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Journal articles on the topic 'Crosslinking mass spectrometry'

Author: Grafiati

Published: 15 June 2024

Last updated: 31 July 2025

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1

Sinz, Andrea. "Crosslinking Mass Spectrometry Goes In-Tissue." Cell Systems 6, no. 1 (2018): 10–12. http://dx.doi.org/10.1016/j.cels.2018.01.005.

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2

Schneider, Michael, Adam Belsom, and Juri Rappsilber. "Protein Tertiary Structure by Crosslinking/Mass Spectrometry." Trends in Biochemical Sciences 43, no. 3 (2018): 157–69. http://dx.doi.org/10.1016/j.tibs.2017.12.006.

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3

Chen, Zhuo Angel, and Juri Rappsilber. "Protein structure dynamics by crosslinking mass spectrometry." Current Opinion in Structural Biology 80 (June 2023): 102599. http://dx.doi.org/10.1016/j.sbi.2023.102599.

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4

Xia, Yingzi. "Exploring misfolded proteins with crosslinking mass spectrometry." Biophysical Journal 123, no. 3 (2024): 206a. http://dx.doi.org/10.1016/j.bpj.2023.11.1301.

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5

Petrotchenko, Evgeniy V., and Christoph H. Borchers. "Crosslinking combined with mass spectrometry for structural proteomics." Mass Spectrometry Reviews 29, no. 6 (2010): 862–76. http://dx.doi.org/10.1002/mas.20293.

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6

Dancy, Beverley M., Fan Liu, Philip Lössl, Albert J. R. Heck, and Robert S. Balaban. "The mitochondrial interactome visualized by crosslinking mass spectrometry." Biochimica et Biophysica Acta (BBA) - Bioenergetics 1857 (August 2016): e22. http://dx.doi.org/10.1016/j.bbabio.2016.04.045.

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7

Singh, Arunima. "Crosslinking mass spectrometry data bolster protein structure prediction." Nature Methods 20, no. 5 (2023): 633. http://dx.doi.org/10.1038/s41592-023-01890-3.

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8

Graziadei, Andrea, and Juri Rappsilber. "Leveraging crosslinking mass spectrometry in structural and cell biology." Structure 30, no. 1 (2022): 37–54. http://dx.doi.org/10.1016/j.str.2021.11.007.

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9

Chen, Zhuo A., and Juri Rappsilber. "Protein Dynamics in Solution by Quantitative Crosslinking/Mass Spectrometry." Trends in Biochemical Sciences 43, no. 11 (2018): 908–20. http://dx.doi.org/10.1016/j.tibs.2018.09.003.

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10

Bullock, Joshua Matthew Allen, Neeladri Sen, Konstantinos Thalassinos, and Maya Topf. "Modeling Protein Complexes Using Restraints from Crosslinking Mass Spectrometry." Structure 26, no. 7 (2018): 1015–24. http://dx.doi.org/10.1016/j.str.2018.04.016.

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11

Kim, Samuel, Jae Kyoo Lee, Hong Gil Nam, and Richard N. Zare. "Photo-Activated Crosslinking Mass Spectrometry for Studying Biomolecular Interactions." Biophysical Journal 106, no. 2 (2014): 459a. http://dx.doi.org/10.1016/j.bpj.2013.11.2601.

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12

Ciancone, Anthony, and Francis J. O'Reilly. "Photo-crosslinkers boost structural information from crosslinking mass spectrometry." Current Opinion in Structural Biology 93 (August 2025): 103102. https://doi.org/10.1016/j.sbi.2025.103102.

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13

Makepeace, Karl A. T., Yassene Mohammed, Elena L. Rudashevskaya, et al. "Improving Identification of In-organello Protein-Protein Interactions Using an Affinity-enrichable, Isotopically Coded, and Mass Spectrometry-cleavable Chemical Crosslinker." Molecular & Cellular Proteomics 19, no. 4 (2020): 624–39. http://dx.doi.org/10.1074/mcp.ra119.001839.

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An experimental and computational approach for identification of protein-protein interactions by ex vivo chemical crosslinking and mass spectrometry (CLMS) has been developed that takes advantage of the specific characteristics of cyanurbiotindipropionylsuccinimide (CBDPS), an affinity-tagged isotopically coded mass spectrometry (MS)-cleavable crosslinking reagent. Utilizing this reagent in combination with a crosslinker-specific data-dependent acquisition strategy based on MS2 scans, and a software pipeline designed for integrating crosslinker-specific mass spectral information led to demonst

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14

Wang, Haodong, Min Zhang, and Liang Ge. "Crosslinking and Mass Spectrometry to Identify Regulators in Unconventional Secretion." Trends in Biochemical Sciences 46, no. 8 (2021): 701–2. http://dx.doi.org/10.1016/j.tibs.2021.03.006.

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15

Xia, Yingzi, and Stephen D. Fried. "Studying the refoldability of the proteome using crosslinking mass spectrometry." Biophysical Journal 121, no. 3 (2022): 184a. http://dx.doi.org/10.1016/j.bpj.2021.11.1800.

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16

Donelan, Chelsee A., Rathna Veeramachaneni, David J. Lapinsky, and Michael Cascio. "Using Crosslinking and Mass Spectrometry to Study Glycine Receptor Allostery." Biophysical Journal 102, no. 3 (2012): 612a. http://dx.doi.org/10.1016/j.bpj.2011.11.3336.

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17

Muizebelt, W. J., and M. W. F. Nielen. "Oxidative Crosslinking of Unsaturated Fatty Acids Studied with Mass Spectrometry." Journal of Mass Spectrometry 31, no. 5 (1996): 545–54. http://dx.doi.org/10.1002/(sici)1096-9888(199605)31:5<545::aid-jms329>3.0.co;2-1.

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18

Hagen, Susan E., Kun Liu, Yafei Jin, Lolita Piersimoni, Philip C. Andrews, and Hollis D. Showalter. "Synthesis of CID-cleavable protein crosslinking agents containing quaternary amines for structural mass spectrometry." Organic & Biomolecular Chemistry 16, no. 37 (2018): 8245–48. http://dx.doi.org/10.1039/c8ob00329g.

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Two novel cyclic quaternary amine crosslinking probes are synthesized for structural mass spectrometry of protein complexes in solution and for analysis of protein interactions in organellar and whole cell extracts.

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19

Tang, Xiaoting, Helisa H. Wippel, Juan D. Chavez, and James E. Bruce. "Crosslinking mass spectrometry: A link between structural biology and systems biology." Protein Science 30, no. 4 (2021): 773–84. http://dx.doi.org/10.1002/pro.4045.

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20

Topf, Maya. "Modeling Protein Monomers and Complexes using Restraints from Crosslinking Mass Spectrometry." Biophysical Journal 116, no. 3 (2019): 330a. http://dx.doi.org/10.1016/j.bpj.2018.11.1790.

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21

Perdivara, Irina, Mitsuo Yamauchi, and Kenneth B. Tomer. "Molecular Characterization of Collagen Hydroxylysine O-Glycosylation by Mass Spectrometry: Current Status." Australian Journal of Chemistry 66, no. 7 (2013): 760. http://dx.doi.org/10.1071/ch13174.

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The most abundant proteins in vertebrates – the collagen family proteins – play structural and biological roles in the body. The predominant member, type I collagen, provides tissues and organs with structure and connectivity. This protein has several unique post-translational modifications that take place intra- and extra-cellularly. With growing evidence of the relevance of such post-translational modifications in health and disease, the biological significance of O-linked collagen glycosylation has recently drawn increased attention. However, several aspects of this unique modification – th

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22

HAH, Sang Soo. "Determination of Protein-Ligand Interactions Using Accelerator Mass Spectrometry: Modified Crosslinking Assay." Analytical Sciences 25, no. 5 (2009): 731–33. http://dx.doi.org/10.2116/analsci.25.731.

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23

Felker, Dana, Haoming Zhang, Zhiyuan Bo, et al. "Mapping protein-protein interactions in homodimeric CYP102A1 by crosslinking and mass spectrometry." Biophysical Chemistry 274 (July 2021): 106590. http://dx.doi.org/10.1016/j.bpc.2021.106590.

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24

Fasci, Domenico, Hugo van Ingen, Richard A. Scheltema, and Albert J. R. Heck. "Histone Interaction Landscapes Visualized by Crosslinking Mass Spectrometry in Intact Cell Nuclei." Molecular & Cellular Proteomics 17, no. 10 (2018): 2018–33. http://dx.doi.org/10.1074/mcp.ra118.000924.

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25

Castellano, Elizabeth. "Identification of Fluoxetine-Serotonin Transporter Interactions using Crosslinking-Mass Spectrometry (CX-MS)." Biophysical Journal 112, no. 3 (2017): 343a. http://dx.doi.org/10.1016/j.bpj.2016.11.1861.

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26

Müller, Fränze, Andrea Graziadei, and Juri Rappsilber. "Quantitative Photo-crosslinking Mass Spectrometry Revealing Protein Structure Response to Environmental Changes." Analytical Chemistry 91, no. 14 (2019): 9041–48. http://dx.doi.org/10.1021/acs.analchem.9b01339.

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27

Castellano, Elizabeth. "Mapping the Extracellular Loops of the Serotonin Transporter Using Crosslinking-Mass Spectrometry." Biophysical Journal 116, no. 3 (2019): 52a. http://dx.doi.org/10.1016/j.bpj.2018.11.327.

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28

Stevenson Keller, T. C., Brant E. Isakson, and Linda Columbus. "Molecular Modeling of the Alpha Globin/eNOS Complex via Crosslinking Mass Spectrometry." Biophysical Journal 116, no. 3 (2019): 168a. http://dx.doi.org/10.1016/j.bpj.2018.11.933.

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29

Nagy, Lajos, Bence Vadkerti, Csilla Lakatos, Péter Pál Fehér, Miklós Zsuga, and Sándor Kéki. "Kinetically Equivalent Functionality and Reactivity of Commonly Used Biocompatible Polyurethane Crosslinking Agents." International Journal of Molecular Sciences 22, no. 8 (2021): 4059. http://dx.doi.org/10.3390/ijms22084059.

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In this paper, the kinetics of the reaction of phenyl isocyanate with crosslinking agents such as sucrose, sorbitol, and glycerol are reported. Crosslinking agents were used in high molar excess to isocyanate to obtain pseudo-first-order rate dependencies, and the reaction products were separated by high-performance liquid chromatography and detected by UV spectroscopy and mass spectrometry. It was found that the glycerol’s primary hydroxyl groups were approximately four times reactive than the secondary ones. However, in the case of sorbitol, the two primary OH groups were found to be the mos

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30

Röth, Daniel, Jessica Molina-Franky, John C. Williams, and Markus Kalkum. "Mass Spectrometric Detection of Formaldehyde-Crosslinked PBMC Proteins in Cell-Free DNA Blood Collection Tubes." Molecules 28, no. 23 (2023): 7880. http://dx.doi.org/10.3390/molecules28237880.

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Streck tubes are commonly used to collect blood samples to preserve cell-free circulating DNA. They contain imidazolidinyl urea as a formaldehyde-releasing agent to stabilize cells. We investigated whether the released formaldehyde leads to crosslinking of intracellular proteins. Therefore, we employed a shotgun proteomics experiment on human peripheral blood mononuclear cells (PBMCs) that were isolated from blood collected in Streck tubes, EDTA tubes, EDTA tubes containing formaldehyde, or EDTA tubes containing allantoin. The identified crosslinks were validated in parallel reaction monitorin

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31

Faustino, Anneliese M., and Stephen D. Fried. "Mapping Structural Intermediates during Co-Translational Folding of Hsp70 with Crosslinking Mass Spectrometry." Biophysical Journal 120, no. 3 (2021): 197a. http://dx.doi.org/10.1016/j.bpj.2020.11.1356.

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32

Livney, Y. D., A. L. Schwan та D. G. Dalgleish. "A Study of β-Casein Tertiary Structure by Intramolecular Crosslinking and Mass Spectrometry". Journal of Dairy Science 87, № 11 (2004): 3638–47. http://dx.doi.org/10.3168/jds.s0022-0302(04)73502-x.

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33

HAH, Sang Soo. "Retraction: Determination of Protein-Ligand Interactions Using Accelerator Mass Spectrometry: Modified Crosslinking Assay." Analytical Sciences 28, no. 8 (2012): 827. http://dx.doi.org/10.2116/analsci.28.827.

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34

Bullock, Joshua M. A., Konstantinos Thalassinos, and Maya Topf. "Jwalk and MNXL web server: model validation using restraints from crosslinking mass spectrometry." Bioinformatics 34, no. 20 (2018): 3584–85. http://dx.doi.org/10.1093/bioinformatics/bty366.

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35

Debelyy, Mykhaylo O., Patrice Waridel, Manfredo Quadroni, Roger Schneiter, and Andreas Conzelmann. "Chemical crosslinking and mass spectrometry to elucidate the topology of integral membrane proteins." PLOS ONE 12, no. 10 (2017): e0186840. http://dx.doi.org/10.1371/journal.pone.0186840.

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36

Fukumoto, Jutaro, Helena Hernández-Cuervo, Venkata Ramireddy Narala, et al. "Identification of ALDH2 Interacting Proteins by Chemical Crosslinking, Co-Immunoprecipitation and Mass Spectrometry." Journal of Allergy and Clinical Immunology 141, no. 2 (2018): AB176. http://dx.doi.org/10.1016/j.jaci.2017.12.559.

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37

Chavez, Juan D., Chi Fung Lee, Arianne Caudal, Andrew Keller, Rong Tian, and James E. Bruce. "Chemical Crosslinking Mass Spectrometry Analysis of Protein Conformations and Supercomplexes in Heart Tissue." Cell Systems 6, no. 1 (2018): 136–41. http://dx.doi.org/10.1016/j.cels.2017.10.017.

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38

Zhou, Xiangzhe, Feng Liu, Nuomin Li, and Yongqian Zhang. "Large-Scale Qualitative and Quantitative Assessment of Dityrosine Crosslinking Omics in Response to Endogenous and Exogenous Hydrogen Peroxide in Escherichia coli." Antioxidants 12, no. 4 (2023): 786. http://dx.doi.org/10.3390/antiox12040786.

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Excessive hydrogen peroxide causes oxidative stress in cells. The oxidation of two tyrosine residues in proteins can generate o,o′-dityrosine, a putative biomarker for protein oxidation, which plays critical roles in a variety of organisms. Thus far, few studies have investigated dityrosine crosslinking under endogenous or exogenous oxidative conditions at the proteome level, and its physiological function remains largely unknown. In this study, to investigate qualitative and quantitative dityrosine crosslinking, two mutant Escherichia coli strains and one mutant strain supplemented with H2O2

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39

Endres, Kevin J., Rodger A. Dilla, Matthew L. Becker, and Chrys Wesdemiotis. "Poly(ethylene glycol) Hydrogel Crosslinking Chemistries Identified via Atmospheric Solids Analysis Probe Mass Spectrometry." Macromolecules 54, no. 17 (2021): 7754–64. http://dx.doi.org/10.1021/acs.macromol.1c00765.

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40

Sinz, Andrea. "Investigation of protein–protein interactions in living cells by chemical crosslinking and mass spectrometry." Analytical and Bioanalytical Chemistry 397, no. 8 (2010): 3433–40. http://dx.doi.org/10.1007/s00216-009-3405-5.

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41

Muizebelt, W. J., J. J. Donkerbroek, M. W. F. Nielen, et al. "Oxidative crosslinking of alkyd resins studied with mass spectrometry and NMR using model compounds." Journal of Coatings Technology 70, no. 1 (1998): 83–93. http://dx.doi.org/10.1007/bf02720501.

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42

Cammarata, Michael B., and Jennifer S. Brodbelt. "Characterization of Intra- and Intermolecular Protein Crosslinking by Top Down Ultraviolet Photodissociation Mass Spectrometry." ChemistrySelect 1, no. 3 (2016): 590–93. http://dx.doi.org/10.1002/slct.201600140.

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43

Al-Eryani, Yusra, Morten Ib Rasmussen, Sven Kjellström, Peter Højrup, Cecilia Emanuelsson, and Claes von Wachenfeldt. "Exploring structure and interactions of the bacterial adaptor protein YjbH by crosslinking mass spectrometry." Proteins: Structure, Function, and Bioinformatics 84, no. 9 (2016): 1234–45. http://dx.doi.org/10.1002/prot.25072.

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44

Faustino, Anneliese M., and Stephen D. Fried. "Progress toward proteome-wide photo-crosslinking mass spectrometry to interrogate protein networks in vivo." Biophysical Journal 123, no. 3 (2024): 347a—348a. http://dx.doi.org/10.1016/j.bpj.2023.11.2112.

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45

van Ooli, W. J., and M. Nahmias. "Surface Characterization of Rubber by Secondary Ion Mass Spectrometry." Rubber Chemistry and Technology 62, no. 4 (1989): 656–82. http://dx.doi.org/10.5254/1.3536267.

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Abstract It has been demonstrated that static SIMS is potentially a very useful technique for the characterization of rubber surfaces. Its major capability is to provide molecular structural information of the polymer in addition to elemental analysis, which would also be possible with other surface techniques such as XPS or AES. The SIMS spectra are in many cases highly characteristic, and they can be used to identify the type and structure of the hydrocarbon polymer. In addition, structural changes in the rubber surface can be detected, and very useful information on the types and amounts of

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46

Gómez-de-Miranda-Jiménez-de-Aberasturi, Olga, Javier Calvo, Ingemar Svensson, Noelia Blanco, Leire Lorenzo, and Raquel Rodriguez. "Novel Determination of Functional Groups in Partially Acrylated Epoxidized Soybean Oil." Molecules 29, no. 19 (2024): 4582. http://dx.doi.org/10.3390/molecules29194582.

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The acrylation degree of vegetable oils plays a relevant role in determining the mechanical properties of the resulting polymers. Both epoxide and acrylate functionalities participate in polymerization reactions, producing various types of chemical bonds in the polymer network, which contribute to specific properties such as molecular size distribution, crosslinking degree, and glass transition temperature (Tg). The accurate identification of epoxide and acrylated groups in triglyceride molecules helps to predict their behavior during the polymerization process. A methodology based on analytic

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47

Argo, Andrew S., Chunxiao Shi, Fan Liu, and Michael B. Goshe. "Performing protein crosslinking using gas-phase cleavable chemical crosslinkers and liquid chromatography-tandem mass spectrometry." Methods 89 (November 2015): 64–73. http://dx.doi.org/10.1016/j.ymeth.2015.06.011.

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48

Ferraro, Nicholas A., and Michael Cascio. "Differential State-Dependent Crosslinking of Azi-Cholesterol with Human A1 Glycine Receptor using Mass Spectrometry." Biophysical Journal 116, no. 3 (2019): 223a. http://dx.doi.org/10.1016/j.bpj.2018.11.1227.

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49

Tomcho, Kayce A., Hannah E. Gering, Rathna J. Veeramachaneni, David J. Lapinsky, and Michael Cascio. "Targeted State Dependent Crosslinking Mass Spectrometry (CXMS) of the Human Alpha 1 Glycine Receptor (GLyR)." Biophysical Journal 116, no. 3 (2019): 392a. http://dx.doi.org/10.1016/j.bpj.2018.11.2120.

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50

Lloyd, Sarah M., Elizabeth J. Sande, Kenneth Ruterbories, et al. "Rapid LC-MS/MS Evaluation of Collagen and Elastin Crosslinks in Human and Mouse Lung Tissue with a Novel Bioanalytical Surrogate Matrix Approach." International Journal of Molecular Sciences 25, no. 23 (2024): 13026. https://doi.org/10.3390/ijms252313026.

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Alterations to post-translational crosslinking modifications in the extracellular matrix (ECM) are known to drive the pathogenesis of fibrotic diseases, including idiopathic pulmonary fibrosis (IPF). Thus, the methodology for measuring crosslinking dynamics is valuable for understanding disease progression. The existing crosslinking analysis sample preparation and liquid chromatography tandem mass spectrometry (LC-MS/MS) methods are typically labor-intensive and time-consuming which limits throughput. We, therefore, developed a rapid approach minimizing specialized equipment and hands-on time.

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