Ryan, C. J., Kennedy, S., Bajrami, I., Matallanas, D. & Lord, C. J. A compendium of co-regulated protein complexes in breast cancer reveals collateral loss events. Cell Syst. 5, 399–409 (2017).
Smith, L. M., Kelleher, N. L. & Consortium for Top Down Proteomics Proteoform: a single term describing protein complexity. Nat Methods 10, 186–187 (2013).
Jensen, M. H., Morris, E. J., Tran, H., Nash, M. A. & Tan, C. Stochastic ordering of complexoform protein assembly by genetic circuits. PLoS Comput. Biol. 16, e1007997 (2020).
Gomes, F. P. & Yates, J. R. 3rd Recent trends of capillary electrophoresis–mass spectrometry in proteomics research. Mass Spectrom. Rev. 38, 445–460 (2019).
Zhou, M. et al. Higher-order structural characterisation of native proteins and complexes by top-down mass spectrometry. Chem. Sci. 11, 12918–12936 (2020).
Zhai, Z. et al. Characterization of complex proteoform mixtures by online nanoflow ion-exchange chromatography-native mass spectrometry. Anal. Chem. 96, 8880–8885 (2024).
Brown, K. A., Melby, J. A., Roberts, D. S. & Ge, Y. Top-down proteomics: challenges, innovations, and applications in basic and clinical research. Expert Rev. Proteomics 17, 719–733 (2020).
Li, H., Nguyen, H. H., Loo, R. R. O., Campuzano, I. D. G. & Loo, J. A. An integrated native mass spectrometry and top-down proteomics method that connects sequence to structure and function of macromolecular complexes. Nat. Chem. 10, 139–148 (2018).
Skinner, O. S. et al. Top-down characterization of endogenous protein complexes with native proteomics. Nat. Chem. Bio. 14, 36–41 (2017).
Gault, J. et al. Combining native and ‘omics’ mass spectrometry to identify endogenous ligands bound to membrane proteins. Nat Methods 17, 505–508 (2020).
Shen, X. et al. Native proteomics in discovery mode using size-exclusion chromatography–capillary zone electrophoresis–tandem mass spectrometry. Anal. Chem. 90, 10095–10099 (2018).
Li, H., Wongkongkathep, P., Van Orden, S. L., Ogorzalek Loo, R. R. & Loo, J. A. Revealing ligand binding sites and quantifying subunit variants of noncovalent protein complexes in a single native top-down FTICR MS experiment. J. Am. Soc. Mass. Spectrom. 25, 2060–2068 (2014).
Chapman, E. A. Native top-down mass spectrometry for characterizing sarcomeric proteins directly from cardiac tissue lysate. J. Am. Soc. Mass. Spectrom. 35, 738–745 (2024).
Jooß, K. et al. Separation and characterization of endogenous nucleosomes by native capillary zone electrophoresis-top-down mass spectrometry. Anal. Chem. 93, 5151–5160 (2021).
Mehaffey, M. R., Xia, Q. & Brodbelt, J. S. Uniting native capillary electrophoresis and multistage ultraviolet photodissociation mass spectrometry for online separation and characterization of Escherichia coli ribosomal proteins and protein complexes. Anal. Chem. 92, 15202–15211 (2020).
Chapman, E. A. et al. Structure and dynamics of endogenous cardiac troponin complex in human heart tissue captured by native nanoproteomics. Nat. Commun. 14, 8400 (2023).
Vimer, S., Ben-Nissan, G. & Sharon, M. Direct characterization of overproduced proteins by native mass spectrometry. Nat. Protoc. 15, 236–265 (2020).
Rogawski, R. & Sharon, M. Characterizing endogenous protein complexes with biological mass spectrometry. Chem. Rev. 122, 7386–7414 (2022).
Razavi, P. et al. The genomic landscape of endocrine-resistant advanced breast cancers. Cancer Cell 34, 427–438 (2018).
Min, J. et al. Dual-mechanism estrogen receptor inhibitors. Proc. Natl Acad. Sci. USA 118, e2101657118 (2021).
Durbin, K. R. et al. ProSight Native: defining protein complex composition from native top-down mass spectrometry data. J. Proteome Res. 22, 2660–2668 (2023).
Chen, D., Geis-Asteggiante, L., Gomes, F. P., Ostrand-Rosenberg, S. & Fenselau, C. Top-down proteomic characterization of truncated proteoforms. J. Proteome Res. 18, 4013–4019 (2019).
Pekel, G. & Ari, F. Therapeutic targeting of cancer metabolism with triosephosphate isomerase. Chem. Biodivers. 17, e2000012 (2020).
Stein, B. D. et al. LKB1-dependent regulation of TPI1 creates a divergent metabolic liability between human and mouse lung adenocarcinoma. Cancer Discov. 13, 1002–1025 (2023).
Schachner, L. F. et al. Revving an engine of human metabolism: activity enhancement of triosephosphate isomerase via hemi-phosphorylation. ACS Chem. Biol. 17, 2769–2780 (2022).
Kulkarni, Y. S. et al. Enzyme architecture: modeling the operation of a hydrophobic clamp in catalysis by triosephosphate isomerase. J. Am. Chem. Soc. 139, 10514–10525 (2017).
Yüksel, K. U. & Gracy, R. W. In vitro deamidation of human triosephosphate isomerase. Arch. Biochem. Biophys. 248, 452–459 (1986).
Ugur, I., Marion, A., Aviyente, V. & Monard, G. Why does Asn71 deamidate faster than Asn15 in the enzyme triosephosphate isomerase? Answers from microsecond molecular dynamics simulation and QM/MM free energy calculations. Biochemistry 54, 1429–1439 (2015).
De La Mora-De La Mora, I. et al. The E104D mutation increases the susceptibility of human triosephosphate isomerase to proteolysis. Asymmetric cleavage of the two monomers of the homodimeric enzyme. Biochim. Biophys. Acta 1834, 2702–2711 (2013).
Schindler, L., Dickerhof, N., Hampton, M. B. & Bernhagen, J. Post-translational regulation of macrophage migration inhibitory factor: basis for functional fine-tuning. Redox Biol. 15, 135–142 (2018).
Xiao, Z. et al. Structure-activity relationships for binding of 4-substituted triazole-phenols to macrophage migration inhibitory factor (MIF). Eur. J. Med. Chem. 186, 111849 (2020).
Luedike, P. et al. Cardioprotection through S-nitros(yl)ation of macrophage migration inhibitory factor. Circulation 125, 1880–1889 (2012).
Gomez, M. L., Shah, N., Kenny, T. C., Jenkins, E. C. & Germain, D. SOD1 is essential for oncogene-driven mammary tumor formation but dispensable for normal development and proliferation. Oncogene 38, 5751–5765 (2019).
Li, H. et al. Structural characterization of native proteins and protein complexes by electron ionization dissociation-mass spectrometry. Anal. Chem. 89, 2731–2738 (2017).
Schachner, L. F. et al. Reassembling protein complexes after controlled disassembly by top-down mass spectrometry in native mode. Int. J. Mass Spectrom. 465, 116591 (2021).
Smith, L. M. et al. A five-level classification system for proteoform identifications. Nat. Methods 16, 939–940 (2019).
Małecki, J. M., Davydova, E. & Falnes, P. Protein methylation in mitochondria. J. Biol. Chem. 298, 101791 (2022).
Steggerda, S. M., Black, B. E. & Paschal, B. M. Monoclonal antibodies to NTF2 inhibit nuclear protein import by preventing nuclear translocation of the GTPase Ran. Mol. Biol. Cell 11, 703–719 (2000).
Lui, K. & Huang, Y. RanGTPase: a key regulator of nucleocytoplasmic trafficking. Mol. Cell. Pharmacol. 1, 148–156 (2009).
Stewart, M., Kent, H. M. & McCoy, A. J. Structural basis for molecular recognition between nuclear transport factor 2 (NTF2) and the GDP-bound form of the Ras-family GTPase Ran. J. Mol. Biol. 277, 635–646 (1998).
Bayliss, R. et al. Structural basis for the interaction between NTF2 and nucleoporin FxFG repeats. EMBO J. 21, 2843–2853 (2002).
Jozwik, K. M. & Carroll, J. S. Pioneer factors in hormone-dependent cancers. Nat. Rev. Cancer 12, 381–385 (2012).
Hurtado, A., Holmes, K. A., Ross-Innes, C. S., Schmidt, D. & Carroll, J. S. FOXA1 is a key determinant of estrogen receptor function and endocrine response. Nat. Genet. 43, 27–33 (2011).
VanAernum, Z. L. et al. Surface-induced dissociation of noncovalent protein complexes in an extended mass range orbitrap mass spectrometer. Anal. Chem. 91, 3611–3618 (2019).
Larson, E. J. et al. High-throughput multi-attribute analysis of antibody-drug conjugates enabled by trapped ion mobility spectrometry and top-down mass spectrometry. Anal. Chem. 93, 10013–10021 (2021).
Qin, Q. et al. Lisa: inferring transcriptional regulators through integrative modeling of public chromatin accessibility and ChIP–seq data. Genome Biol. 21, 32 (2020).
VanAernum, Z. L. et al. Rapid online buffer exchange for screening of proteins, protein complexes and cell lysates by native mass spectrometry. Nat. Protoc. 15, 1132–1157 (2020).
Tucholski, T. et al. A top-down proteomics platform coupling serial size exclusion chromatography and Fourier transform ion cyclotron resonance mass spectrometry. Anal. Chem. 91, 3835–3844 (2019).
Chernushevich, I. V. & Thomson, B. A. Collisional cooling of large ions in electrospray mass spectrometry. Anal. Chem. 76, 1754–1760 (2004).
DeHart, C. J., Fellers, R. T., Fornelli, L., Kelleher, N. L. & Thomas, P. M. Bioinformatics analysis of top-down mass spectrometry data with ProSight Lite. Methods Mol. Biol. 1558, 381–394 (2017).
Bookout, A. L., Cummins, C. L., Mangelsdorf, D. J., Pesola, J. M. & Kramer, M. F. High-throughput real-time quantitative reverse transcription PCR. Curr. Protoc. Mol. Biol., https://doi.org/10.1002/0471142727.mb1508s73 (2006).
Meers, M. P., Bryson, T. D., Henikoff, J. G. & Henikoff, S. Improved CUT&RUN chromatin profiling tools. eLife 24, e46314 (2019).
Ewels, P. A. et al. The nf-core framework for community-curated bioinformatics pipelines. Nat. Biotechnol. 38, 276–278 (2020).
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
Li, H. et al. The sequence alignment/map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
Zhang, Y. et al. ChIP–seq (MACS). Genome Biol. 9, R137 (2008).
Ross-Innes, C. S. et al. Differential oestrogen receptor binding is associated with clinical outcome in breast cancer. Nature 481, 389–393 (2012).
Jayaram, N., Usvyat, D. & AC, R. M. Evaluating tools for transcription factor binding site prediction. BMC Bioinformatics 17, 547 (2016).
Tan, G. & Lenhard, B. TFBSTools: an R/bioconductor package for transcription factor binding site analysis. Bioinformatics 32, 1555–1556 (2016).
Rauluseviciute, I. et al. JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles. Nucleic Acids Res. 52, D174–d182 (2024).
Machanick, P. & Bailey, T. L. MEME-ChIP: motif analysis of large DNA datasets. Bioinformatics 27, 1696–1697 (2011).
Galaxy Community. The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2022 update. Nucleic Acids Res. 50, W345–W351 (2022).
Kim, D., Langmead, B. & Salzberg, S. L. HISAT: a fast spliced aligner with low memory requirements. Nat. Methods 12, 357–360 (2015).
Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
Szklarczyk, D. et al. STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res. 47, D607–D613 (2018).
Li, S. et al. Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP–seq peaks. Nucleic Acids Res. 47, W206–w211 (2019).
Tan, B. et al. An optimized protocol for proximity biotinylation in confluent epithelial cell cultures using the peroxidase APEX2. STAR Protoc. 1, 100074 (2020).
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