B. E., & Warner, J. R. (1990) · Molecular and Cellular Biology · doi:10.1128/mcb.10.10.5226 · Cited by 136 · see citing works

Nonsense-mediated mRNA decay in Saccharomyces cerevisiae

Gonzalez, C. I., Bhattacharya, A., Wang, W., & Peltz, S. W. (2001) · Gene · doi:10.1016/s0378-1119(01)00552-2 · Cited by 135 · see citing works

Fragments of the internal transcribed spacer 1 of pre-rRNA accumulate in Saccharomyces cerevisiae lacking 5'----3' exoribonuclease 1

Stevens, A., HSU, C. L., Isham, K. R., et al. (1991) · Journal of Bacteriology · doi:10.1128/jb.173.21.7024-7028.1991 · Cited by 124 · see citing works

Reproducibility of Quantitative Proteomic Analyses of Complex Biological Mixtures by Multidimensional Protein Identification Technology

Washburn, M. P., Ulaszek, R. R., & Yates, J. R. (2003) · Analytical Chemistry · doi:10.1021/ac034120b · Cited by 120 · see citing works

Bms1p, a G-domain-containing protein, associates with Rcl1p and is required for 18S rRNA biogenesis in yeast

Węgierski, T., Billy, É., Nasr, F., & Filipowicz, W. (2001) · RNA · doi:10.1017/s1355838201012079 · Cited by 118 · see citing works

Upf1p Control of Nonsense mRNA Translation Is Regulated by Nmd2p and Upf3p

Maderazo, A. B., He, F., Mangus, D. A., & Jacobson, A. (2000) · Molecular and Cellular Biology · doi:10.1128/mcb.20.13.4591-4603.2000 · Cited by 114 · see citing works

A Novel Proteomic Approach for Specific Identification of Tyrosine Kinase Substrates Using [13C]Tyrosine

Ibarrola, N., Molina, H., Iwahori, A., & Pandey, A. (2004) · Journal of Biological Chemistry · doi:10.1074/jbc.m311714200 · Cited by 105 · see citing works

Selective incorporation of isotopically labeled amino acids for identification of intact proteins on a proteome‐wide level

Martinović, S., Veenstra, T. D., Anderson, G., Paša‐Tolić, L., & Smith, R. D. (2001) · Journal of Mass Spectrometry · doi:10.1002/jms.263 · Cited by 92 · see citing works

Sec24p and Iss1p Function Interchangeably in Transport Vesicle Formation from the Endoplasmic Reticulum inSaccharomyces cerevisiae

Kurihara, T., Hamamoto, S., Gimeno, R. E., et al. (2000) · Molecular Biology of the Cell · doi:10.1091/mbc.11.3.983 · Cited by 82 · see citing works

Comparison of two-dimensional electrophoresis patterns of heat shock protein Hsp27 species in normal and cardiomyopathic hearts

Scheler, C., Li, X., Salnikow, J., Dunn, M. J., & Jungblut, P. R. (1999) · Electrophoresis · doi:10.1002/(sici)1522-2683(19991201)20:18 · Cited by 72 · see citing works

Purification and characterization of yeast RNA polymerase II general initiation factor g

Henry, N. L., Sayre, M. H., & Kornberg, R. D. (1992) · Journal of Biological Chemistry · doi:10.1016/s0021-9258(18)50103-4 · Cited by 58 · see citing works

Depth of Proteome Issues

Parker, K. C., Patterson, D. H., Williamson, B., Marchese, J., Graber, A., He, F., Jacobson, A., Juhász, P., & Martin, S. A. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m300110-mcp200 · Cited by 38 · see citing works

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

Cox, J., Hein, M. Y., Luber, C. A., Paron, I., Nagaraj, N., & Mann, M. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.031591 · Cited by 5,180 · see citing works

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

Vogel, C., & Marcotte, E. M. (2012) · Nature Reviews Genetics · doi:10.1038/nrg3185 · Cited by 4,195 · see citing works

Organoid models of human and mouse ductal pancreatic cancer

Boj, S. F., Hwang, C.-I., Baker, L. A., Chio, I. I. C., Engle, D. D., Corbo, V., Jager, M., Ponz-Sarvise, M., Tiriac, H., Spector, M. S., et al. (2015) · Cell · doi:10.1016/j.cell.2014.12.021 · Cited by 2,150 · see citing works

Correlation of mRNA and protein in complex biological samples

Maier, T., Güell, M., & Serrano, L. (2009) · FEBS Letters · doi:10.1016/j.febslet.2009.10.036 · Cited by 1,802 · 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

McAlister, G. C., Nusinow, D. P., Jedrychowski, M. P., Wühr, M., Huttlin, E. L., Erickson, B. K., Rad, R., Haas, W., & Gygi, S. P. (2014) · Analytical Chemistry · doi:10.1021/ac502040v · Cited by 1,263 · see citing works

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

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

Zhang, H., Liu, T., Zhang, Z., Payne, S. H., Zhang, B., McDermott, J. E., Zhou, J.-Y., Petyuk, V. A., Chen, L., Ray, D., et al. (2016) · Cell · doi:10.1016/j.cell.2016.05.069 · Cited by 1,029 · see citing works

Proteomics by Mass Spectrometry: Approaches, Advances, and Applications

Yates, J. R., Ruse, C. I., & Nakorchevsky, A. (2009) · Annual Review of Biomedical Engineering · doi:10.1146/annurev-bioeng-061008-124934 · Cited by 1,078 · see citing works

MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics

Ting, L., Rad, R., Gygi, S. P., & Haas, W. (2011) · Nature Methods · doi:10.1038/nmeth.1714 · Cited by 1,009 · 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

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 · see citing works

Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma

Clark, D. J., Dhanasekaran, S. M., Petralia, F., Pan, J., Song, X., Hu, Y., da Veiga Leprevost, F., Reva, B., Lih, T.-S. M., Chang, H.-Y., et al. (2019) · Cell · doi:10.1016/j.cell.2019.10.007 · Cited by 730 · see citing works

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

Widespread protein aggregation as an inherent part of aging in C. elegans

David, D. C., Ollikainen, N., Trinidad, J. C., Cary, M. P., Burlingame, A. L., & Kenyon, C. (2010) · PLoS Biology · doi:10.1371/journal.pbio.1000450 · Cited by 627 · 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

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

Analysis of Nucleolar Protein Dynamics Reveals the Nuclear Degradation of Ribosomal Proteins

Lam, Y. W., Lamond, A. I., Mann, M., & Andersen, J. S. (2007) · Current Biology · doi:10.1016/j.cub.2007.03.064 · Cited by 369 · see citing works

NRF2 Promotes Tumor Maintenance by Modulating mRNA Translation in Pancreatic Cancer

Chio, I. I. C., Jafarnejad, S. M., Ponz-Sarvise, M., Park, Y., Rivera, K., Palm, W., Wilson, J., Sangar, V., Hao, Y., Öhlund, D., et al. (2016) · Cell · doi:10.1016/j.cell.2016.06.056 · Cited by 378 · see citing works

Significance Analysis of Spectral Count Data in Label-free Shotgun Proteomics

Choi, H., Fermin, D., & Nesvizhskii, A. I. (2008) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m800203-mcp200 · Cited by 364 · see citing works

Synergistic lipid compositions for albumin receptor mediated delivery of mRNA to the liver

Miao, L., Lin, J., Huang, Y., Li, L., Delcassian, D., Ge, Y., Shi, Y., & Anderson, D. G. (2020) · Nature Communications · doi:10.1038/s41467-020-16248-y · Cited by 343 · see citing works

Proteomics of Integral Membrane ProteinsTheory and Application

Speers, A. E., & Wu, C. C. (2007) · Chemical Reviews · doi:10.1021/cr068286z · Cited by 325 · see citing works

A Review on Quantitative Multiplexed Proteomics

Pappireddi, N., Martin, L., & Wühr, M. (2019) · ChemBioChem · doi:10.1002/cbic.201800650 · Cited by 299 · see citing works

Thermal proteome profiling for interrogating protein interactions

Mateus, A., Kurzawa, N., Becher, I., Sridharan, S., Helm, D., Stein, F., Typas, A., & Savitski, M. M. (2020) · Molecular Systems Biology · doi:10.15252/msb.20199232 · Cited by 258 · see citing works

Trans-Omics: How To Reconstruct Biochemical Networks Across Multiple ‘Omic’ Layers

Yugi, K., Kubota, H., Hatano, A., & Kuroda, S. (2016) · Trends in Biotechnology · doi:10.1016/j.tibtech.2015.12.013 · Cited by 258 · see citing works

Growth control of the eukaryote cell: a systems biology study in yeast

Castrillo, J. I., Zeef, L. A., Hoyle, D. C., Zhang, N., Hayes, A., Gardner, D. C., Cornell, M. J., Petty, J., Hakes, L., Wardleworth, L., et al. (2007) · Journal of Biology · doi:10.1186/jbiol54 · Cited by 263 · see citing works

Methods for samples preparation in proteomic research

Bodzon-Kulakowska, A., Bierczynska-Krzysik, A., Dylag, T., Drabik, A., Suder, P., Noga, M., Jarzebinska, J., & Silberring, J. (2007) · Journal of Chromatography B · doi:10.1016/j.jchromb.2006.10.040 · Cited by 254 · see citing works

Derivatization for liquid chromatography-mass spectrometry

Qi, B.-L., Liu, P., Wang, Q.-Y., Cai, W.-J., Yuan, B.-F., & Feng, Y.-Q. (2014) · TrAC Trends in Analytical Chemistry · doi:10.1016/j.trac.2014.03.013 · Cited by 254 · see citing works

Identification and Quantification of Proteoforms by Mass Spectrometry

Schaffer, L. V., Millikin, R. J., Miller, R. M., Anderson, L. C., Fellers, R. T., Ge, Y., Kelleher, N. L., LeDuc, R. D., Liu, X., Payne, S. H., et al. (2019) · PROTEOMICS · doi:10.1002/pmic.201800361 · Cited by 209 · see citing works

Triplex protein quantification based on stable isotope labeling by peptide dimethylation applied to cell and tissue lysates

Boersema, P. J., Aye, T. T., van Veen, T. A. B., Heck, A. J. R., & Mohammed, S. (2008) · PROTEOMICS · doi:10.1002/pmic.200800297 · Cited by 220 · see citing works

Multibatch TMT reveals false positives, batch effects and missing values

Brenes, A., Hukelmann, J., Bensaddek, D., & Lamond, A. I. (2019) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra119.001472 · Cited by 196 · see citing works

Behavioral and Structural Responses to Chronic Cocaine Require a Feedforward Loop Involving ΔFosB and Calcium/Calmodulin-Dependent Protein Kinase II in the Nucleus Accumbens Shell

Robison, A. J., Vialou, V., Mazei-Robison, M., Feng, J., Kourrich, S., Collins, M., Wee, S., Koob, G., Turecki, G., Neve, R., et al. (2013) · The Journal of Neuroscience · doi:10.1523/jneurosci.5192-12.2013 · Cited by 190 · see citing works

Quantitative Measurement of Intact Alpha-Synuclein Proteoforms from Post-Mortem Control and Parkinson's Disease Brain Tissue by Intact Protein Mass Spectrometry

Kellie, J. F., Higgs, R. E., Ryder, J. W., Major, A., Beach, T. G., Adler, C. H., Merchant, K., & Knierman, M. D. (2014) · Scientific Reports · doi:10.1038/srep05797 · Cited by 182 · see citing works

Mass spectrometry identifies and quantifies 74 unique histone H4 isoforms in differentiating human embryonic stem cells

Phanstiel, D., Brumbaugh, J., Berggren, W. T., Conard, K., Feng, X., Levenstein, M. E., McAlister, G. C., Thomson, J. A., & Coon, J. J. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0710515105 · Cited by 166 · see citing works

A new cross-linking strategy: protein interaction reporter (PIR) technology for protein–protein interaction studies

Tang, X., & Bruce, J. E. (2010) · Molecular BioSystems · doi:10.1039/b920876c · Cited by 143 · see citing works

Identification of Protein Interactions Involved in Cellular Signaling

Westermarck, J., Ivaska, J., & Corthals, G. L. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r113.027771 · Cited by 143 · see citing works

The Revolution and Evolution of Shotgun Proteomics for Large-Scale Proteome Analysis

Yates, J. R. (2013) · Journal of the American Chemical Society · doi:10.1021/ja3094313 · Cited by 131 · see citing works

Importance of systems biology in engineering microbes for biofuel production

Mukhopadhyay, A., Redding, A. M., Rutherford, B. J., & Keasling, J. D. (2008) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2008.05.003 · Cited by 129 · see citing works

Proteome response of Phaeodactylum tricornutum , during lipid accumulation induced by nitrogen depletion

Longworth, J., Wu, D., Huete-Ortega, M., Wright, P. C., & Vaidyanathan, S. (2016) · Algal Research · doi:10.1016/j.algal.2016.06.015 · Cited by 127 · see citing works

Proteomic analysis reveals the role of synaptic vesicle cycling in sustaining the suprachiasmatic circadian clock

Deery, M. J., Maywood, E. S., Chesham, J. E., Sládek, M., Karp, N. A., Green, E. W., Charles, P. D., Reddy, A. B., Kyriacou, C. P., Lilley, K. S., et al. (2009) · Current Biology · doi:10.1016/j.cub.2009.10.024 · Cited by 125 · see citing works

Comparative proteomics analysis suggests that placental mitochondria are involved in the development of pre-eclampsia

Shi, Z., Long, W., Zhao, C., Guo, X., Shen, R., & Ding, H. (2013) · PLoS ONE · doi:10.1371/journal.pone.0064351 · Cited by 118 · see citing works

Comparative proteomic and transcriptomic profiling of the fission yeast Schizosaccharomyces pombe

Schmidt, M. W., Houseman, A., Ivanov, A. R., & Wolf, D. A. (2007) · Molecular Systems Biology · doi:10.1038/msb4100117 · Cited by 114 · see citing works

Extensive Peptide Fractionation and <i>y</i>₁ Ion-Based Interference Detection Method for Enabling Accurate Quantification by Isobaric Labeling and Mass Spectrometry

Niu, M., Cho, J.-H., Kodali, K., Pagala, V., High, A. A., Wang, H., Wu, Z., Li, Y., Bi, W., Zhang, H., et al. (2017) · Analytical Chemistry · doi:10.1021/acs.analchem.6b04415 · Cited by 118 · see citing works

Cell wall-related bionumbers and bioestimates of Saccharomyces cerevisiae and Candida albicans

Klis, F. M., de Koster, C. G., & Brul, S. (2014) · Eukaryotic Cell · doi:10.1128/ec.00250-13 · Cited by 109 · see citing works

Peptide-level Robust Ridge Regression Improves Estimation, Sensitivity, and Specificity in Data-dependent Quantitative Label-free Shotgun Proteomics

Goeminne, L. E., Gevaert, K., & Clement, L. (2016) · Molecular &amp; Cellular Proteomics · doi:10.1074/mcp.m115.055897 · Cited by 110 · see citing works

Tumour suppressor p16^INK4a – anoikis‐favouring decrease in <scp>N</scp>/<scp>O</scp>‐glycan/cell surface sialylation by down‐regulation of enzymes in sialic acid biosynthesis in tandem in a pancreatic carcinoma model

Amano, M., Eriksson, H., Manning, J. C., Detjen, K. M., André, S., Nishimura, S., Lehtiö, J., & Gabius, H. (2012) · The FEBS Journal · doi:10.1111/febs.12001 · Cited by 111 · see citing works

Absolute Quantification of Transcription Factors Reveals Principles of Gene Regulation in Erythropoiesis

Gillespie, M. A., Palii, C. G., Sanchez-Taltavull, D., Shannon, P., Longabaugh, W. J. R., Downes, D. J., Sivaraman, K., Espinoza, H. M., Hughes, J. R., Price, N. D., et al. (2020) · Molecular Cell · doi:10.1016/j.molcel.2020.03.031 · Cited by 110 · see citing works

Proteomics-Based Methods for Discovery, Quantification, and Validation of Protein–Protein Interactions

Miteva, Y. V., Budayeva, H. G., & Cristea, I. M. (2013) · Analytical Chemistry · doi:10.1021/ac3033257 · Cited by 105 · see citing works

Catch me if you can: Mass spectrometry‐based phosphoproteomics and quantification strategies

Eyrich, B., Sickmann, A., & Zahedi, R. P. (2011) · PROTEOMICS · doi:10.1002/pmic.201000489 · Cited by 104 · see citing works

A quantitative proteomic analysis of biofilm adaptation by the periodontal pathogen <i>Tannerella forsythia</i>

Pham, T. K., Roy, S., Noirel, J., Douglas, I., Wright, P. C., & Stafford, G. P. (2010) · PROTEOMICS · doi:10.1002/pmic.200900448 · Cited by 95 · see citing works

Recent advances on multidimensional liquid chromatography–mass spectrometry for proteomics: From qualitative to quantitative analysis—A review

Wu, Q., Yuan, H., Zhang, L., & Zhang, Y. (2012) · Analytica Chimica Acta · doi:10.1016/j.aca.2012.04.010 · Cited by 94 · see citing works

Capillary Electrophoresis-Electrospray Ionization-Mass Spectrometry for Quantitative Analysis of Glycans Labeled with Multiplex Carbonyl-Reactive Tandem Mass Tags

Zhong, X., Chen, Z., Snovida, S., Liu, Y., Rogers, J. C., & Li, L. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b01835 · Cited by 92 · see citing works

Decreased serum thrombospondin-1 levels in pancreatic cancer patients up to 24 months prior to clinical diagnosis: association with diabetes mellitus

Jenkinson, C., Elliott, V. L., Evans, A., Oldfield, L., Jenkins, R. E., O'Brien, D. P., Apostolidou, S., Gentry-Maharaj, A., Fourkala, E.-O., Jacobs, I. J., et al. (2016) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-0879 · Cited by 87 · see citing works

Quantitative analysis of intact apolipoproteins in human HDL by top-down differential mass spectrometry

Mazur, M. T., Cardasis, H. L., Spellman, D. S., Liaw, A., Yates, N. A., & Hendrickson, R. C. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0910776107 · Cited by 87 · see citing works

iTRAQ reveals candidate pancreatic cancer serum biomarkers: influence of obstructive jaundice on their performance

Tonack, S., Jenkinson, C., Cox, T., Elliott, V, Jenkins, R. E., Kitteringham, N. R., Greenhalf, W., Shaw, V, Michalski, C. W., Friess, H., et al. (2013) · British Journal of Cancer · doi:10.1038/bjc.2013.150 · Cited by 70 · see citing works

Decreased Laminin Expression by Human Lung Epithelial Cells and Fibroblasts Cultured in Acellular Lung Scaffolds from Aged Mice

Godin, L. M., Sandri, B. J., Wagner, D. E., Meyer, C. M., Price, A. P., Akinnola, I., Weiss, D. J., & Panoskaltsis-Mortari, A. (2016) · PLOS ONE · doi:10.1371/journal.pone.0150966 · Cited by 68 · see citing works

Label-free quantitative phosphoproteomics with novel pairwise abundance normalization reveals synergistic RAS and CIP2A signaling

Kauko, O., Laajala, T. D., Jumppanen, M., Hintsanen, P., Suni, V., Haapaniemi, P., Corthals, G., Aittokallio, T., Westermarck, J., & Imanishi, S. Y. (2015) · Scientific Reports · doi:10.1038/srep13099 · Cited by 61 · see citing works

Mass Spectrometric Analysis of Histone Proteoforms

Yuan, Z.-F., Arnaudo, A. M., & Garcia, B. A. (2014) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-071213-015959 · Cited by 64 · see citing works

Connecting metabolome and phenotype: recent advances in functional metabolomics tools for the identification of bioactive natural products

Vitale, G. A., Geibel, C., Minda, V., Wang, M., Aron, A. T., & Petras, D. (2024) · Natural Product Reports · doi:10.1039/d3np00050h · Cited by 66 · see citing works

Mass spectrometry: A platform for biomarker discovery and validation for Alzheimer's and Parkinson's diseases

Cilento, E. M., Jin, L., Stewart, T., Shi, M., Sheng, L., & Zhang, J. (2019) · Journal of Neurochemistry · doi:10.1111/jnc.14635 · Cited by 60 · see citing works

A perspective on proteomics in cell biology

Ahmad, Y., & Lamond, A. I. (2014) · Trends in Cell Biology · doi:10.1016/j.tcb.2013.10.010 · Cited by 54 · see citing works

Proteomic analysis of microglial contribution to mouse strain-dependent dopaminergic neurotoxicity

McLaughlin, P., Zhou, Y., Ma, T., Liu, J., Zhang, W., Hong, J., Kovacs, M., & Zhang, J. (2006) · Glia · doi:10.1002/glia.20294 · Cited by 55 · see citing works

Improved Proteomics-Based Drug Mechanism-of-Action Studies Using 16-Plex Isobaric Mass Tags

Zinn, N., Werner, T., Doce, C., Mathieson, T., Boecker, C., Sweetman, G., Fufezan, C., & Bantscheff, M. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00900 · Cited by 49 · see citing works

Mixed-effects statistical model for comparative LC–MS proteomics studies

Daly, D. S., Anderson, K. K., Panisko, E. A., Purvine, S. O., Fang, R., Monroe, M. E., & Baker, S. E. (2008) · Journal of Proteome Research · doi:10.1021/pr070441i · Cited by 50 · see citing works

A Review of Imputation Strategies for Isobaric Labeling-Based Shotgun Proteomics

Bramer, L. M., Irvahn, J., Piehowski, P. D., Rodland, K. D., & Webb-Robertson, B.-J. M. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00123 · Cited by 47 · see citing works

Comparison of two label-free global quantitation methods, APEX and 2D gel electrophoresis, applied to the Shigella dysenteriae proteome

Kuntumalla, S., Braisted, J. C., Huang, S.-T., Parmar, P. P., Clark, D. J., Alami, H., Zhang, Q., Donohue-Rolfe, A., Tzipori, S., Fleischmann, R. D., et al. (2009) · Proteome Science · doi:10.1186/1477-5956-7-22 · Cited by 35 · see citing works

Analysis of the Hippocampal Proteome in ME7 Prion Disease Reveals a Predominant Astrocytic Signature and Highlights the Brain-restricted Production of Clusterin in Chronic Neurodegeneration

Asuni, A. A., Gray, B., Bailey, J., Skipp, P., Perry, V. H., & O'Connor, V. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.502690 · Cited by 31 · see citing works

Accurate Determination of Peptide Phosphorylation Stoichiometry Via Automated Diagonal Capillary Electrophoresis Coupled with Mass Spectrometry: Proof of Principle

Mou, S., Sun, L., & Dovichi, N. J. (2013) · Analytical Chemistry · doi:10.1021/ac402858a · Cited by 22 · see citing works

iTRAQ-Based Quantitative Proteomic Analysis of Spirulina platensis in Response to Low Temperature Stress

Li, Q., Chang, R., Sun, Y., & Li, B. (2016) · PLOS ONE · doi:10.1371/journal.pone.0166876 · Cited by 19 · see citing works

Proteomic Analysis Reveals Dab2 Mediated Receptor Endocytosis Promotes Liver Sinusoidal Endothelial Cell Dedifferentiation

Lao, Y., Li, Y., Hou, Y., Chen, H., Qiu, B., Lin, W., Sun, A., Wei, H., Jiang, Y., & He, F. (2017) · Scientific Reports · doi:10.1038/s41598-017-13917-9 · Cited by 5 · see citing works

Increased N,N-Dimethyl Leucine Isobaric Tag Multiplexing by a Combined Precursor Isotopic Labeling and Isobaric Tagging Approach

Frost, D. C., Rust, C. J., Robinson, R. A. S., & Li, L. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.8b01301 · Cited by 40 · see citing works

Differential quantification of isobaric phosphopeptides using data-independent acquisition mass spectrometry

Sidoli, S., Fujiwara, R., Kulej, K., & Garcia, B. A. (2016) · Molecular BioSystems · doi:10.1039/c6mb00385k · Cited by 11 · see citing works

Mass Defect-Based Pseudo-Isobaric Dimethyl Labeling for Proteome Quantification

Zhou, Y., Shan, Y., Wu, Q., Zhang, S., Zhang, L., & Zhang, Y. (2013) · Analytical Chemistry · doi:10.1021/ac402834w · Cited by 44 · see citing works

Protein labeling by iTRAQ: A new tool for quantitative mass spectrometry in proteome research

Wiese, S., Reidegeld, K. A., Meyer, H. E., & Warscheid, B. (2006) · PROTEOMICS · doi:10.1002/pmic.200600422 · Cited by 803 · see citing works

In Vivo Termini Amino Acid Labeling for Quantitative Proteomics

Nie, A., Zhang, L., Yan, G., Yao, J., Zhang, Y., Lu, H., Yang, P., & He, F. (2011) · Analytical Chemistry · doi:10.1021/ac201035f · Cited by 25 · see citing works