A Review on Quantitative Multiplexed Proteomics

Electrospray Ionization for Mass Spectrometry of Large Biomolecules

Fenn, J. B., Mann, M., Meng, C. K., Wong, S. F., & Whitehouse, C. M. (1989) · Science · doi:10.1126/science.2675315 · Cited by 7,634 · see citing works

An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

Eng, J. K., McCormack, A. L., & Yates, J. R. (1994) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(94)80016-2 · Cited by 6,484 · see citing works

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

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

Andromeda: A Peptide Search Engine Integrated into the MaxQuant Environment

Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., & Mann, M. (2011) · Journal of Proteome Research · doi:10.1021/pr101065j · Cited by 5,349 · 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

A statistical model for identifying proteins by tandem mass spectrometry.

Nesvizhskii, A., Keller, A., Kolker, E., & Aebersold, R. (2003) · Analytical Chemistry · doi:10.1021/ac0341261 · Cited by 4,902 · 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 · see citing works

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

Ross, P. L., Huang, Y. N., Marchese, J. N., Williamson, B., Parker, K., Hattan, S., Khainovski, N., Pillai, S., Dey, S., Daniels, S., et al. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m400129-mcp200 · Cited by 4,401 · see citing works

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

Letter to the editors

Roepstorff, P., & Fohlman, J. (1984) · Journal of Mass Spectrometry · doi:10.1002/bms.1200111109 · Cited by 2,637 · 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

Quantitative mass spectrometry in proteomics: a critical review

Bantscheff, M., Schirle, M., Sweetman, G. M. A., Rick, J. M., & Küster, B. (2007) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-007-1486-6 · Cited by 1,659 · 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

Comet: An open‐source <scp>MS</scp> / <scp>MS</scp> sequence database search tool

Eng, J. K., Jahan, T. A., & Hoopmann, M. R. (2013) · PROTEOMICS · doi:10.1002/pmic.201200439 · Cited by 1,474 · see citing works

Selected reaction monitoring for quantitative proteomics: a tutorial

Lange, V., Picotti, P., Domon, B., & Aebersold, R. H. (2008) · Molecular Systems Biology · doi:10.1038/msb.2008.61 · Cited by 1,396 · see citing works

Proteomic characterization of the human centrosome by protein correlation profiling

Andersen, J. S., Wilkinson, C. J., Mayor, T., Mortensen, P., Nigg, E. A., & Mann, M. (2003) · Nature · doi:10.1038/nature02166 · Cited by 1,319 · 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 &amp; Cellular Proteomics · doi:10.1074/mcp.o112.020131 · Cited by 1,288 · 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

Trypsin Cleaves Exclusively C-terminal to Arginine and Lysine Residues

Olsen, J. V., Ong, S., & Mann, M. (2004) · Molecular & Cellular Proteomics · doi:10.1074/mcp.t400003-mcp200 · Cited by 1,258 · 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 &amp; Cellular Proteomics · doi:10.1074/mcp.m114.044305 · Cited by 1,238 · see citing works

Protein sequencing by tandem mass spectrometry.

Hunt, D. F., Yates, J. R., Shabanowitz, J., Winston, S., & Hauer, C. (1986) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.83.17.6233 · Cited by 1,189 · see citing works

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

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

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

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

Data‐independent acquisition‐based SWATH‐MS for quantitative proteomics: a tutorial

Ludwig, C., Gillet, L. C. J., Rosenberger, G., Amon, S., Collins, B. C., & Aebersold, R. H. (2018) · Molecular Systems Biology · doi:10.15252/msb.20178126 · Cited by 999 · see citing works

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

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

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present

Bantscheff, M., Lemeer, S., Savitski, M. M., & Kuster, B. (2012) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-012-6203-4 · Cited by 801 · see citing works

A two-dimensional quadrupole ion trap mass spectrometer

Schwartz, J. C., Senko, M. W., & Syka, J. E. P. (2002) · Journal of the American Society for Mass Spectrometry · doi:10.1016/s1044-0305(02)00384-7 · Cited by 800 · see citing works

Automated approach for quantitative analysis of complex peptide mixtures from tandem mass spectra

Venable, J. D., Dong, M., Wohlschlegel, J. A., Dillin, A. G., & Yates, J. R. (2004) · Nature Methods · doi:10.1038/nmeth705 · Cited by 798 · see citing works

OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data

Röst, H. L., Rosenberger, G., Navarro, P., Gillet, L. C. J., Miladinović, S. M., Schubert, O. T., Wolski, W., Collins, B. C., Malmström, J. A., Malmström, L., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.2841 · Cited by 770 · see citing works

Missing Value Imputation Approach for Mass Spectrometry-based Metabolomics Data

Wei, R., Wang, J., Su, M., Jia, E., Chen, S., Chen, T., & Ni, Y. (2018) · Scientific Reports · doi:10.1038/s41598-017-19120-0 · Cited by 720 · see citing works

Quantification of Proteins and Metabolites by Mass Spectrometry without Isotopic Labeling or Spiked Standards

Wang, W., Zhou, H., Lin, H., Roy, S., Shaler, T. A., Hill, L. R., Norton, S. M., Kumar, P., Anderle, M., & Becker, C. H. (2003) · Analytical Chemistry · doi:10.1021/ac026468x · Cited by 654 · see citing works

Tailored excitation for Fourier transform ion cyclotron mass spectrometry

Marshall, A. G., Wang, T. C. L., & Ricca, T. L. (1985) · Journal of the American Chemical Society · doi:10.1021/ja00312a015 · Cited by 631 · see citing works

DIA-Umpire: comprehensive computational framework for data-independent acquisition proteomics

Tsou, C., Avtonomov, D. M., Larsen, B. G., Tucholska, M., Choi, H., Gingras, A., & Nesvizhskii, A. I. (2015) · Nature Methods · doi:10.1038/nmeth.3255 · Cited by 622 · 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

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

Relative Quantification of Proteins in Human Cerebrospinal Fluids by MS/MS Using 6-Plex Isobaric Tags

Dayon, L., Hainard, A., Licker, V., Turck, N., Kuhn, K., Hochstrasser, D. F., Burkhard, P. R., & Sanchez, J. (2008) · Analytical Chemistry · doi:10.1021/ac702422x · Cited by 565 · see citing works

Accounting for the Multiple Natures of Missing Values in Label-Free Quantitative Proteomics Data Sets to Compare Imputation Strategies

Lazar, C., Gatto, L., Ferro, M., Bruley, C., & Bürger, T. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b00981 · Cited by 532 · see citing works

Chromatogram libraries improve peptide detection and quantification by data independent acquisition mass spectrometry

Searle, B. C., Pino, L. K., Egertson, J. D., Ting, Y. S., Lawrence, R., MacLean, B., Villén, J., & MacCoss, M. J. (2018) · Nature Communications · doi:10.1038/s41467-018-07454-w · Cited by 508 · see citing works

Top Down proteomics: Facts and perspectives

Catherman, A. D., Skinner, O. S., & Kelleher, N. L. (2014) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2014.02.041 · Cited by 507 · see citing works

Addressing Accuracy and Precision Issues in iTRAQ Quantitation

Karp, N. A., Huber, W. K., Sadowski, P. G., Charles, P. D., Hester, S. V., & Lilley, K. S. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m900628-mcp200 · Cited by 497 · see citing works

iTRAQ Underestimation in Simple and Complex Mixtures: “The Good, the Bad and the Ugly”

Ow, S. Y., Salim, M., Noirel, J., Evans, C. A., Rehman, I., & Wright, P. C. (2009) · Journal of Proteome Research · doi:10.1021/pr900634c · Cited by 490 · see citing works

Quantitative Profiling of Proteins in Complex Mixtures Using Liquid Chromatography and Mass Spectrometry

Chelius, D., & Bondarenko, P. V. (2002) · Journal of Proteome Research · doi:10.1021/pr025517j · Cited by 426 · see citing works

Identification and Relative Quantitation of Protein Mixtures by Enzymatic Digestion Followed by Capillary Reversed-Phase Liquid Chromatography−Tandem Mass Spectrometry

Bondarenko, P. V., Chelius, D., & Shaler, T. A. (2002) · Analytical Chemistry · doi:10.1021/ac0256991 · Cited by 390 · see citing works

Defining the consequences of genetic variation on a proteome-wide scale

Chick, J. M., Munger, S. C., Simecek, P., Huttlin, E. L., Choi, K., Gatti, D. M., Raghupathy, N., Svenson, K. L., Churchill, G. A., & Gygi, S. P. (2016) · Nature · doi:10.1038/nature18270 · Cited by 361 · see citing works

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

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

The Q Exactive HF, a Benchtop Mass Spectrometer with a Pre-filter, High-performance Quadrupole and an Ultra-high-field Orbitrap Analyzer

Scheltema, R. A., Hauschild, J.-P., Lange, O., Hornburg, D., Denisov, E. V., Damoc, E., Kuehn, A., Makarov, A., & Mann, M. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.043489 · Cited by 321 · see citing works

Liquid Chromatography – Mass Spectrometry: An Introduction

ARDREY, R. E. (2003) · Analytical techniques in the sciences · doi:10.1002/0470867299 · Cited by 315 · see citing works

Preparation of Proteins and Peptides for Mass Spectrometry Analysis in a Bottom‐Up Proteomics Workflow

Gundry, R. L., White, M. Y., Murray, C. I., Kane, L. A., Fu, Q., Stanley, B. A., & Eyk, J. E. V. (2009) · Current Protocols in Molecular Biology · doi:10.1002/0471142727.mb1025s88 · Cited by 307 · see citing works

Multiplexed MS/MS for improved data-independent acquisition

Egertson, J. D., Kuehn, A., Merrihew, G. E., Bateman, N. W., MacLean, B., Ting, Y. S., Canterbury, J. D., Marsh, D. M., Kellmann, M., Zabrouskov, V., et al. (2013) · Nature Methods · doi:10.1038/nmeth.2528 · Cited by 305 · see citing works

Systematic Comparison of Label-Free, Metabolic Labeling, and Isobaric Chemical Labeling for Quantitative Proteomics on LTQ Orbitrap Velos

Li, Z., Adams, R. M., Chourey, K., Hurst, G. B., Hettich, R. L., & Pan, C. (2011) · Journal of Proteome Research · doi:10.1021/pr200748h · Cited by 302 · see citing works

Review, evaluation, and discussion of the challenges of missing value imputation for mass spectrometry-based label-free global proteomics

Webb-Robertson, B.-J. M., Wiberg, H. K., Matzke, M. M., Brown, J. N., Wang, J., McDermott, J. E., Smith, R. D., Rodland, K. D., Metz, T. O., Pounds, J. G., et al. (2015) · Journal of Proteome Research · doi:10.1021/pr501138h · Cited by 294 · see citing works

Deep Proteomics of the Xenopus laevis Egg using an mRNA-Derived Reference Database

Wühr, M., Freeman, R. M., Presler, M., Horb, M. E., Peshkin, L., Gygi, S. P., & Kirschner, M. W. (2014) · Current Biology · doi:10.1016/j.cub.2014.05.044 · Cited by 257 · see citing works

Eight-channel iTRAQ Enables Comparison of the Activity of Six Leukemogenic Tyrosine Kinases

Pierce, A., Unwin, R. D., Evans, C. A., Griffiths, S., Carney, L., Zhang, L.-Q., Jaworska, E., Lee, C.-F., Blinco, D., Okoniewski, M. J., et al. (2007) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m700251-mcp200 · Cited by 256 · see citing works

Gas-phase purification enables accurate, multiplexed proteome quantification with isobaric tagging

Wenger, C. D., Lee, M. V., Hebert, A. S., McAlister, G. C., Phanstiel, D. H., Westphall, M. S., & Coon, J. J. (2011) · Nature Methods · doi:10.1038/nmeth.1716 · Cited by 244 · see citing works

N,N-Dimethyl Leucines as Novel Isobaric Tandem Mass Tags for Quantitative Proteomics and Peptidomics

Xiang, F., Ye, H., Chen, R., Fu, Q., & Li, L. (2010) · Analytical Chemistry · doi:10.1021/ac902778d · Cited by 201 · see citing works

iTRAQ Labeling is Superior to mTRAQ for Quantitative Global Proteomics and Phosphoproteomics

Mertins, P., Udeshi, N. D., Clauser, K. R., Mani, D. R., Patel, J., Ong, S., Jaffe, J. D., & Carr, S. A. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.014423 · Cited by 191 · see citing works

Quantitative, multiplexed workflow for deep analysis of human blood plasma and biomarker discovery by mass spectrometry

Keshishian, H., Burgess, M. W., Specht, H., Wallace, L., Clauser, K. R., Gillette, M. A., & Carr, S. A. (2017) · Nature Protocols · doi:10.1038/nprot.2017.054 · Cited by 190 · see citing works

High-Resolution Enabled TMT 8-plexing

Werner, T., Becher, I., Sweetman, G. M. A., Doce, C., Savitski, M. M., & Bantscheff, M. (2012) · Analytical Chemistry · doi:10.1021/ac301553x · Cited by 189 · see citing works

Approaching complete peroxisome characterization by gas-phase fractionation

Yi, E. C., Marelli, M., Lee, H., Purvine, S. O., Aebersold, R. H., Aitchison, J. D., & Goodlett, D. R. (2002) · Electrophoresis · doi:10.1002/1522-2683(200209)23:18 · Cited by 183 · see citing works

Neutron-encoded mass signatures for multiplexed proteome quantification

Hebert, A. S., Merrill, A. E., Bailey, D. J., Still, A., Westphall, M. S., Strieter, E. R., Pagliarini, D. J., & Coon, J. J. (2013) · Nature Methods · doi:10.1038/nmeth.2378 · Cited by 179 · see citing works

Peptide Labeling with Isobaric Tags Yields Higher Identification Rates Using iTRAQ 4-Plex Compared to TMT 6-Plex and iTRAQ 8-Plex on LTQ Orbitrap

Pichler, P., Köcher, T., Holzmann, J., Mazanek, M., Taus, T., Ammerer, G., & Mechtler, K. (2010) · Analytical Chemistry · doi:10.1021/ac100890k · Cited by 175 · see citing works

Proteome-Wide Evaluation of Two Common Protein Quantification Methods

O’Connell, J. D., Paulo, J. A., O’Brien, J. J., & Gygi, S. P. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00016 · Cited by 174 · see citing works

Evaluation and Improvement of Quantification Accuracy in Isobaric Mass Tag-Based Protein Quantification Experiments

Ahrné, E., Glatter, T., Viganó, C., von Schubert, C., Nigg, E. A., & Schmidt, A. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00066 · Cited by 165 · see citing works

Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities

Lapek, J. D., Greninger, P., Morris, R. T., Amzallag, A., Pruteanu-Malinici, I., Benes, C. H., & Haas, W. (2017) · Nature Biotechnology · doi:10.1038/nbt.3955 · Cited by 159 · see citing works

A Description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) Common Data Analysis Pipeline

Rudnick, P. A., Markey, S. P., Roth, J. S., Mirokhin, Y. A., Yan, X., Tchekhovskoi, D. V., Edwards, N. J., Thangudu, R. R., Ketchum, K. A., Kinsinger, C. R., et al. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5b01091 · Cited by 154 · see citing works

High-Resolution Enabled 12-Plex DiLeu Isobaric Tags for Quantitative Proteomics

Frost, D. C., Greer, T., & Li, L. (2014) · Analytical Chemistry · doi:10.1021/ac503276z · Cited by 149 · see citing works

Accurate Multiplexed Proteomics at the MS2 Level Using the Complement Reporter Ion Cluster

Wühr, M., Haas, W., McAlister, G. C., Peshkin, L., Rad, R., Kirschner, M. W., & Gygi, S. P. (2012) · Analytical Chemistry · doi:10.1021/ac301962s · Cited by 147 · see citing works

Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry

Ludwig, C., Claassen, M., Schmidt, A., & Aebersold, R. H. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.013987 · Cited by 137 · see citing works

Data-controlled automation of liquid chromatography/tandem mass spectrometry analysis of peptide mixtures

Stahl, D. C., Swiderek, K. M., Davis, M. T., & Lee, T. D. (1996) · Journal of the American Society for Mass Spectrometry · doi:10.1016/1044-0305(96)00057-8 · Cited by 135 · see citing works

A Strategy to Combine Sample Multiplexing with Targeted Proteomics Assays for High-Throughput Protein Signature Characterization

Erickson, B. K., Rose, C. M., Braun, C. R., Erickson, A. R., Knott, J., McAlister, G. C., Wühr, M., Paulo, J. A., Everley, R. A., & Gygi, S. P. (2017) · Molecular Cell · doi:10.1016/j.molcel.2016.12.005 · Cited by 126 · see citing works

High-field asymmetric waveform ion mobility spectrometry for mass spectrometry-based proteomics

Swearingen, K. E., & Moritz, R. L. (2012) · Expert Review of Proteomics · doi:10.1586/epr.12.50 · Cited by 124 · see citing works

The Nuclear Proteome of a Vertebrate

Wühr, M., Guettler, T., Peshkin, L., McAlister, G. C., Sonnett, M., Ishihara, K., Groen, A. C., Presler, M., Erickson, B. K., Mitchison, T. J., et al. (2015) · Current Biology · doi:10.1016/j.cub.2015.08.047 · Cited by 123 · see citing works

A Novel Differential Ion Mobility Device Expands the Depth of Proteome Coverage and the Sensitivity of Multiplex Proteomic Measurements

Pfammatter, S., Bonneil, É., McManus, F. P., Prasad, S., Bailey, D. J., Belford, M. W., Dunyach, J., & Thibault, P. (2018) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir118.000862 · Cited by 123 · see citing works

Deep Profiling of Proteome and Phosphoproteome by Isobaric Labeling, Extensive Liquid Chromatography, and Mass Spectrometry

Bai, B., Tan, H., Pagala, V., High, A. A., Ichhaporia, V. P., Hendershot, L. M., & Peng, J. (2016) · Methods in enzymology on CD-ROM/Methods in enzymology · doi:10.1016/bs.mie.2016.10.007 · Cited by 119 · see citing works

NeuCode Labels for Relative Protein Quantification

Merrill, A. E., Hebert, A. S., MacGilvray, M. E., Rose, C. M., Bailey, D. J., Bradley, J. C., Wood, W. W., Masri, M. E., Westphall, M. S., Gasch, A. P., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.040287 · Cited by 111 · see citing works

Mass Spectrometry-Based Quantitative Proteomics for Dissecting Multiplexed Redox Cysteine Modifications in Nitric Oxide-Protected Cardiomyocyte Under Hypoxia

Pan, K., Chen, Y.-Y., Pu, T.-H., Chao, Y.-S., Yang, C., Bomgarden, R. D., Rogers, J. C., Meng, T., & Khoo, K. (2013) · Antioxidants and Redox Signaling · doi:10.1089/ars.2013.5326 · Cited by 97 · see citing works

EASI-tag enables accurate multiplexed and interference-free MS2-based proteome quantification

Winter, S. V., Meier, F., Wichmann, C., Cox, J., Mann, M., & Meissner, F. (2018) · Nature Methods · doi:10.1038/s41592-018-0037-8 · Cited by 97 · see citing works

Accurate, Sensitive, and Precise Multiplexed Proteomics Using the Complement Reporter Ion Cluster

Sonnett, M., Yeung, E., & Wühr, M. (2018) · Analytical Chemistry · doi:10.1021/acs.analchem.7b04713 · Cited by 91 · see citing works

Multiplexed Quantitative Proteomics for High-Throughput Comprehensive Proteome Comparisons of Human Cell Lines

Edwards, A., & Haas, W. (2015) · Methods in molecular biology · doi:10.1007/978-1-4939-3341-9_1 · Cited by 88 · see citing works

Stored waveform simultaneous mass-selective ejection/excitation for Fourier transform ion cyclotron resonance mass spectrometry

Chen, L., & Marshall, A. G. (1987) · International Journal of Mass Spectrometry and Ion Processes · doi:10.1016/0168-1176(87)80027-7 · Cited by 81 · see citing works

Peptide fractionation in proteomics approaches

Manadas, B. J., Mendes, V. M., English, J., & Dunn, M. J. (2010) · Expert Review of Proteomics · doi:10.1586/epr.10.46 · Cited by 81 · 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

Effects of MEK inhibitors GSK1120212 and PD0325901 in vivo using 10‐plex quantitative proteomics and phosphoproteomics

Paulo, J. A., McAllister, F. E., Everley, R. A., Beausoleil, S. A., Banks, A. S., & Gygi, S. P. (2014) · PROTEOMICS · doi:10.1002/pmic.201400154 · Cited by 67 · see citing works

MS1 Peptide Ion Intensity Chromatograms in MS2 (SWATH) Data Independent Acquisitions. Improving Post Acquisition Analysis of Proteomic Experiments

Rardin, M. J., Schilling, B., Cheng, L.-Y., MacLean, B., Sorensen, D. J., Sahu, A. K., MacCoss, M. J., Olga Vitek, A., & Gibson, B. W. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o115.048181 · Cited by 66 · see citing works

Methods for combining peptide intensities to estimate relative protein abundance

Carrillo, B., Yanofsky, C. M., LaBoissière, S., Nadon, R., & Kearney, R. E. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp610 · Cited by 65 · see citing works

A Framework for Intelligent Data Acquisition and Real-Time Database Searching for Shotgun Proteomics

Graumann, J., Scheltema, R. A., Zhang, Y., Cox, J., & Mann, M. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.013185 · Cited by 63 · see citing works

Defining, Comparing, and Improving iTRAQ Quantification in Mass Spectrometry Proteomics Data

Hultin‐Rosenberg, L., Forshed, J., Branca, R. M., Lehtiö, J., & Johansson, H. J. (2013) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m112.021592 · Cited by 59 · see citing works

High pH Reversed-Phase Micro-Columns for Simple, Sensitive, and Efficient Fractionation of Proteome and (TMT labeled) Phosphoproteome Digests

Ruprecht, B., Zecha, J., Zolg, D. P., & Küster, B. (2017) · Methods in molecular biology · doi:10.1007/978-1-4939-6747-6_8 · Cited by 53 · see citing works

Compositional Proteomics: Effects of Spatial Constraints on Protein Quantification Utilizing Isobaric Tags

O’Brien, J. J., O’Connell, J. D., Paulo, J. A., Thakurta, S. G., Rose, C. M., Weekes, M. P., Huttlin, E. L., & Gygi, S. P. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.7b00699 · Cited by 50 · see citing works

Evaluation of different peptide fragmentation types and mass analyzers in data‐dependent methods using an Orbitrap Fusion Lumos Tribrid mass spectrometer

Espadas, G., Borràs, E., Chiva, C., & Sabidó, E. (2017) · PROTEOMICS · doi:10.1002/pmic.201600416 · Cited by 49 · see citing works

Multiplexed proteome analysis with neutron-encoded stable isotope labeling in cells and mice

Overmyer, K. A., Tyanova, S., Hebert, A. S., Westphall, M. S., Cox, J., & Coon, J. J. (2018) · Nature Protocols · doi:10.1038/nprot.2017.121 · Cited by 48 · see citing works

A comprehensive proteomic and phosphoproteomic analysis of yeast deletion mutants of 14‐3‐3 orthologs and associated effects of rapamycin

Paulo, J. A., & Gygi, S. P. (2014) · PROTEOMICS · doi:10.1002/pmic.201400155 · Cited by 47 · see citing works

Generation of Multiple Reporter Ions from a Single Isobaric Reagent Increases Multiplexing Capacity for Quantitative Proteomics

Braun, C. R., Bird, G. H., Wühr, M., Erickson, B. K., Rad, R., Walensky, L. D., Gygi, S. P., & Haas, W. (2015) · Analytical Chemistry · doi:10.1021/acs.analchem.5b02307 · Cited by 43 · see citing works

Quantitative Proteomics Using Reductive Dimethylation for Stable Isotope Labeling

Tolonen, A. C., & Haas, W. (2014) · Journal of Visualized Experiments · doi:10.3791/51416 · Cited by 39 · see citing works

Filter Diagonalization Method-Based Mass Spectrometry for Molecular and Macromolecular Structure Analysis

Kozhinov, A. N., & Tsybin, Y. O. (2012) · Analytical Chemistry · doi:10.1021/ac203391z · Cited by 35 · see citing works

Novel method to investigate protein carbonylation by iTRAQ strategy

Palmese, A., Rosa, C. D., Chiappetta, G., Marino, G., & Amoresano, A. (2012) · Analytical and Bioanalytical Chemistry · doi:10.1007/s00216-012-6324-9 · Cited by 30 · see citing works

Index-ion Triggered MS2 Ion Quantification: A Novel Proteomics Approach for Reproducible Detection and Quantification of Targeted Proteins in Complex Mixtures

Yan, W., Luo, J., Robinson, M., Eng, J. K., Aebersold, R. H., & Ranish, J. A. (2010) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m110.005611 · Cited by 30 · see citing works

Bayesian Confidence Intervals for Multiplexed Proteomics Integrate Ion-statistics with Peptide Quantification Concordance*[S]

Peshkin, L., Gupta, M., Ryazanova, L. V., & Wühr, M. (2019) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir119.001317 · Cited by 28 · see citing works

Abundance-based Classifier for the Prediction of Mass Spectrometric Peptide Detectability Upon Enrichment (PPA)

Muntel, J., Boswell, S. A., Tang, S., Ahmed, S., Wapinski, I., Foley, G., Steen, H., & Springer, M. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m114.044321 · Cited by 26 · see citing works

Hadamard transform and "no-peak" enhancement in measurement of tandem Fourier transform mass spectra

McLafferty, F. W., Stauffer, D. B., Loh, S. Y., & Williams, E. R. (1987) · Analytical Chemistry · doi:10.1021/ac00144a044 · Cited by 24 · see citing works

A Sulfoxide‐Based Isobaric Labelling Reagent for Accurate Quantitative Mass Spectrometry

Stadlmeier, M., Bogena, J., Wallner, M., Wühr, M., & Carell, T. (2018) · Angewandte Chemie International Edition · doi:10.1002/anie.201708867 · Cited by 24 · see citing works

Efficient Microscale Basic Reverse Phase Peptide Fractionation for Global and Targeted Proteomics

Lee, H., Kim, H., & Liebler, D. C. (2016) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00102 · Cited by 18 · see citing works

Ein auf Sulfoxid basierendes, isobares Derivatisierungsreagens für die präzise quantitative Massenspektrometrie

Stadlmeier, M., Bogena, J., Wallner, M., Wühr, M., & Carell, T. (2018) · Angewandte Chemie · doi:10.1002/ange.201708867 · Cited by 2 · see citing works

Measuring biological age using omics data

Rutledge, J., Oh, H., & Wyss-Coray, T. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00511-7 · Cited by 570 · see citing works

TMTpro reagents: a set of isobaric labeling mass tags enables simultaneous proteome-wide measurements across 16 samples

Li, J., Vranken, J. G. V., Vaites, L. P., Schweppe, D. K., Huttlin, E. L., Etienne, C. L., Nandhikonda, P., Viner, R., Robitaille, A. M., Thompson, A. H., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-0781-4 · Cited by 449 · see citing works

Quantitative Mass Spectrometry-Based Proteomics: An Overview

Rozanova, S., Barkovits, K., Nikolov, M., Schmidt, C., Urlaub, H., & Marcus, K. (2021) · Methods in molecular biology · doi:10.1007/978-1-0716-1024-4_8 · Cited by 279 · see citing works

Bioinformatics Methods for Mass Spectrometry-Based Proteomics Data Analysis

Chen, C., Hou, J., Tanner, J. J., & Cheng, J. (2020) · International Journal of Molecular Sciences · doi:10.3390/ijms21082873 · Cited by 280 · see citing works

Unbiased spatial proteomics with single-cell resolution in tissues

Mund, A., Brunner, A.-D., & Mann, M. (2022) · Molecular Cell · doi:10.1016/j.molcel.2022.05.022 · Cited by 259 · see citing works

A Pragmatic Guide to Enrichment Strategies for Mass Spectrometry–Based Glycoproteomics

Riley, N. M., Bertozzi, C. R., & Pitteri, S. J. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r120.002277 · Cited by 234 · see citing works

Labeling Preferences of Diazirines with Protein Biomolecules

West, A. V., Muncipinto, G., Wu, H., Huang, A. C., Labenski, M., Jones, L. H., & Woo, C. M. (2021) · Journal of the American Chemical Society · doi:10.1021/jacs.1c02509 · Cited by 211 · see citing works

MSstatsTMT: Statistical Detection of Differentially Abundant Proteins in Experiments with Isobaric Labeling and Multiple Mixtures

Huang, T. C., Choi, M., Tzouros, M., Golling, S., Pandya, N. J., Bánfai, B., Dunkley, T. P. J., & Olga Vitek, A. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra120.002105 · Cited by 178 · see citing works

Analytical and Biochemical Perspectives of Protein O-GlcNAcylation

Ma, J., Wu, C., & Hart, G. W. (2021) · Chemical Reviews · doi:10.1021/acs.chemrev.0c00884 · Cited by 171 · see citing works

MS-Based Proteomics of Body Fluids: The End of the Beginning

Bader, J. M., Albrecht, V., & Mann, M. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2023.100577 · Cited by 171 · see citing works

Quantitative Mass Spectrometry-Based Proteomics: An Overview

Nikolov, M., Schmidt, C., & Urlaub, H. (2012) · Methods in molecular biology · doi:10.1007/978-1-61779-885-6_7 · Cited by 166 · see citing works

Omics-Driven Biotechnology for Industrial Applications

Amer, B., & Baidoo, E. E. K. (2021) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2021.613307 · Cited by 148 · see citing works

Proteomic analysis of archival breast cancer clinical specimens identifies biological subtypes with distinct survival outcomes

Asleh, K., Negri, G. L., Miko, S. E. S., Colborne, S., Hughes, C. S., Wang, X. Q., Gao, D., Gilks, C. B., Chia, S., Nielsen, T. O., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-28524-0 · Cited by 127 · see citing works

Identification and characterization of post-translational modifications: Clinical implications

Hermann, J., Schurgers, L. J., & Jankowski, V. (2022) · Molecular Aspects of Medicine · doi:10.1016/j.mam.2022.101066 · Cited by 123 · see citing works

Systems-based proteomics to resolve the biology of Alzheimer’s disease beyond amyloid and tau

Rayaprolu, S., Higginbotham, L., Bagchi, P., Watson, C. M., Zhang, T., Levey, A. I., Rangaraju, S., & Seyfried, N. T. (2021) · Neuropsychopharmacology · doi:10.1038/s41386-020-00840-3 · Cited by 118 · see citing works

Cell type-specific biotin labeling in vivo resolves regional neuronal and astrocyte proteomic differences in mouse brain

Rayaprolu, S., Bitarafan, S., Santiago, J. V., Betarbet, R. S., Sunna, S. N., Cheng, L., Xiao, H., Nelson, R. S., Kumar, P., Bagchi, P., et al. (2022) · Nature Communications · doi:10.1038/s41467-022-30623-x · Cited by 109 · see citing works

Extracellular vesicle-based liquid biopsy biomarkers and their application in precision immuno-oncology

Asleh, K., Dery, V., Taylor, C., Davey, M., Djeungoue‐Petga, M., & Ouellette, R. J. (2023) · Biomarker Research · doi:10.1186/s40364-023-00540-2 · Cited by 112 · see citing works

Recent Developments in Data Independent Acquisition (DIA) Mass Spectrometry: Application of Quantitative Analysis of the Brain Proteome

Li, K. W., Gonzalez‐Lozano, M. A., Koopmans, F., & Smit, A. B. (2020) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2020.564446 · Cited by 102 · see citing works

A guide to mass spectrometric analysis of extracellular vesicle proteins for biomarker discovery

Jalaludin, I., Lubman, D. M., & Kim, J. (2021) · Mass Spectrometry Reviews · doi:10.1002/mas.21749 · Cited by 98 · see citing works

PROTAC technology: From drug development to probe technology for target deconvolution

Yan, S., Zhang, G., Luo, W., Xu, M., Peng, R., Du, Z., Liu, Y., Bai, Z., Xiao, X., & Qin, S. (2024) · European Journal of Medicinal Chemistry · doi:10.1016/j.ejmech.2024.116725 · Cited by 92 · see citing works

Overview and Considerations in Bottom-Up Proteomics

Miller, R. M., & Smith, L. (2022) · In Analysis · doi:10.1039/d2an01246d · Cited by 60 · see citing works

Instrumentation at the leading edge of proteomics

Peters-Clarke, T. M., Coon, J., & Riley, N. (2024) · Analytical Chemistry · doi:10.1021/acs.analchem.3c04497 · Cited by 78 · see citing works

Perfluorocarbons in Chemical Biology

Miller, M. A., & Sletten, E. M. (2020) · ChemBioChem · doi:10.1002/cbic.202000297 · Cited by 81 · see citing works

Uncovering the Depths of the Human Proteome: Antibody-based Technologies for Ultrasensitive Multiplexed Protein Detection and Quantification

Ren, A. H., Diamandis, E. P., & Kulasingam, V. (2021) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2021.100155 · Cited by 79 · see citing works

Recent advances in isobaric labeling and applications in quantitative proteomics

Sivanich, M. K., Gu, T., Tabang, D. N., & Li, L. (2022) · PROTEOMICS · doi:10.1002/pmic.202100256 · Cited by 78 · see citing works

Novel insights into the emerging roles of tRNA-derived fragments in mammalian development

Guzzi, N., & Bellodi, C. (2020) · RNA Biology · doi:10.1080/15476286.2020.1732694 · Cited by 77 · see citing works

Pick-up single-cell proteomic analysis for quantifying up to 3000 proteins in a Mammalian cell

Wang, Y., Guan, Z.-Y., Shi, S.-W., Jiang, Y., Zhang, J., Yang, Y., Wu, Q., Wu, J., Chen, J., Ying, W.-X., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-45659-4 · Cited by 85 · see citing works

Deciphering the regulatory genome of Escherichia coli, one hundred promoters at a time

Ireland, W. T., Beeler, S. M., Flores‐Bautista, E., McCarty, N. S., Röschinger, T., Belliveau, N. M., Sweredoski, M. J., Moradian, A., Kinney, J. B., & Phillips, R. (2020) · eLife · doi:10.7554/elife.55308 · Cited by 73 · see citing works

Plant Proteome Dynamics

Mergner, J., & Küster, B. (2022) · Annual Review of Plant Biology · doi:10.1146/annurev-arplant-102620-031308 · Cited by 67 · see citing works

Automated proteomic sample preparation: The key component for high throughput and quantitative mass spectrometry analysis

Fu, Q., Murray, C. I., Karpov, O. A., & Eyk, J. E. V. (2021) · Mass Spectrometry Reviews · doi:10.1002/mas.21750 · Cited by 66 · see citing works

Data-independent acquisition boosts quantitative metaproteomics for deep characterization of gut microbiota

Zhao, J., Yang, Y., Xu, H., Zheng, J., Shen, C., Tian, C., Wang, T., Wang, B., Yi, J., Zhao, D., et al. (2023) · npj Biofilms and Microbiomes · doi:10.1038/s41522-023-00373-9 · Cited by 62 · see citing works

Precise Temporal Regulation of Post-transcriptional Repressors Is Required for an Orderly Drosophila Maternal-to-Zygotic Transition

Cao, W. X., Kabelitz, S., Gupta, M., Yeung, E., Lin, S., Rammelt, C., Ihling, C. H., Pekovic, F., Low, T. C. H., Siddiqui, N. U., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.107783 · Cited by 61 · see citing works

Activity-based RNA-modifying enzyme probing reveals DUS3L-mediated dihydrouridylation

Dai, W. H., Li, A., Yu, N. J., Nguyen, T., Leach, R. W., Wühr, M., & Kleiner, R. E. (2021) · Nature Chemical Biology · doi:10.1038/s41589-021-00874-8 · Cited by 58 · see citing works

A Tutorial Review of Labeling Methods in Mass Spectrometry-Based Quantitative Proteomics

Wang, Z., Liu, P.-K., & Li, L. (2024) · ACS Measurement Science Au · doi:10.1021/acsmeasuresciau.4c00007 · Cited by 57 · see citing works

High-Throughput Single-Cell Proteomic Analysis of Organ-Derived Heterogeneous Cell Populations by Nanoflow Dual-Trap Single-Column Liquid Chromatography

Kreimer, S. D., Binek, A., Chazarin, B., Cho, J. H., Haghani, A., Hutton, A., Marbán, E., Mastali, M., Meyer, J. G., Mesquita, T., et al. (2023) · Analytical Chemistry · doi:10.1021/acs.analchem.3c00213 · Cited by 53 · 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

Crossing the Halfway Point: Aptamer-Based, Highly Multiplexed Assay for the Assessment of the Proteome

Kraemer, S., Schneider, D., Paterson, C., Perry, D., Westacott, M. J., Hagar, Y., Katilius, E., Lynch, S., Russell, T. M., Johnson, T., et al. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00411 · Cited by 41 · see citing works

Chemical isotope labeling for quantitative proteomics

Tian, X., Permentier, H. P., & Bischoff, R. (2021) · Mass Spectrometry Reviews · doi:10.1002/mas.21709 · Cited by 52 · see citing works

Protein Abundance of Clinically Relevant Drug Transporters in The Human Kidneys

Oswald, S., Müller, J., Neugebauer, U., Schröter, R., Herrmann, E., Pavenstädt, H. J., & Ciarimboli, G. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20215303 · Cited by 49 · see citing works

Current trends in isotope‐coded derivatization liquid chromatographic‐mass spectrometric analyses with special emphasis on their biomedical application

El‐Maghrabey, M., Kishikawa, N., & Kuroda, N. (2019) · Biomedical Chromatography · doi:10.1002/bmc.4756 · Cited by 46 · see citing works

Photoaffinity labelling with small molecules

Homan, R. A., Lapek, J. D., Woo, C. M., Niessen, S., Jones, L. H., & Parker, C. G. (2024) · Nature Reviews Methods Primers · doi:10.1038/s43586-024-00308-4 · Cited by 52 · see citing works

Discovery of a Redox Thiol Switch: Implications for Cellular Energy Metabolism

Gao, X., Li, L., Parisien, M., Wu, J., Bederman, I. R., Gao, Z., Krokowski, D., Chirieleison, S. M., Abbott, D. W., Wang, B., et al. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra119.001910 · Cited by 45 · see citing works

Commentary on a combined approach to the problem of developing biomarkers for the prediction of spontaneous preterm labor that leads to preterm birth

Lamont, R., Richardson, L., Boniface, J. J., Cobo, T., Exner, M. M., Christensen, I. B., Forslund, S. K., Gaba, A., Helmer, H., Jørgensen, J. S., et al. (2020) · Placenta · doi:10.1016/j.placenta.2020.05.007 · Cited by 44 · see citing works

TMTpro Complementary Ion Quantification Increases Plexing and Sensitivity for Accurate Multiplexed Proteomics at the MS2 Level

Johnson, A. N. T., Stadlmeier, M., & Wühr, M. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00813 · Cited by 42 · see citing works

A Universal and High-Throughput Proteomics Sample Preparation Platform

Burns, A. P., Zhang, Y., Xu, T., Wei, Z., Yao, Q., Fang, Y., Cebotaru, V., Xia, M., Hall, M. D., Huang, R., et al. (2021) · Analytical Chemistry · doi:10.1021/acs.analchem.1c00265 · Cited by 36 · see citing works

Discovering Nature’s Fingerprints: Isotope Ratio Analysis on Bioanalytical Mass Spectrometers

Neubauer, C., Kantnerová, K., Lamothe, A., Savarino, J., Hilkert, A. W., Juchelka, D., Hinrichs, K., Elvert, M., Heuer, V. B., Elsner, M., et al. (2023) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.2c00363 · Cited by 38 · see citing works

Photoaffinity Labeling Chemistries Used to Map Biomolecular Interactions

West, A. V., & Woo, C. M. (2022) · Israel Journal of Chemistry · doi:10.1002/ijch.202200081 · Cited by 37 · see citing works

Parallelization with Dual-Trap Single-Column Configuration Maximizes Throughput of Proteomic Analysis

Kreimer, S. D., Haghani, A., Binek, A., Hauspurg, A. K., Seyedmohammad, S., Rivas, A., Momenzadeh, A., Meyer, J. G., Raedschelders, K., & Eyk, J. E. V. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c02609 · Cited by 35 · see citing works

Quantification of snake venom proteomes by mass spectrometry‐considerations and perspectives

Calvete, J. J., Lomonte, B., Saviola, A. J., Calderón‐Celis, F., & Encinar, J. R. (2023) · Mass Spectrometry Reviews · doi:10.1002/mas.21850 · Cited by 35 · see citing works

Global protein turnover quantification in Escherichia coli reveals cytoplasmic recycling under nitrogen limitation

Gupta, M., Johnson, A. N. T., Cruz, E. R., Costa, E. J., Guest, R. L., Li, H., Hart, E. M., Nguyen, T., Stadlmeier, M., Bratton, B. P., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-49920-8 · Cited by 36 · see citing works

Proteomic profiling reveals engineered chitosan nanoparticles mediated cellular crosstalk and immunomodulation for therapeutic application in apical periodontitis

Hussein, H., & Kishen, A. (2021) · Bioactive Materials · doi:10.1016/j.bioactmat.2021.09.032 · Cited by 35 · see citing works

Multi-omics approaches for deciphering the microbial modulation of plants' genetic potentials: What's known and what's next?

Doni, F., Miranti, M., Mispan, M. S., Mohamed, Z., & Uphoff, N. T. (2022) · Rhizosphere · doi:10.1016/j.rhisph.2022.100613 · Cited by 34 · see citing works

Progress and pitfalls of using isobaric mass tags for proteome profiling

Dayon, L., & Affolter, M. (2020) · Expert Review of Proteomics · doi:10.1080/14789450.2020.1731309 · Cited by 34 · see citing works

Recent advances in proteome‐wide label‐free target deconvolution for bioactive small molecules

Sun, J., Prabhu, N., Tang, J., Yang, F., Jia, L., Guo, J., Xiao, K., Tam, W. L., Nordlund, P., & Dai, L. (2021) · Medicinal Research Reviews · doi:10.1002/med.21788 · Cited by 34 · see citing works

The protein repertoire in early vertebrate embryogenesisPreprint

Peshkin, L., Lukyanov, A., Kalocsay, M., Gage, R. M., Wang, D., Pells, T. J., Karimi, K., Vize, P. D., Wühr, M., & Kirschner, M. W. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/571174 · Cited by 34 · see citing works

Ion mobility-high resolution mass spectrometry in anti-doping analysis. Part I: Implementation of a screening method with the assessment of a library of substances prohibited in sports

Plachká, K., Pezzatti, J., Musenga, A., Nicoli, R., Kuuranne, T., Rudaz, S. L., Nováková, L., & Guillarme, D. (2021) · Analytica Chimica Acta · doi:10.1016/j.aca.2021.338257 · Cited by 33 · see citing works

Proteomics and plant biology: contributions to date and a look towards the next decade

Jorrín-Novo, J. V. (2021) · Expert Review of Proteomics · doi:10.1080/14789450.2021.1910028 · Cited by 35 · see citing works

Cerebrospinal Fluid Biomarkers for Diagnosis and the Prognostication of Acute Ischemic Stroke: A Systematic Review

Naik, A., Adeleye, O., Koester, S. W., Winkler, E. A., Hartke, J. N., Karahalios, K., Mihaljević, S., Rani, A., Raikwar, S. P., Rulney, J. D., et al. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms241310902 · Cited by 32 · see citing works

Multiplex Digital Immunoassays with Reduced Pre-partition Reaction via Massively Parallel Reagent Delivery on a Bead-Based SlipChip

Lyu, W., Yi, J., Guo, Q., Wang, Y., Zhang, J., Sun, T., Ma, H., Tang, T., Quan, X., Xu, H. Y., et al. (2023) · ACS Nano · doi:10.1021/acsnano.3c03044 · Cited by 32 · see citing works

Robust proteome profiling of cysteine-reactive fragments using label-free chemoproteomics

Biggs, G. S., Cawood, E. E., Vuorinen, A., McCarthy, W. J., Wilders, H., Riziotis, I. G., van der Zouwen, A. J., Pettinger, J., Nightingale, L., Chen, P., et al. (2025) · Nature Communications · doi:10.1038/s41467-024-55057-5 · Cited by 36 · see citing works

Quantitative proteomic strategies to study reproduction in farm animals: Female reproductive fluids

Mayrhofer, C., & Brem, G. (2020) · Journal of Proteomics · doi:10.1016/j.jprot.2020.103884 · 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

Advances in stable isotope labeling: dynamic labeling for spatial and temporal proteomic analysis

Beller, N. C., & Hummon, A. B. (2022) · Molecular Omics · doi:10.1039/d2mo00077f · Cited by 29 · see citing works

Proteomic Approaches to Study Cysteine Oxidation: Applications in Neurodegenerative Diseases

Pham, T. K., Buczek, W. A., Mead, R. J., Shaw, P. J., & Collins, M. O. (2021) · Frontiers in Molecular Neuroscience · doi:10.3389/fnmol.2021.678837 · Cited by 28 · see citing works

Proteomic Applications in Aquatic Environment Studies

Gamage, N. T. G., MIYASHITA, R., Takahashi, K., Asakawa, S., & Senevirathna, J. D. M. (2022) · Proteomes · doi:10.3390/proteomes10030032 · Cited by 27 · see citing works

Proteomics: An Essential Tool to Study Plant-Specialized Metabolism

Martínez-Esteso, M. J., Morante-Carriel, J., Samper-Herrero, A., Martínez-Márquez, A., Sellés-Marchart, S., Nájera, H., & Bru-Martínez, R. (2024) · Biomolecules · doi:10.3390/biom14121539 · Cited by 17 · see citing works

Single-cell proteomics: A treasure trove in neurobiology

Goto‐Silva, L., & Junqueira, M. (2021) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2021.140658 · Cited by 27 · see citing works

29‐Plex tandem mass tag mass spectrometry enabling accurate quantification by interference correction

Sun, H., Poudel, S., Vanderwall, D., Lee, D. G., Li, Y., & Peng, J. (2022) · PROTEOMICS · doi:10.1002/pmic.202100243 · Cited by 26 · see citing works

Proximity labeling for investigating protein-protein interactions

Pfeiffer, C. T., Paulo, J. A., Gygi, S. P., & Rockman, H. A. (2022) · Methods in cell biology · doi:10.1016/bs.mcb.2021.12.006 · Cited by 26 · see citing works

Tidyproteomics: an open-source R package and data object for quantitative proteomics post analysis and visualization

Jones, J., MacKrell, E. J., Wang, T., Lomenick, B., Roukes, M. L., & Chou, T. (2023) · BMC Bioinformatics · doi:10.1186/s12859-023-05360-7 · Cited by 26 · see citing works

Comprehensive Quantitative Proteome Analysis of Aedes aegypti Identifies Proteins and Pathways Involved in Wolbachia pipientis and Zika Virus Interference Phenomenon

Martins, M. R., Ramos, L. F. C., Murillo, J. R., Torres, A., de Carvalho, S. S., Domont, G. B., de Oliveira, D. M. P., Mesquita, R. D., Nogueira, F. C. S., Maciel‐de‐Freitas, R., et al. (2021) · Frontiers in Physiology · doi:10.3389/fphys.2021.642237 · Cited by 26 · see citing works

Advances in neuroproteomics for neurotrauma: unraveling insights for personalized medicine and future prospects

Kobeissy, F. H., Goli, M., Yadikar, H., Shakkour, Z., Kurup, M., Haidar, M. A., Alroumi, S., Mondello, S., Wang, K., & Mechref, Y. S. (2023) · Frontiers in Neurology · doi:10.3389/fneur.2023.1288740 · Cited by 27 · see citing works

Fibre-specific mitochondrial protein abundance is linked to resting and post-training mitochondrial content in the muscle of men

Reisman, E. G., Botella, J., Huang, C., Schittenhelm, R. B., Stroud, D. A., Granata, C., Chandrasiri, O. S., Ramm, G., Oorschot, V. M. J., Caruana, N. J., et al. (2024) · Nature Communications · doi:10.1038/s41467-024-50632-2 · Cited by 27 · see citing works

Derivatization-based sample-multiplexing for enhancing throughput in liquid chromatography/tandem mass spectrometry quantification of metabolites: an overview

Higashi, T., & Ogawa, S. (2020) · Journal of Chromatography A · doi:10.1016/j.chroma.2020.461679 · Cited by 25 · see citing works

Photoredox-Catalyzed Decarboxylative C -Terminal Differentiation for Bulk- and Single-Molecule Proteomics

Zhang, L., Floyd, B. M., Chilamari, M., Mapes, J. P., Swaminathan, J., Bloom, S. H., Marcotte, E. M., & Anslyn, E. V. (2021) · ACS Chemical Biology · doi:10.1021/acschembio.1c00631 · Cited by 25 · see citing works

15N Metabolic Labeling Quantification Workflow in Arabidopsis Using Protein Prospector

Shrestha, R., Reyes, A. V., Baker, P. R., Wang, Z., Chalkley, R. J., & Xu, S. (2022) · Frontiers in Plant Science · doi:10.3389/fpls.2022.832562 · Cited by 25 · see citing works

Pathway‐based integration of multi‐omics data reveals lipidomics alterations validated in an Alzheimer's disease mouse model and risk loci carriers

Garcia‐Segura, M. E., Durainayagam, B. R., Liggi, S., Graça, G., Jiménez, B., Dehghan, A., Tzoulaki, I., Karaman, İ., Elliott, P., & Griffin, J. L. (2022) · Journal of Neurochemistry · doi:10.1111/jnc.15719 · Cited by 25 · see citing works

An Update on MRMAssayDB: A Comprehensive Resource for Targeted Proteomics Assays in the Community

Bhowmick, P., Roome, S., Borchers, C. H., Goodlett, D. R., & Mohammed, Y. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00961 · Cited by 27 · see citing works

Mass spectrometry methods for analysis of extracellular matrix components in neurological diseases

Downs, M. J., Zaia, J., & Sethi, M. K. (2022) · Mass Spectrometry Reviews · doi:10.1002/mas.21792 · Cited by 23 · see citing works

The ataxin-1 interactome reveals direct connection with multiple disrupted nuclear transport pathways

Zhang, S., Williamson, N. A., Duvick, L. A., Lee, A., Orr, H. T., Korlin-Downs, A., Yang, P., Mok, Y.-F., Jans, D. A., & Bogoyevitch, M. A. (2020) · Nature Communications · doi:10.1038/s41467-020-17145-0 · Cited by 23 · see citing works

Data acquisition approaches for single cell proteomics

Ghosh, G., Shannon, A. E., & Searle, B. C. (2024) · PROTEOMICS · doi:10.1002/pmic.202400022 · Cited by 23 · see citing works

Mass Spectrometric Characterization of HSV-1 L-Particles From Human Dendritic Cells and BHK21 Cells and Analysis of Their Functional Role

Birzer, A., Kraner, M., Heilingloh, C. S., Mühl-Zürbes, P., Hofmann, J., Steinkasserer, A., & Popella, L. (2020) · Frontiers in Microbiology · doi:10.3389/fmicb.2020.01997 · Cited by 22 · see citing works

Detecting Cardiovascular Protein-Protein Interactions by Proximity Proteomics

Kushner, J., Liu, G., Eisert, R. J., Bradshaw, G. A., Pitt, G. S., Hinson, J. T., Kalocsay, M., & Marx, S. O. (2022) · Circulation Research · doi:10.1161/circresaha.121.319810 · Cited by 22 · see citing works

Protein constraints in genome‐scale metabolic models: Data integration, parameter estimation, and prediction of metabolic phenotypes

Ferreira, M. A. D. M., da Silveira, W. B., & Nikoloski, Z. (2024) · Biotechnology and Bioengineering · doi:10.1002/bit.28650 · Cited by 21 · see citing works

Contemporary proteomic strategies for cysteine redoxome profiling

Willems, P., Breusegem, F. V., & Huang, J. (2020) · PLANT PHYSIOLOGY · doi:10.1093/plphys/kiaa074 · Cited by 21 · see citing works

Integrative Multi-PTM Proteomics Reveals Dynamic Global, Redox, Phosphorylation, and Acetylation Regulation in Cytokine-Treated Pancreatic Beta Cells

Gluth, A., Li, X., Gritsenko, M. A., Gaffrey, M. J., Kim, D. N., Lalli, P. M., Chu, R., Day, N. J., Sagendorf, T. J., Monroe, M. E., et al. (2024) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2024.100881 · Cited by 21 · see citing works

Integrated Analysis of Proteome and Transcriptome Profiling Reveals Pan-Cancer-Associated Pathways and Molecular Biomarkers

Hu, G.-S., Zheng, Z.-Z., He, Y.-H., Wang, D.-C., Nie, R., & Liu, W. (2025) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2025.100919 · Cited by 18 · see citing works

Comparative Analysis of Quantitative Mass Spectrometric Methods for Subcellular Proteomics

Tannous, A., Boonen, M., Zheng, H., Zhao, C., Germain, C. J., Moore, D. F., Sleat, D. E., Jadot, M., & Lobel, P. (2020) · Journal of Proteome Research · doi:10.1021/acs.jproteome.9b00862 · Cited by 20 · see citing works

IL-17A and TNF-α inhibitors induce multiple molecular changes in psoriasis

Dong, Q., Li, D., Xie, B., Hu, L. H., Huang, J., Jia, X. X., Tang, Y. L., Liu, G. H., Shen, N. N., & Yu, X. B. (2022) · Frontiers in Immunology · doi:10.3389/fimmu.2022.1015182 · Cited by 20 · see citing works

Proteomics techniques in protein biomarker discovery

Babaei, M., Kashanian, S., Lee, H., & Harding, F. J. (2024) · Quantitative Biology · doi:10.1002/qub2.35 · Cited by 18 · see citing works

Considerations for reproducible omics in aging research

Singh, P. P., & Benayoun, B. A. (2023) · Nature Aging · doi:10.1038/s43587-023-00448-4 · Cited by 18 · see citing works

Protein biomarkers for radiation injury and testing of medical countermeasure efficacy: promises, pitfalls, and future directions

Singh, V. K., Srivastava, M., & Seed, T. M. (2023) · Expert Review of Proteomics · doi:10.1080/14789450.2023.2263652 · Cited by 18 · see citing works

Protein Abundance Prediction Through Machine Learning Methods

Ferreira, M. A. D. M., Ventorim, R. Z., de Almeida, E. L. M., Silveira, S. D. A., & da Silveira, W. B. (2021) · Journal of Molecular Biology · doi:10.1016/j.jmb.2021.167267 · Cited by 18 · see citing works

Proteomic dissection of the chloroplast: Moving beyond photosynthesis

Lande, N. V., Barua, P., Gayen, D., Kumar, S., Chakraborty, S., & Chakraborty, N. (2019) · Journal of Proteomics · doi:10.1016/j.jprot.2019.103542 · Cited by 18 · see citing works

Proteomic Profiling of IgG1 Producing CHO Cells Using LC/LC-SPS-MS3: The Effects of Bioprocessing Conditions on Productivity and Product Quality

Strasser, L., Farrell, A., Ho, J. T. C., Scheffler, K., Cook, K., Pankert, P., Mowlds, P., Viner, R., Karger, B. L., & Bones, J. (2021) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2021.569045 · Cited by 17 · see citing works

Multi-omics approach to identifying isoform variants as therapeutic targets in cancer patients

Shaw, T. I., Zhao, B., Li, Y., Wang, H., Wang, L., Manley, B. J., Stewart, P. A., & Karolak, A. M. (2022) · Frontiers in Oncology · doi:10.3389/fonc.2022.1051487 · Cited by 16 · see citing works

A reflection on the improvement of Chinese hamster ovary cell-based bioprocesses through advances in proteomic techniques

Nguyen, M., & Zimmer, A. (2023) · Biotechnology Advances · doi:10.1016/j.biotechadv.2023.108141 · Cited by 17 · see citing works

Breast cancers that disseminate to bone marrow acquire aggressive phenotypes through CX43-related tumor-stroma tunnels

Sinha, S., Callow, B. W., Farfel, A. P., Roy, S., Chen, S., Masotti, M., Rajendran, S., Buschhaus, J. M., Espinoza, C. R., Luker, K. E., et al. (2024) · Journal of Clinical Investigation · doi:10.1172/jci170953 · Cited by 16 · see citing works

Liquid Chromatography-Mass Spectrometry for Clinical Metabolomics: An Overview

Furlani, I. L., Nunes, E. D. C., Canuto, G. A. B., de Macedo, A. N., & Oliveira, R. V. (2021) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-77252-9_10 · Cited by 17 · see citing works

Determining Plasma Protein Variation Parameters as a Prerequisite for Biomarker Studies—A TMT-Based LC-MSMS Proteome Investigation

Andersen, L. C., Palstrøm, N. B., Diederichsen, A., Lindholt, J., Rasmussen, L., & Beck, H. C. (2021) · Proteomes · doi:10.3390/proteomes9040047 · Cited by 20 · see citing works

Multiplexing Techniques in Quantitative Proteomics to Study Disease

Evans, A. R. (2015) · D-Scholarship@Pitt (University of Pittsburgh)

Isobaric labeling: Expanding the breadth, accuracy, depth, and diversity of sample multiplexing

Paulo, J. A. (2022) · PROTEOMICS · doi:10.1002/pmic.202200328 · Cited by 10 · see citing works

Recent advances in isobaric labeling and applications in quantitative proteomics

Sivanich, M. K., Gu, T., Tabang, D. N., & Li, L. (2022) · PROTEOMICS · doi:10.1002/pmic.202100256 · Cited by 78 · see citing works

Taming the isobaric tagging elephant in the room in quantitative proteomics

Christoforou, A., & Lilley, K. S. (2011) · Nature Methods · doi:10.1038/nmeth.1736 · Cited by 25 · see citing works

Multi-Q 2 software facilitates isobaric labeling quantitation analysis with improved accuracy and coverage

Chen, C.-T., Wang, J.-H., Cheng, C.-W., Hsu, W.-C., Ko, C.-L., Choong, W.-K., & Sung, T. (2021) · Scientific Reports · doi:10.1038/s41598-021-81740-4 · Cited by 6 · see citing works