Systematic detection of functional proteoform groups from bottom-up proteomic datasets
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Abstract
To a large extent functional diversity in cells is achieved by the expansion of molecular complexity beyond that of the coding genome. Various processes create multiple distinct but related proteins per coding gene – so-called proteoforms – that expand the functional capacity of a cell. Evaluating proteoforms from classical bottom-up proteomics datasets, where peptides instead of intact proteoforms are measured, has remained difficult. Here we present COPF, a tool for COrrelation-based functional ProteoForm assessment in bottom-up proteomics data. It leverages the concept of peptide correlation analysis to systematically assign peptides to co-varying proteoform groups. We show applications of COPF to protein complex co-fractionation data as well as to more typical protein abundance vs. sample data matrices, demonstrating the systematic detection of assembly- and tissue-specific proteoform groups, respectively, in either dataset. We envision that the presented approach lays the foundation for a systematic assessment of proteoforms and their functional implications directly from bottom-up proteomic datasets.
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Cites
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nature Protocols · doi:10.1038/nprot.2008.211 · Cited by 35,890 · see citing works
Huang, D. W., Sherman, B. T., & Lempicki, R. A. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkn923 · Cited by 14,108 · see citing works
UniProt: a worldwide hub of protein knowledge
The UniProt Consortium (2019) · Nucleic Acids Research · doi:10.1093/nar/gky1049 · Cited by 7,698 · see citing works
Mass spectrometry-based proteomics
Aebersold, R., & Mann, M. (2003) · Nature · doi:10.1038/nature01511 · Cited by 6,955 · see citing works
Self-citationPérez-Riverol, Y., Csordas, A., Bai, J.-W., Bernal-Llinares, M., Hewapathirana, S., Kundu, D. J., Inuganti, A., Griss, J., Mayer, G., Eisenacher, M., et al. (2018) · Nucleic Acids Res. · doi:10.1093/nar/gky1106 · Cited by 6,216 · see citing works
Finishing the euchromatic sequence of the human genome
International Human Genome Sequencing Consortium (2004) · Nature · doi:10.1038/nature03001 · Cited by 4,971 · see citing works
Skyline: an open source document editor for creating and analyzing targeted proteomics experiments
MacLean, B., Tomazela, D. M., Shulman, N., Chambers, M., Finney, G. L., Frewen, B., Kern, R., Tabb, D. L., Liebler, D. C., & MacCoss, M. J. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq054 · Cited by 4,697 · see citing works
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
Self-citationMass-spectrometric exploration of proteome structure and function
Aebersold, R., & Mann, M. (2016) · Nature · doi:10.1038/nature19949 · Cited by 2,334 · see citing works
Self-citationA draft map of the human proteome
Kim, M.-S., Pinto, S. M., Getnet, D., Nirujogi, R. S., Manda, S. S., Chaerkady, R., Madugundu, A. K., Kelkar, D. S., Isserlin, R., Jain, S., et al. (2014) · Nature · doi:10.1038/nature13302 · Cited by 2,198 · see citing works
Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R
Langfelder, P., Zhang, B., & Horvath, S. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btm563 · Cited by 1,892 · see citing works
Mass-spectrometry-based draft of the human proteome
Wilhelm, M., Schlegl, J., Hahne, H., Gholami, A. M., Lieberenz, M., Savitski, M. M., Ziegler, E., Butzmann, L., Gessulat, S., Marx, H., et al. (2014) · Nature · doi:10.1038/nature13319 · Cited by 1,820 · see citing works
Single-cell RNA sequencing technologies and bioinformatics pipelines
Hwang, B., Lee, J. H., & Bang, D. (2018) · Experimental & Molecular Medicine · doi:10.1038/s12276-018-0071-8 · Cited by 1,793 · see citing works
Proteoform: a single term describing protein complexity
The Consortium for Top Down Proteomics, Smith, L. M., & Kelleher, N. L. (2013) · Nature Methods · doi:10.1038/nmeth.2369 · Cited by 1,528 · see citing works
Function of alternative splicing
Stamm, S., Ben‐Ari, S., Rafalska, I., Tang, Y., Zhang, Z., Toiber, D., Thanaraj, T. A., & Soreq, H. (2004) · Gene · doi:10.1016/j.gene.2004.10.022 · Cited by 1,373 · see citing works
Alternative splicing as a regulator of development and tissue identity
Baralle, F. E., & Giudice, J. (2017) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2017.27 · Cited by 1,333 · see citing works
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
Interpretation of Shotgun Proteomic Data
Nesvizhskii, A. I., & Aebersold, R. (2005) · Molecular & Cellular Proteomics · doi:10.1074/mcp.r500012-mcp200 · Cited by 1,025 · see citing works
Self-citationHow many human proteoforms are there?
Aebersold, R., Agar, J. N., Amster, I. J., Baker, M. S., Bertozzi, C. R., Boja, E. S., Costello, C. E., Cravatt, B. F., Fenselau, C., Garcia, B. A., et al. (2018) · Nature Chemical Biology · doi:10.1038/nchembio.2576 · Cited by 907 · see citing works
Self-citationdiaPASEF: parallel accumulation–serial fragmentation combined with data-independent acquisition
Meier, F., Brunner, A., Frank, M., Ha, A., Bludau, I., Voytik, E., Kaspar‐Schoenefeld, S., Lubeck, M., Raether, O., Bache, N., et al. (2020) · Nature Methods · doi:10.1038/s41592-020-00998-0 · Cited by 902 · see citing works
Self-citationThe Skyline ecosystem: Informatics for quantitative mass spectrometry proteomics
Pino, L. K., Searle, B. C., Bollinger, J. G., Nunn, B. L., MacLean, B., & MacCoss, M. J. (2017) · Mass Spectrometry Reviews · doi:10.1002/mas.21540 · Cited by 786 · see citing works
Proteogenomics: concepts, applications and computational strategies
Nesvizhskii, A. I. (2014) · Nature Methods · doi:10.1038/nmeth.3144 · Cited by 763 · see citing works
A deep proteome and transcriptome abundance atlas of 29 healthy human tissues
Wang, D., Eraslan, B., Wieland, T., Hallström, B., Hopf, T., Zolg, D. P., Zecha, J., Asplund, A., Li, L., Meng, C., et al. (2019) · Molecular Systems Biology · doi:10.15252/msb.20188503 · Cited by 750 · see citing works
Function of alternative splicing
Kelemen, O., Convertini, P., Zhang, Z., Wen, Y., Shen, M., Falaleeva, M., & Stamm, S. (2013) · Gene · doi:10.1016/j.gene.2012.07.083 · Cited by 743 · 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 741 · see citing works
Self-citationThe nuclear pore complex: understanding its function through structural insight
Beck, M., & Hurt, E. (2016) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm.2016.147 · Cited by 680 · see citing works
Mapping intact protein isoforms in discovery mode using top-down proteomics
Tran, J. C., Zamdborg, L., Ahlf, D. R., Lee, J. E., Catherman, A. D., Durbin, K. R., Tipton, J. D., Vellaichamy, A., Kellie, J. F., Li, M., et al. (2011) · Nature · doi:10.1038/nature10575 · Cited by 665 · see citing works
Use of an oriented peptide library to determine the optimal substrates of protein kinases
Songyang, Z., Blechner, S., Hoagland, N., Hoekstra, M. F., Piwnica-Worms, H. M., & Cantley, L. C. (1994) · Current Biology · doi:10.1016/s0960-9822(00)00221-9 · Cited by 654 · see citing works
Spotlight on protein N-terminal acetylation
Ree, R., Varland, S., & Arnesen, T. (2018) · Experimental & Molecular Medicine · doi:10.1038/s12276-018-0116-z · Cited by 648 · 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
Collins, B. C., Hunter, C. L., Liu, Y., Schilling, B., Rosenberger, G., Bader, S. L., Chan, D. W., Gibson, B. W., Gingras, A.-C., Held, J. M., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-00249-5 · Cited by 576 · see citing works
Self-citationBruderer, R., Bernhardt, O. M., Gandhi, T., Xuan, Y., Sondermann, J. R., Schmidt, M., Gómez‐Varela, D., & Reiter, L. (2017) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra117.000314 · Cited by 479 · see citing works
Substrates for p34cdc2: In vivo veritas?
Moreno, S., & Nurse, P. (1990) · Cell · doi:10.1016/0092-8674(90)90463-o · Cited by 476 · see citing works
Bekker‐Jensen, D. B., Martínez‐Val, A., Steigerwald, S., Rüther, P. L., Fort, K. L., Arrey, T. N., Harder, A., Makarov, A., & Olsen, J. V. (2020) · Molecular & Cellular Proteomics · doi:10.1074/mcp.tir119.001906 · Cited by 409 · see citing works
Phenotypic consequences of 1,000 generations of selection at elevated CO2 in a green alga
Collins, S., & Bell, G. (2004) · Nature · doi:10.1038/nature02945 · Cited by 394 · see citing works
Alternative Splicing May Not Be the Key to Proteome Complexity
Tress, M. L., Abascal, F., & Valencia, A. (2016) · Trends in Biochemical Sciences · doi:10.1016/j.tibs.2016.08.008 · Cited by 341 · see citing works
Proteomic and interactomic insights into the molecular basis of cell functional diversity
Bludau, I., & Aebersold, R. (2020) · Nature Reviews Molecular Cell Biology · doi:10.1038/s41580-020-0231-2 · Cited by 297 · see citing works
Self-citationFontoura, B. M. A., Blobel, G., & Matunis, M. J. (1999) · The Journal of Cell Biology · doi:10.1083/jcb.144.6.1097 · Cited by 267 · see citing works
RNA-Seq and human complex diseases: recent accomplishments and future perspectives
Costa, V., Aprile, M., Esposito, R., & Ciccodicola, A. (2012) · European Journal of Human Genetics · doi:10.1038/ejhg.2012.129 · Cited by 266 · see citing works
Region and cell-type resolved quantitative proteomic map of the human heart
Doll, S., Dreßen, M., Geyer, P. E., Itzhak, D. N., Braun, C., Doppler, S. A., Meier, F., Deutsch, M.-A., Lahm, H., Lange, R., et al. (2017) · Nature Communications · doi:10.1038/s41467-017-01747-2 · Cited by 265 · see citing works
Cellular substrates of p34cdc2 and its companion cyclin-dependent kinases
Nigg, E. A. (1993) · Trends in Cell Biology · doi:10.1016/0962-8924(93)90011-o · Cited by 234 · 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
Rosenberger, G., Bludau, I., Schmitt, U., Heusel, M., Hunter, C. L., Liu, Y., MacCoss, M. J., MacLean, B. X., Nesvizhskii, A. I., Pedrioli, P. G. A., et al. (2017) · Nature Methods · doi:10.1038/nmeth.4398 · Cited by 203 · see citing works
Self-citationA splice variant of human Bmal1 acts as a negative regulator of the molecular circadian clock
Lee, J., Park, E., Kim, G. H., Kwon, I., & Kim, K. (2018) · Experimental & Molecular Medicine · doi:10.1038/s12276-018-0187-x · Cited by 200 · see citing works
Role of Nucleoporin Induction in Releasing an mRNA Nuclear Export Block
Enninga, J., Levy, D. E., Blobel, G., & Fontoura, B. M. A. (2002) · Science · doi:10.1126/science.1067861 · Cited by 196 · see citing works
Goloborodko, A. A., Levitsky, L. I., Ivanov, M. V., & Gorshkov, M. V. (2013) · Journal of the American Society for Mass Spectrometry · doi:10.1007/s13361-012-0516-6 · Cited by 184 · see citing works
Ting, Y. S., Egertson, J. D., Payne, S. H., Kim, S., MacLean, B., Käll, L., Aebersold, R., Smith, R. D., Noble, W. S., & MacCoss, M. J. (2015) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o114.047035 · Cited by 175 · see citing works
Self-citationPyteomics 4.0: Five Years of Development of a Python Proteomics Framework
Levitsky, L. I., Klein, J., Ivanov, M. V., & Gorshkov, M. V. (2018) · Journal of Proteome Research · doi:10.1021/acs.jproteome.8b00717 · Cited by 174 · see citing works
Alexander, J., Lim, D., Joughin, B. A., Hegemann, B., Hutchins, J. R. A., Ehrenberger, T., Ivins, F. J., Sessa, F., Hudecz, O., Nigg, E. A., et al. (2011) · Science Signaling · doi:10.1126/scisignal.2001796 · Cited by 174 · see citing works
An Introduction to Ecological Genomics
van Straalen, N. M., & Roelofs, D. (2011) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199594689.001.0001 · Cited by 168 · see citing works
Characterization of the Histone H1-binding Protein, NASP, as a Cell Cycle-regulated Somatic Protein
Richardson, R. T., Batova, I. N., Widgren, E. E., Zheng, L.-X., Whitfield, M. L., Marzluff, W. F., & O’Rand, M. G. (2000) · Journal of Biological Chemistry · doi:10.1074/jbc.m003781200 · Cited by 154 · see citing works
Complex‐centric proteome profiling by SEC‐SWATH‐MS
Heusel, M., Bludau, I., Rosenberger, G., Hafen, R., Frank, M., Banaei‐Esfahani, A., van Drogen, A., Collins, B. C., Gstaiger, M., & Aebersold, R. (2019) · Molecular Systems Biology · doi:10.15252/msb.20188438 · Cited by 141 · see citing works
Self-citationIdentification of substrates for cyclin dependent kinases
Errico, A., Deshmukh, K., Tanaka, Y., Pozniakovsky, A., & Hunt, T. (2010) · Advances in Enzyme Regulation · doi:10.1016/j.advenzreg.2009.12.001 · Cited by 128 · see citing works
Autoproteolysis in nucleoporin biogenesis
Rosenblum, J. S., & Blobel, G. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.20.11370 · Cited by 124 · see citing works
Hodel, A. E., Hodel, M. R., Griffis, E. R., Hennig, K. A., Ratner, G. A., Xu, S., & Powers, M. A. (2002) · Molecular Cell · doi:10.1016/s1097-2765(02)00589-0 · Cited by 123 · see citing works
Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS
Rosenberger, G., Liu, Y., Röst, H. L., Ludwig, C., Buil, A., Bensimon, A., Soste, M., Spector, T. D., Dermitzakis, E. T., Collins, B. C., et al. (2017) · Nature Biotechnology · doi:10.1038/nbt.3908 · Cited by 121 · see citing works
Self-citationWhat we know about TMEM106B in neurodegeneration
Nicholson, A. M., & Rademakers, R. (2016) · Acta Neuropathologica · doi:10.1007/s00401-016-1610-9 · Cited by 107 · see citing works
Characterization and in Vivo Functional Analysis of Splice Variants of Cypher
Huang, C., Zhou, Q., Liang, P., Hollander, M. S., Sheikh, F., Li, X., Greaser, M., Shelton, G. D., Evans, S., & Chen, J. (2003) · Journal of Biological Chemistry · doi:10.1074/jbc.m211875200 · Cited by 105 · see citing works
Sheynkman, G., Shortreed, M. R., Cesnik, A. J., & Smith, L. M. (2016) · Annual Review of Analytical Chemistry · doi:10.1146/annurev-anchem-071015-041722 · Cited by 99 · see citing works
Anderson, L. C., DeHart, C. J., Kaiser, N. K., Fellers, R. T., Smith, D. F., Greer, J. B., LeDuc, R. D., Blakney, G. T., Thomas, P. M., Kelleher, N. L., et al. (2017) · Journal of Proteome Research · doi:10.1021/acs.jproteome.6b00696 · Cited by 94 · see citing works
Kawabe, H., Hata, Y., Takeuchi, M., Ide, N., Mizoguchi, A., & Takai, Y. (1999) · Journal of Biological Chemistry · doi:10.1074/jbc.274.43.30914 · Cited by 88 · see citing works
Splicing heterogeneity: separating signal from noise
Wan, Y., & Larson, D. R. (2018) · Genome biology · doi:10.1186/s13059-018-1467-4 · Cited by 79 · see citing works
Alternative splicing and muscular dystrophy
Pistoni, M., Ghigna, C., & Gabellini, D. (2010) · RNA Biology · doi:10.4161/rna.7.4.12258 · Cited by 78 · see citing works
A Global Screen for Assembly State Changes of the Mitotic Proteome by SEC-SWATH-MS
Heusel, M., Frank, M., Köhler, M., Amon, S., Frommelt, F., Rosenberger, G., Bludau, I., Aulakh, S. K., Linder, M. I., Liu, Y., et al. (2020) · Cell Systems · doi:10.1016/j.cels.2020.01.001 · Cited by 72 · see citing works
Self-citationImpaired Dendritic Development and Memory inSorbs2Knock-Out Mice
Zhang, Q., Gao, X., Li, C., Feliciano, C., Wang, D., Zhou, D., Yuan, M., Monteiro, P., Anand, M., Itohara, S., et al. (2016) · Journal of Neuroscience · doi:10.1523/jneurosci.2528-15.2016 · Cited by 71 · see citing works
Covariation of Peptide Abundances Accurately Reflects Protein Concentration Differences
Zhang, B., Pirmoradian, M., Zubarev, R., & Käll, L. (2017) · Molecular & Cellular Proteomics · doi:10.1074/mcp.o117.067728 · Cited by 68 · see citing works
Gu, Z. C., & Enenkel, C. (2014) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-014-1699-8 · Cited by 66 · see citing works
Bludau, I., Heusel, M., Frank, M., Rosenberger, G. A., Hafen, R., Banaei‐Esfahani, A., van Drogen, A., Collins, B. C., Gstaiger, M., & Aebersold, R. (2019) · Nature Protocols · doi:10.1038/s41596-020-0332-6 · Cited by 65 · see citing works
Self-citationQuantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population
Williams, E. G., Wu, Y., Wolski, W., Kim, J. Y., Lan, J., Hasan, M., Halter, C., Jha, P., Ryu, D., Auwerx, J. H., et al. (2018) · Molecular & Cellular Proteomics · doi:10.1074/mcp.ra118.000554 · Cited by 50 · see citing works
Self-citationBrady, O. A., Zhou, X., & Hu, F. (2014) · Journal of Biological Chemistry · doi:10.1074/jbc.m113.515700 · Cited by 48 · see citing works
Peptide Correlation Analysis (PeCorA) Reveals Differential Proteoform Regulation
Dermit, M., Peters-Clarke, T. M., Shishkova, E., & Meyer, J. G. (2021) · Journal of Proteome Research · doi:10.1021/acs.jproteome.0c00602 · Cited by 40 · see citing works
Bayesian Proteoform Modeling Improves Protein Quantification of Global Proteomic Measurements
Webb‐Robertson, B., Matzke, M. M., Datta, S., Payne, S., Kang, J., Bramer, L., Nicora, C., Shukla, A. K., Metz, T., Rodland, K., et al. (2014) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m113.030932 · Cited by 39 · see citing works
Forshed, J., Johansson, H. J., Pernemalm, M., Branca, R. M. M., Sandberg, A., & Lehtiö, J. (2011) · Molecular & Cellular Proteomics · doi:10.1074/mcp.m111.010264 · Cited by 32 · see citing works
Deducing the presence of proteins and proteoforms in quantitative proteomics
Bamberger, C., Martínez‐Bartolomé, S., Montgomery, M., Pankow, S., Hulleman, J. D., Kelly, J. W., & Yates, J. R. (2018) · Nature Communications · doi:10.1038/s41467-018-04411-5 · Cited by 30 · see citing works
Meier, F., Brunner, A., Frank, M., Ha, A., Bludau, I., Voytik, E., Kaspar‐Schoenefeld, S., Lubeck, M., Raether, O., Aebersold, R. H., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/656207 · Cited by 27 · see citing works
Self-citationProtein Inference Using Peptide Quantification Patterns
Lukasse, P., & America, A. H. P. (2014) · Journal of Proteome Research · doi:10.1021/pr401072g · Cited by 13 · see citing works
nArgBP2-SAPAP-SHANK, the core postsynaptic triad associated with psychiatric disorders
Lee, S., Kim, J. A., & Chang, S. (2018) · Experimental & Molecular Medicine · doi:10.1038/s12276-017-0018-5 · Cited by 12 · see citing works
Domain‐specific CD 6 monoclonal antibodies identify CD 6 isoforms generated by alternative‐splicing
Santos, R. F., Oliveira, L., Brown, M. H., & Carmo, A. M. (2019) · Immunology · doi:10.1111/imm.13087 · Cited by 12 · see citing works
Karayel, Ö., Şanal, E., Giese, S. H., Kagıalı, Z. C. Ü., Polat, A. N., Hu, C., Renard, B. Y., Tunçbağ, N., & Özlü, N. (2018) · Scientific Reports · doi:10.1038/s41598-018-20231-5 · Cited by 9 · see citing works
ibludau/ProteoformAnanlysis: COPF analysis
Ibludau (2021) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.4762046 · Cited by 1 · see citing works
CCprofiler/CCprofiler: CCprofiler - COPF release
Ibludau, Frank, M., Hafen, R., Heuselm, Schmitt, U., Lee, C. H., & Cai, Y. (2021) · Zenodo (CERN European Organization for Nuclear Research) · doi:10.5281/zenodo.4761980 · Cited by 1 · see citing works
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An Introduction to Mass Spectrometry-Based Proteomics
Shuken, S. R. (2023) · Journal of Proteome Research · doi:10.1021/acs.jproteome.2c00838 · Cited by 225 · see citing works
Comprehensive Overview of Bottom-Up Proteomics Using Mass Spectrometry
Jiang, Y., Balaya, R. D. A., Schuster, D., Neely, B. A., Rosano, G. L., Volkmar, N., Momenzadeh, A., Peters-Clarke, T. M., Egbert, S., Kreimer, S. D., et al. (2024) · ACS Measurement Science Au · doi:10.1021/acsmeasuresciau.3c00068 · Cited by 200 · see citing works
Analysis and Visualization of Quantitative Proteomics Data Using FragPipe-Analyst
Hsiao, Y., Zhang, H., Li, G. X., Deng, Y., Yu, F., Kahrood, H. V., Steele, J. R., Schittenhelm, R. B., & Nesvizhskii, A. I. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00294 · Cited by 152 · see citing works
Protein complexes in cells by AI‐assisted structural proteomics
(2023) · doi:10.15252/msb.202311544 · Cited by 147 · see citing works
Plubell, D. L., Käll, L., Webb-Robertson, B.-J., Bramer, L. M., Ives, A., Kelleher, N. L., Smith, L. M., Montine, T. J., Wu, C. C., & MacCoss, M. J. (2022) · Journal of Proteome Research · doi:10.1021/acs.jproteome.1c00894 · Cited by 85 · see citing works
Accurate Label-Free Quantification by directLFQ to Compare Unlimited Numbers of Proteomes
Ammar, C., Schessner, J. P., Willems, S., Michaelis, A. C., & Mann, M. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2023.100581 · Cited by 64 · see citing works
Ferdosi, S., Stukalov, A., Hasan, M., Tangeysh, B., Brown, T. R., Wang, T., Elgierari, E. M., Zhao, X., Huang, Y., Alavi, A., et al. (2022) · Advanced Materials · doi:10.1002/adma.202206008 · Cited by 61 · see citing works
Skinnider, M. A., & Foster, L. J. (2021) · Nature Methods · doi:10.1038/s41592-021-01194-4 · Cited by 57 · see citing works
Deep thermal profiling for detection of functional proteoform groups
Kurzawa, N., Leo, I. R., Stahl, M. M. S., Kunold, E., Becher, I., Audrey, A., Mermelekas, G., Huber, W. K., Mateus, A., Savitski, M. M., et al. (2023) · Nature Chemical Biology · doi:10.1038/s41589-023-01284-8 · Cited by 45 · see citing works
InstaNovo enables diffusion-powered de novo peptide sequencing in large-scale proteomics experiments
Eloff, K., Kalogeropoulos, K., Mabona, A., Morell, O., Catzel, R., Rivera‐de‐Torre, E., Jespersen, J. B., Williams, W., van Beljouw, S. P. B., Skwark, M. J., et al. (2025) · Nature Machine Intelligence · doi:10.1038/s42256-025-01019-5 · Cited by 47 · see citing works
Zemaitis, K. J., Veličković, D., Kew, W. R., Fort, K. L., Reinhardt-Szyba, M., Pamreddy, A., Ding, Y., Kaushik, D., Sharma, K., Makarov, A., et al. (2022) · Analytical Chemistry · doi:10.1021/acs.analchem.2c01034 · Cited by 33 · see citing works
Thermal proteome profiling: Insights into protein modifications, associations, and functions.
Sueur, C. L., Hammarén, H. M., Sridharan, S., & Savitski, M. (2022) · Current Opinion in Chemical Biology · doi:10.1016/j.cbpa.2022.102225 · Cited by 31 · see citing works
Systematic identification of structure-specific protein–protein interactions
(2024) · doi:10.1038/s44320-024-00037-6 · Cited by 34 · see citing works
Self-citationProteoforms expand the world of microproteins and short open reading frame-encoded peptides
Cassidy, L., Kaulich, P. T., & Tholey, A. (2023) · iScience · doi:10.1016/j.isci.2023.106069 · Cited by 32 · see citing works
Liao, Y., Fulcher, J. M., Degnan, D. J., Williams, S. M., Bramer, L., Veličković, D., Zemaitis, K. J., Veličković, M., Sontag, R. L., Moore, R. J., et al. (2023) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2022.100491 · Cited by 29 · see citing works
Rapid Profiling of Protein Complex Reorganization in Perturbed Systems
Bludau, I., Nicod, C., Martelli, C., Xue, P., Heusel, M., Fossati, A., Uliana, F., Frommelt, F., Aebersold, R., & Collins, B. C. (2021) · bioRxiv · doi:10.1021/acs.jproteome.3c00125 · Cited by 26 · see citing works
Self-citationCoorssen, J. R., & Padula, M. P. (2024) · Proteomes · doi:10.3390/proteomes12020014 · Cited by 27 · see citing works
Defining proteoform-specific interactions for drug targeting in a native cell signalling environment
Lutomski, C. A., Bennett, J. L., El‐Baba, T. J., Wu, D., Hinkle, J. D., Burnap, S. A., Liko, I., Mullen, C., Syka, J. E. P., Struwe, W. B., et al. (2025) · Nature Chemistry · doi:10.1038/s41557-024-01711-w · Cited by 29 · see citing works
Proteoform medicine: characterizing and targeting protein forms in human disease
Korchak, J. A., Yi, S. S., Kelleher, N. L., Sahni, N., & Sheynkman, G. (2026) · Nature Reviews Genetics · doi:10.1038/s41576-025-00915-1 · Cited by 25 · see citing works
Donovan, M. K. R., Huang, Y., Blume, J. E., Wang, J., Hornburg, D., Ferdosi, S., Mohtashemi, I., Kim, S., Ko, M., Benz, R. W., et al. (2023) · PLoS ONE · doi:10.1371/journal.pone.0282821 · Cited by 21 · see citing works
Eloff, K., Kalogeropoulos, K., Morell, O., Mabona, A., Jespersen, J. B., Williams, W., van Beljouw, S. P. B., Skwark, M. J., Laustsen, A. H., Brouns, S. J. J., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.08.30.555055 · Cited by 24 · see citing works
Uncovering hidden protein modifications with native top-down mass spectrometry
Bennett, J. L., El‐Baba, T. J., Zouboulis, K., Kirschbaum, C., Song, H., Butroid, F. I., Benesch, J. L. P., Lutomski, C. A., & Robinson, C. V. (2025) · Nature Methods · doi:10.1038/s41592-025-02846-5 · Cited by 26 · see citing works
Schär, S., Raess, L., Malinovska, L., Savickas, S., Cavallo, F., Below, C., Tognetti, M., Shichkova, P., Gourdet, B., Robles, G., et al. (2025) · Analytical Chemistry · doi:10.1021/acs.analchem.5c03829 · Cited by 21 · see citing works
Tian, J., Xing, B., Li, M., Xu, C., Huo, Y., & Guo, S. (2022) · International Journal of Molecular Sciences · doi:10.3390/ijms23094853 · Cited by 20 · see citing works
Top‐Down Proteomics: Why and When?
Kaulich, P. T., & Tholey, A. (2025) · Proteomics · doi:10.1002/pmic.202400338 · Cited by 19 · see citing works
Gallo, M. C. R., Li, Q., Mehta, D., & Uhrig, R. (2022) · BMC Plant Biology · doi:10.1186/s12870-022-03870-9 · Cited by 17 · see citing works
Chowdhury, T., Cupp-Sutton, K. A., Guo, Y., Gao, K., Zhao, Z.-T., Burgett, A. W. G., & Wu, S. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00778 · Cited by 18 · see citing works
Pauper, M., Hentschel, A., Tiburcy, M., Beltrán, S., Ruck, T., Schara, U., & Roos, A. (2025) · Biomolecules · doi:10.3390/biom15010130 · Cited by 17 · see citing works
Larréché, S., Bousquet, A., Chevillard, L., Gahoual, R., Jourdi, G., Dupart, A.-L., Bachelot‐Loza, C., Gaussem, P., Siguret, V., Chippaux, J., et al. (2023) · Toxins · doi:10.3390/toxins15100614 · Cited by 15 · see citing works
Zolotovskaia, M., Kovalenko, M. A., Pugacheva, P. A., Tkachev, V., Simonov, A., Sorokin, M., Seryakov, A. P., Garazha, A., Гайфуллин, Н., Sekacheva, M. I., et al. (2023) · Proteomes · doi:10.3390/proteomes11030026 · Cited by 14 · see citing works
A peptidoform based proteomic strategy for studying functions of post‐translational modifications
Liu, Y. (2021) · PROTEOMICS · doi:10.1002/pmic.202100316 · Cited by 12 · see citing works
Strategies for mass spectrometry-based phosphoproteomics using isobaric tagging
Liu, X., Fields, R., Schweppe, D. K., & Paulo, J. A. (2021) · Expert Review of Proteomics · doi:10.1080/14789450.2021.1994390 · Cited by 11 · see citing works
Jamwal, S., Jena, M., Tyagi, N., Kancharla, S., Kolli, P., Mandadapu, G., Kumar, S., & Mohanty, A. (2023) · Journal of Developmental Biology · doi:10.3390/jdb12010002 · Cited by 10 · see citing works
Alternative proteoforms and proteoform-dependent assemblies in humans and plants
McWhite, C. D., Sae-Lee, W., Yuan, Y., Mallam, A. L., Gort-Freitas, N. A., Ramundo, S., Onishi, M., & Marcotte, E. M. (2024) · Molecular Systems Biology · doi:10.1038/s44320-024-00048-3 · Cited by 10 · see citing works
Molecular probes for cellular imaging of post-translational proteoforms
Suraritdechachai, S., Lakkanasirorat, B., & Uttamapinant, C. (2022) · RSC Chemical Biology · doi:10.1039/d1cb00190f · Cited by 9 · see citing works
A Database of Accurate Electrophoretic Migration Patterns for Human Proteins
Mylonas, R., Potts, A., Waridel, P., Barblan, J., Rubio, M. D. C. C., Widmann, C., & Quadroni, M. (2022) · Journal of Molecular Biology · doi:10.1016/j.jmb.2022.167933 · Cited by 6 · see citing works
Yu, H.-Y., Tai, Q., Yang, C.-J., Gao, M.-X., & Zhang, X.-M. (2023) · Journal of Chromatography A · doi:10.1016/j.chroma.2023.464048 · Cited by 7 · see citing works
Comprehensive Overview of Bottom-up Proteomics using Mass SpectrometryPreprint
Jiang, Y., Rex, D. A. B., Schuster, D., Neely, B. A., Rosano, G. L., Volkmar, N., Momenzadeh, A., Peters-Clarke, T. M., Egbert, S., Kreimer, S. D., et al. (2023) · PubMed · doi:10.48550/arxiv.2311.07791 · Cited by 8 · see citing works
Tree-based quantification infers proteoform regulation in bottom-up proteomics dataPreprint
Ammar, C., Thielert, M., Weiss, C. A. M., Rodriguez, E., Strauss, M. T., Rosenberger, F., Zeng, W.-F., & Mann, M. (2025) · bioRxiv · doi:10.1101/2025.03.06.641844 · Cited by 5 · see citing works
Functional proteoform group deconvolution reveals a broader spectrum of ibrutinib off-targets
Leo, I. R., Kunold, E., Audrey, A., Tampere, M., Eirich, J., Lehtiö, J., & Jafari, R. (2025) · Nature Communications · doi:10.1038/s41467-024-54654-8 · Cited by 6 · see citing works
Evolution of Protein Functional Annotation: Text Mining Study
Ilgisonis, E. V., Pogodin, P. V., Kiseleva, O. I., Tarbeeva, S. N., & Ponomarenko, E. A. (2022) · Journal of Personalized Medicine · doi:10.3390/jpm12030479 · Cited by 6 · see citing works
Hornburg, D., Ferdosi, S., Hasan, M., Tangeysh, B., Brown, T. R., Wang, T., Elgierari, E. M., Zhao, X., Alavi, A., Chu, J., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.01.08.475439 · Cited by 6 · see citing works
Doron-Mandel, E., Bokor, B. J., Ma, Y.-Z., Street, L., Tang, L. C., Abdou, A. A., Shah, N. H., Rosenberger, G. A., & Jovanovic, M. (2025) · Nature Communications · doi:10.1038/s41467-025-56303-0 · Cited by 4 · see citing works
Self-citationMembrane Protein Glycosylation Revisited: Functional Dynamics and Emerging Clinical Insights
Kim, K. D., & Yoo, B. C. (2026) · International Journal of Molecular Sciences · doi:10.3390/ijms27083575 · Cited by 4 · see citing works
Recent advances in proteomic-based diagnostics of cystic fibrosis
Nimer, R. M., & Rahman, A. M. A. (2023) · Expert Review of Proteomics · doi:10.1080/14789450.2023.2258282 · Cited by 4 · see citing works
Ergin, E. K., Myung, J. J. K., & Lange, P. F. (2024) · Journal of Proteome Research · doi:10.1021/acs.jproteome.4c00131 · Cited by 4 · see citing works
IS-PRM-Based Peptide Targeting Informed by Long-Read Sequencing for Alternative Proteome Detection
Korchak, J. A., Jeffery, E. D., Bandyopadhyay, S., Jordan, B. T., Lehe, M. D., Watts, E. F., Fenix, A. M., Wilhelm, M., & Sheynkman, G. (2024) · Journal of the American Society for Mass Spectrometry · doi:10.1021/jasms.4c00119 · Cited by 5 · see citing works
Top‐down proteomics and proteoforms – special issue
Tholey, A., & Schlüter, H. (2024) · Proteomics · doi:10.1002/pmic.202200375 · Cited by 4 · see citing works
Decoding Ubiquitin Modifications by Mass Spectrometry
Gong, Y., & Dai, L. (2024) · Advances in experimental medicine and biology · doi:10.1007/978-981-97-7288-9_1 · Cited by 3 · see citing works
An integrated landscape of mRNA and protein isoforms
Kedan, A., Zauber, H., Wang, M., Kim, S., Zhu, Q., Fang, L., Lilley, K. S., Chen, W., & Selbach, M. (2026) · Cell Reports · doi:10.1016/j.celrep.2026.117898 · Cited by 2 · see citing works
Multiplex Targeted Proteomic Analysis of Cytokine Ratios for ICU Mortality in Severe COVID-19
Araújo, R., Rekowski, C. P. V., Fonseca, T. A. H., Calado, C. R. C., Ramalhete, L., & Bento, L. F. N. (2025) · Proteomes · doi:10.3390/proteomes13030035 · Cited by 3 · see citing works
Rapid profiling of protein complex re-organization in perturbed systemsPreprint
Bludau, I., Nicod, C., Martelli, C., Xue, P., Heusel, M., Fossati, A., Uliana, F., Frommelt, F., Aebersold, R. H., & Collins, B. C. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.12.17.473177 · Cited by 3 · see citing works
Self-citationDeep thermal proteome profiling for detection of proteoforms and drug sensitivity biomarkersPreprint
Kurzawa, N., Stahl, M. M. S., Leo, I. R., Kunold, E., Becher, I., Audrey, A., Mermelekas, G., Huber, W. K., Mateus, A., Savitski, M. M., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.06.10.495491 · Cited by 3 · see citing works
Detecting Differential Alternative Splicing in Mass Spectrometry-based Proteomics DataPreprint
Ammar, C., Csaba, G., Hadziahmetovic, A., Vasilopoulou, C. G., Gruber, M., Mann, M., & Zimmer, R. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.09.19.558203 · Cited by 3 · see citing works
Considering Measurement Time and Depth in diaPASEF Plasma Proteomics
Smit, E. R., van der Zwaan, C., Groten, S. A., van den Biggelaar, M., Hoogendijk, A. J., & Langerhorst, P. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5c00637 · Cited by 2 · see citing works
Need for speed: advances in the era of high throughput interaction proteomics
Frommelt, F., Uliana, F., Aebersold, R. H., & Fossati, A. (2026) · Molecular Omics · doi:10.1093/molecular-omics/aaiag012 · Cited by 2 · see citing works
Self-citationVitorino, R. (2026) · Proteomes · doi:10.3390/proteomes14020020 · Cited by 3 · see citing works
Schär, S., Räss, L., Malinovska, L., Savickas, S., Cavallo, F., Below, C., Tognetti, M., Shichkova, P., Gourdet, B., Robles, G., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.23.655690 · Cited by 2 · see citing works
Staniak, M., Huang, T. C., Figueroa‐Navedo, A. M., Kohler, D., Choi, M., Hinkle, T. B., Kleinheinz, T., Blake, R., Rose, C. M., Xu, Y., et al. (2025) · Bioinformatics · doi:10.1093/bioinformatics/btaf046 · Cited by 1 · see citing works
ProteoformDB: A Built-in Application to Generate Proteoform Database
Hoàng, T., Hu, Y., & Zhang, H. (2025) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5c00461 · Cited by 1 · see citing works
Low, T., Chen, Y.-J., Ishihama, Y., Chung, M. C. M., Cordwell, S., Poon, T. C. W., & Kwon, H. (2022) · Molecular & Cellular Proteomics · doi:10.1016/j.mcpro.2022.100436 · Cited by 1 · see citing works
Liu, Y.-S. (2021) · Preprints.org · doi:10.20944/preprints202111.0333.v1
Doron‐Mandel, E., Bokor, B. J., Ma, Y., Street, L. A., Tang, L. C., Abdou, A. A., Shah, N. H., Rosenberger, G., & Jovanović, M. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.01.12.523793 · Cited by 1 · see citing works
Self-citationProteoPy: an AnnData-based framework for integrated proteomics analysisPreprint
Fichtner, I. D., Temesvari-Nagy, L., Sahm, F., Gerstung, M., & Bludau, I. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.03.31.715273 · Cited by 1 · see citing works
Self-citationProtein N-Terminomics Reveals Major Proteases in Regulating Beige Adipocyte DifferentiationPreprint
Chang, H., Chang, C., Nishida, H., Takamuro, K., Ogata, K., Peng, K., Lin, L.-C., Lo, Y., Huang, T., & Ishihama, Y. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.07.31.502230
Protein Complexes in Bacillus subtilis by AI-Assisted Structural ProteomicsPreprint
O'Reilly, F. J., Graziadei, A., Forbrig, C., Bremenkamp, R., Charles, K., Lenz, S., Elfmann, C., Fischer, L., Stülke, J., & Rappsilber, J. (2022) · SSRN Electronic Journal · doi:10.2139/ssrn.4186259
Campbell, T. L., & Drown, B. S. (2023) · Nature Chemical Biology · doi:10.1038/s41589-023-01285-7
Gallo, M. C. R., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384283
Gallo, M. C. R., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384295
Gallo, M. C. R., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384244
Gallo, M. C. R., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384280
Gallo, M. C. R., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384286
Gallo, M. C. R., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384238
Gallo, M. C. R., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384250
Gallo, M. C. R., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384292
Gallo, M. C. R., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384235
Gallo, M. C. R., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384301
Gallo, M. C. R., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384298
Gallo, M. C. R., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384247
Ergin, E. K., Conrrero, A., Ferguson, K. M., & Lange, P. F. (2026) · Journal of Proteome Research · doi:10.1021/acs.jproteome.5c01235
Rodriguez Gallo, M. C., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384265
Rodriguez Gallo, M. C., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384253
Rodriguez Gallo, M. C., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384241
Rodriguez Gallo, M. C., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384274
Rodriguez Gallo, M. C., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384256
Rodriguez Gallo, M. C., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384259
Rodriguez Gallo, M. C., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384262
Rodriguez Gallo, M. C., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384268
Rodriguez Gallo, M. C., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384277
Rodriguez Gallo, M. C., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384271
Rodriguez Gallo, M. C., Li, Q., Mehta, D., & Uhrig, R. G. (2022) · Figshare · doi:10.6084/m9.figshare.21384289
Proteomics of aging: biomarkers for physiological systems and diseases
Luo, Y., Xiao, Y.-L., Chen, J.-H., Wang, H., Luo, S., Dong, H., & Huang, R.-P. (2026) · Frontiers in Aging · doi:10.3389/fragi.2026.1895104
Papatziamou, D., Singh, A., Makwana, M. V., & Patel, S. K. (2026) · Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics · doi:10.1016/j.bbapap.2026.141180
A draft atlas of the human plasma proteome at isoform resolutionPreprint
Zühlke, B. M., Schwecke, T., Shapira, T., Niewienda, A., Yang, A., Amari, F., Textoris‐Taube, K., Sinn, L. R., Lehmann, K., Gille, C., et al. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.09.26.754256
Quantitative Top‐Down Proteomics: A Review
Cupp‐Sutton, K. A., Atallah, M. A., Zhao, Z., Anjum, S., Chowdhury, T., Sunny, A. T., Szamweber, P., & Wu, S. (2026) · Mass Spectrometry Reviews · doi:10.1002/mas.70051
- Authors
- Bludau, I., Frank, M., Dörig, C., Cai, Y., Heusel, M., Rosenberger, G., Picotti, P., Collins, B. C., Röst, H., & Aebersold, R.
- Affiliations
- ETH Zurich (CH)
- University of Toronto (CA)
- Lund University (SE)
- Queen's University Belfast (GB)
- University of Zurich (CH)
- Corresponding author
- Röst, Hannes
- Aebersold, Ruedi
- ORCID
- Venue
- Nature Communications
- Published
- 2021-06-21
- Volume
- 12
- Issue
- 1
- Pages
- 3810-3810
- ISSN
- 2041-1723 (ISSN-L)
- PMC
- PMC8217233
- OpenAlex
- W3175993123
- Cited by
- 88
- References
- 82
- Citations by year
- 2026: 11 · 2025: 16 · 2024: 10 · 2023: 19 · 2022: 26 · 2021: 6
- FWCI
- 6.66
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Nature Communications (publishedVersion, cc-by)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- Repository for Publications and Research Data (ETH Zurich) (submittedVersion, cc-by)
- RePEc: Research Papers in Economics (submittedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Lund University Publications (Lund University) (submittedVersion)
- ETH Zürich Research Collection (cc-by)
- Funders
- National Science Foundation
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (175127, 173572, ERC-20140AdG 670821, 183933, 161435, 310030E, 191046)
- SystemsX.ch
- Topics
- Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Advanced Biosensing Techniques and Applications
- Keywords
- proteoforms, shotgun proteomics, protein abundance, protein assembly, post-translational modification
- MeSH terms
- Algorithms, Animals, Humans, Peptides, Benchmarking, Protein Isoforms, Proteomics, Mice, Tandem Mass Spectrometry, Workflow
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