Aebersold, R. et al. What number of human proteoforms are there? Nat. Chem. Biol. 14, 206–214 (2018).
Kim, H. Okay., Pham, M. H. C., Ko, Okay. S., Rhee, B. D. & Han, J. Different splicing isoforms in well being and illness. Pflügers Arch. 470, 995–1016 (2018).
Paronetto, M. P., Passacantilli, I. & Sette, C. Different splicing and cell survival: from tissue homeostasis to illness. Cell Loss of life Differ. 23, 1919–1929 (2016).
Lin, H. & Caroll, Okay. S. Introduction: posttranslational protein modification. Chem. Rev. 118, 887–888 (2018).
Carbonara, Okay., Andonovski, M. & Coorssen, J. R. Proteomes are of proteoforms: embracing the complexity. Proteomes 9, 38 (2021).
Benson, M. D., Ngo, D., Ganz, P. & Gerszten, R. E. Rising affinity reagents for top throughput proteomics: belief, however confirm. Circulation 140, 1610–1612 (2019).
Yang, Y. et al. Hybrid mass spectrometry approaches in glycoprotein evaluation and their utilization in scoring biosimilarity. Nat. Commun. 7, 13397 (2016).
Čaval, T., Tian, W., Yang, Z., Clausen, H. & Heck, A. J. R. Direct high quality management of glycoengineered erythropoietin variants. Nat. Commun. 9, 3342 (2018).
Siuti, N. & Kelleher, N. L. Decoding protein modifications utilizing top-down mass spectrometry. Nat. Strategies 410, 817–821 (2007).
Wang, Y., Zhao, Y., Bollas, A., Wang, Y. & Au, Okay. F. Nanopore sequencing expertise, bioinformatics and purposes. Nat. Biotechnol. 39, 1348–1365 (2021).
Ardui, S., Ameur, A., Vermeesch, J. R. & Hestand, M. S. Single molecule real-time (SMRT) sequencing comes of age: purposes and utilities for medical diagnostics. Nucleic Acids Res. 46, 2159–2168 (2018).
Restrepo-Pérez, L., Joo, C. & Dekker, C. Paving the best way to single-molecule protein sequencing. Nat. Nanotechnol. 13, 786–796 (2018).
Alfaro, J. A. et al. The rising panorama of single-molecule protein sequencing applied sciences. Nat. Strategies 18, 604–617 (2021).
Floyd, B. M. & Marcotte, E. M. Protein sequencing, one molecule at a time. Annu. Rev. Biophys. 51, 181–200 (2022).
Timp, W. & Timp, G. Past mass spectrometry, the following step in proteomics. Sci. Adv. 6, eaax8978 (2020).
Swaminathan, J., Boulgakov, A. A. & Marcotte, E. M. A theoretical justification for single molecule peptide sequencing. PLoS Comput. Biol. 11, e1004080 (2015).
Rodriques, S. G., Marblestone, A. H. & Boyden, E. S. A theoretical evaluation of single molecule protein sequencing by way of weak binding spectra. PLoS ONE 14, e0212868 (2019).
Yao, Y., Docter, M., Van Ginkel, J., De Ridder, D. & Joo, C. Single-molecule protein sequencing by way of fingerprinting: computational evaluation. Phys. Biol. 12, 10–16 (2015).
de Lannoy, C. V. et al. Analysis of FRET X for single-molecule protein fingerprinting. iScience 24, 103239 (2021).
Yu, L. et al. Unidirectional single-file transport of full-length proteins by way of a nanopore. Nat. Biotechnol. 41, 1130–1139 (2023).
van Ginkel, J. et al. Single-molecule peptide fingerprinting. Proc. Natl Acad. Sci. USA 115, 3338–3343 (2018).
Swaminathan, J. et al. Extremely parallel single-molecule identification of proteins in zeptomole-scale mixtures. Nat. Biotechnol. 36, 1076–1082 (2018).
Shrestha, P. et al. Single-molecule mechanical fingerprinting with DNA nanoswitch calipers. Nat. Nanotechnol. 16, 1362–1370 (2021).
Filius, M., Kim, S. H., Severins, I. & Joo, C. Excessive-resolution single-molecule FRET by way of DNA trade (FRET X). Nano Lett. 21, 3295–3301 (2021).
Filius, M., van Wee, R. & Joo, C. in Single Molecule Evaluation: Strategies and Protocols (eds Heller, I. et al.) 203–213 (Springer, 2024).
Van Wee, R., Filius, M. & Joo, C. Finishing the canvas: advances and challenges for DNA-PAINT super-resolution imaging. Traits Biochem. Sci. 11, 918–930 (2021).
Schnitzbauer, J., Strauss, M. T., Schlichthaerle, T., Schueder, F. & Jungmann, R. Tremendous-resolution microscopy with DNA-PAINT. Nat. Protoc. 12, 1198–1228 (2017).
Shi, X. et al. Quantitative fluorescence labeling of aldehyde-tagged proteins for single-molecule imaging. Nat. Strategies 9, 499–503 (2012).
Schuler, B. & Hofmann, H. Single-molecule spectroscopy of protein folding dynamics—increasing scope and timescales. Curr. Opin. Struct. Biol. 23, 36–47 (2013).
Yang, X. & Qian, Okay. Protein O-GlcNAcylation: rising mechanisms and capabilities. Nat. Rev. Mol. Cell Biol. 18, 452–465 (2017).
Vellosillo, P. & Minguez, P. A worldwide map of associations between kinds of protein posttranslational modifications and human genetic illnesses. iScience 24, 102917 (2021).
Mauri, T. et al. O-GlcNAcylation prediction: an unattained goal. Adv. Appl. Bioinform. Chem. 14, 87–102 (2021).
Shi, J., Ruijtenbeek, R. & Pieters, R. J. Demystifying O-GlcNAcylation: hints from peptide substrates. Glycobiology 28, 814–824 (2018).
Shen, D. L. et al. Catalytic promiscuity of O-GlcNAc transferase allows sudden metabolic engineering of cytoplasmic proteins with 2-azido-2-deoxy-glucose. ACS Chem. Biol. 12, 206–213 (2017).
Mayer, A., Gloster, T. M., Chou, W. Okay., Vocadlo, D. J. & Tanner, M. E. 6′-Azido-6′-deoxy-UDP-N-acetylglucosamine as a glycosyltransferase substrate. Bioorg. Med. Chem. Lett. 21, 1199–1201 (2011).
Macdonald, J. I., Munch, H. Okay., Moore, T. & Francis, M. B. One-step site-specific modification of native proteins with 2-pyridinecarboxyaldehydes. Nat. Chem. Biol. 11, 326–331 (2015).
Wang, S. et al. S100A8/A9 in irritation. Entrance. Immunol. 9, 1298 (2018).
Vijayan, A. L. et al. Procalcitonin: a promising diagnostic marker for sepsis and antibiotic remedy. J. Intensive Care 5, 51 (2017).
Senior, A. W. et al. Improved protein construction prediction utilizing potentials from deep studying. Nature 577, 706–710 (2020).
Jumper, J. et al. Extremely correct protein construction prediction with AlphaFold. Nature 596, 583–589 (2021).
Jungmann, R. et al. Multiplexed 3D mobile super-resolution imaging with DNA-PAINT and Alternate-PAINT. Nat. Strategies 11, 313–318 (2014).
Erickson, H. P. Measurement and form of protein molecules on the nanometer stage decided by sedimentation, gel filtration, and electron microscopy. Biol. Proced. On-line 11, 32–51 (2009).
Ree, R., Varland, S. & Arnesen, T. Highlight on protein N-terminal acetylation. Exp. Mol. Med. 50, 1–13 (2018).
Bloom, S. et al. Decarboxylative alkylation for site-selective bioconjugation of native proteins by way of oxidation potentials. Nat. Chem. 10, 205–211 (2018).
Ramirez, D. H. et al. Engineering a proximity-directed O-GlcNAc transferase for selective protein O-GlcNAcylation in cells. ACS Chem. Biol. 15, 1059–1066 (2020).
Yang, Y.-Y., Ascano, J. M. & Dangle, H. C. Bioorthogonal chemical reporters for monitoring protein acetylation. J. Am. Chem. Soc. 132, 3640–3641 (2010).
Westcott, N. P., Fernandez, J. P., Molina, H. & Dangle, H. C. Chemical proteomics reveals ADP-ribosylation of small GTPases throughout oxidative stress. Nat. Chem. Biol. 13, 302–308 (2017).
Rabuka, D., Hubbard, S. C., Laughlin, S. T., Argade, S. P. & Bertozzi, C. R. A chemical reporter technique to probe glycoprotein fucosylation. J. Am. Chem. Soc. 128, 12078–12079 (2006).
Boeggeman, E. et al. Direct identification of nonreducing GlcNAc residues on N-glycans of glycoproteins utilizing a novel chemoenzymatic methodology. Bioconjugate Chem. 18, 806–814 (2007).
van Geel, R. et al. Chemoenzymatic conjugation of poisonous payloads to the globally conserved N-glycan of native mAbs supplies homogeneous and extremely efficacious antibody–drug conjugates. Bioconjugate Chem. 26, 2233–2242 (2015).
Tate, E. W., Kalesh, Okay. A., Lanyon-Hogg, T., Storck, E. M. & Thinon, E. World profiling of protein lipidation utilizing chemical proteomic applied sciences. Curr. Opin. Chem. Biol. 24, 48–57 (2015).
Anderson, N. L. & Anderson, N. G. The human plasma proteome: historical past, character, and diagnostic prospects. Mol. Cell. Proteom. 1, 845–867 (2002).
Han, X., Aslanian, A. & Yates, J. R. Mass spectrometry for proteomics. Curr. Opin. Chem. Biol. 12, 483–490 (2008).
Filius, M. et al. Excessive-speed super-resolution imaging utilizing protein-assisted DNA-PAINT. Nano Lett. 20, 2264–2270 (2020).
Kim, S. H., Kim, H., Jeong, H. & Yoon, T. Y. Encoding a number of digital indicators in DNA barcodes with single-molecule FRET. Nano Lett. 21, 1694–1701 (2021).
McCann, J. J., Choi, U. B., Zheng, L., Weninger, Okay. & Bowen, M. E. Optimizing strategies to get well absolute FRET effectivity from immobilized single molecules. Biophys. J. 99, 961–970 (2010).
Cristianini, N. & Shawe-Taylor, J. An Introduction to Assist Vector Machines and Different Kernel-based Studying Strategies (Cambridge College Press, 2000).
Pedregosa, F. et al. Scikit-learn: machine studying in Python. J. Mach. Study. Res. 12, 2825–2830 (2011).
Pabst, M. et al. A normal method to discover prokaryotic protein glycosylation reveals the distinctive floor layer modulation of an anammox bacterium. ISME J. 16, 346–357 (2022).
Chuh, Okay. N., Zaro, B. W., Piller, F., Piller, V. & Pratt, M. R. Adjustments in metabolic chemical reporter construction yield a selective probe of O-GlcNAc modification. J. Am. Chem. Soc. 136, 12283–12295 (2014).