Publications – Rappsilber Laboratory

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Light-Induced Orthogonal Fragmentation of Crosslinked Peptides

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JACS Au, 2023

Chemistry, Crosslinking, Publication
Dual-Bioorthogonal Catalysis by a Palladium Peptide Complex

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Journal of Medicinal Chemistry, 2023

Chemistry, Publication
Improved Peptide Backbone Fragmentation Is the Primary Advantage of MS-Cleavable Crosslinkers

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Analytical Chemistry, 2022

Crosslinking, Publication
Leveraging Parameter Dependencies in High-Field Asymmetric Waveform Ion-Mobility Spectrometry and Size-exclusion Chromatography for Proteome-wide Crosslinking Mass Spectrometry

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Analytical Chemistry, 2022

Chromatography, Crosslinking, Ion-mobility spectrometry, Method development, Publication
Leveraging crosslinking mass spectrometry in structural and cell biology

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Structure, 2021

Crosslinking, Crosslinking (in situ), MS development, Publication, Review, Standardisation, Structural Biology (method)
Proteinanalytik mittels Crosslinking-Massenspektrometrie

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GIT Labor-Fachzeitschrift, 2021

Crosslinking, Publication, Review
Reliable identification of protein-protein interactions by crosslinking mass spectrometry

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Nature Communications, 2021

Crosslinking, Method development, Publication, Software, Structural Biology (application)
Retention Time Prediction Using Neural Networks Increases Identifications in Crosslinking Mass Spectrometry

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Nature Communications, 2021

Chromatography, Crosslinking, Machine learning, Method development, Publication, Software
Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry

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Structure, 2020

Crosslinking, Crosslinking (in situ), MS development, Publication, Review, Standardisation, Structural Biology (method)
Anatomy of a crosslinker

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Current Opinion in Chemical Biology, 2021

Chemistry, Crosslinking, Crosslinking (high density), Crosslinking (quantitative), Publication, Quantitation, Review, Standardisation, Structural Biology (method)
In-cell architecture of an actively transcribing-translating expressome

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Science, 2020

Crosslinking, Crosslinking (in situ), Publication, Structural Biology (application), Structural Biology (method)
Proteomics Using Protease Alternatives to Trypsin Benefits from Sequential Digestion with Trypsin

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Therese Dau, Giulia Bartolomucci, Juri Rappsilber Analytical Chemistry, 2020 https://doi.org/10.1021/acs.analchem.0c00478 Trypsin is the most used enzyme in proteomics....

Method development, Publication
Ultraviolet Photodissociation of Tryptic Peptide Backbones at 213 nm

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Lars Kolbowski, Adam Belsom, Juri Rappsilber Journal of the American Society for Mass Spectrometry, 2020 https://doi.org/10.1021/jasms.0c00106 We analyzed...

Method development, MS development, Publication
The structure of human thyroglobulin

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Nature, 2020

Collaboration highlights, Crosslinking, Publication, Structural Biology (application)
Co-regulation map of the human proteome enables identification of protein functions

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Nature Biotechnology, 2019

Machine learning, Publication, Software
Lamin A molecular compression and sliding as mechanisms behind nucleoskeleton elasticity

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Nature Communications, 2019

Crosslinking, Publication
Quantitative Photo-crosslinking Mass Spectrometry Revealing Protein Structure Response to Environmental Changes

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Analytical Chemistry, 2019

Crosslinking, Method development, Publication, Quantitation
A folded conformation of MukBEF and cohesin

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Nature Structural & Molecular Biology, 2019

Collaboration highlights, Crosslinking, Publication, Structural Biology (application)
Sequential Digestion with Trypsin and Elastase in Cross-Linking Mass Spectrometry.

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Analytical Chemistry, 2019

Crosslinking, Method development, Publication
Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry

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Molecular & Cellular Proteomics, 2019

Crosslinking, Crosslinking (quantitative), Method development, MS development, Publication, Quantitation
Noncovalently Associated Peptides Observed during Liquid Chromatography-Mass Spectrometry and Their Effect on Cross-Link Analyses

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Analytical Chemistry, 2019

Crosslinking, Method development, Publication
Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition

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Molecular & Cellular Proteomics, 2019

Publication
Protein Dynamics in Solution by Quantitative Crosslinking/Mass Spectrometry.

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Trends in Biochemical Sciences, 2018

Crosslinking (quantitative), Publication, Review
In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides

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Journal of Proteome Research, 2018

Crosslinking, Publication
Epigenetic Variability Confounds Transcriptome but Not Proteome Profiling for Coexpression-based Gene Function Prediction

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Molecular & Cellular Proteomics, 2018

Publication
xiSPEC: web-based visualization, analysis and sharing of proteomics data

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Nucleic Acids Research, 2018

Publication, Software, Standardisation, Visualization
Peptide Retention in Hydrophilic Strong Anion Exchange Chromatography Is Driven by Charged and Aromatic Residues.

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Analytical Chemistry, 2018

Chemistry, Chromatography, Machine learning, Publication, Software
Protein Tertiary Structure by Crosslinking/ Mass Spectrometry

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Trends in Biochemical Sciences, 2018

Crosslinking, Publication, Review
On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry

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Journal of the American Society for Mass Spectrometry, 2017

Crosslinking, Publication, Quantitation
Quantitative cross-linking/mass spectrometry to elucidate structural changes in proteins and their complexes.

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Nature Protocols, 2019

Crosslinking (quantitative), Publication
ComplexViewer: visualization of curated macromolecular complexes

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Bioinformatics, 2017

Crosslinking, Publication, Software, Visualization
Complementary Benzophenone Cross-Linking/Mass Spectrometry Photochemistry

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Analytical Chemistry, 2017

Crosslinking, Method development, Publication
Optimizing the Parameters Governing the Fragmentation of Cross-Linked Peptides in a Tribrid Mass Spectrometer

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Analytical Chemistry 2017

Crosslinking, Method development, MS development, Publication
Blind testing crosslinking/mass spectrometry under the auspices of the 11th critical assessment of methods of protein structure prediction (CASP11)

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Wellcome Open Research, 2016

Crosslinking, Method development, Publication
Repression of RNA polymerase by the archaeo-viral regulator ORF145/RIP

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Nature Communications, 2016

Crosslinking, Publication
Optimized fragmentation regime for diazirine photo-cross-linked peptides

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Analytical Chemistry, 2016

Crosslinking, Method development, Publication
Blind Evaluation of Hybrid Protein Structure Analysis Methods based on Cross-Linking

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Trends in Biochemical Sciences, 2016

Publication
Quantitative Cross-linking/Mass Spectrometry Using Isotope-labeled Cross-linkers and MaxQuant.

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molecular & cellular proteomics, 2016

Crosslinking (quantitative), Publication, Software
Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling.

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molecular & cellular proteomics, 2016

Crosslinking (quantitative), Publication, Structural Biology (application)
A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides.

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Molecular & Cellular Proteomics, 2016

Crosslinking, Method development, Publication
Serum Albumin Domain Structures in Human Blood Serum by Mass Spectrometry and Computational Biology

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Molecular & Cellular Proteomics, 2016

Crosslinking, Method development, Publication
A Single α Helix Drives Extensive Remodeling of the Proteasome Lid and Completion of Regulatory Particle Assembly.

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Cell, 2015

Collaboration highlights, Crosslinking (quantitative), Publication, Structural Biology (application)

Latest from Pubmed

Balu, S, Huget, S, Medina Reyes, JJ, Ragueneau, E, Panneerselvam, K, Fischer, SN et al.. Complex portal 2025: predicted human complexes and enhanced visualisation tools for the comparison of orthologous and paralogous complexes. Nucleic Acids Res. 2024; :. doi: 10.1093/nar/gkae1085. PubMed PMID:39558156 .
Lenz, M, Turko, P, Kruse, P, Eichler, A, Chen, ZA, Rappsilber, J et al.. Transcriptomic and de novo proteomic analyses of organotypic entorhino-hippocampal tissue cultures reveal changes in metabolic and signaling regulators in TTX-induced synaptic plasticity. Mol Brain. 2024;17 (1):78. doi: 10.1186/s13041-024-01153-y. PubMed PMID:39511688 PubMed Central PMC11542228.
Kwiatkowski, A, Caserta, G, Schulz, AC, Frielingsdorf, S, Pelmenschikov, V, Weisser, K et al.. ATP-Triggered Fe(CN)₂CO Synthon Transfer from the Maturase HypCD to the Active Site of Apo-[NiFe]-Hydrogenase. J Am Chem Soc. 2024;146 (45):30976-30989. doi: 10.1021/jacs.4c09791. PubMed PMID:39491524 PubMed Central PMC11565642.
Dias Mirandela, M, Zoch, A, Leismann, J, Webb, S, Berrens, RV, Valsakumar, D et al.. Two-factor authentication underpins the precision of the piRNA pathway. Nature. 2024;634 (8035):979-985. doi: 10.1038/s41586-024-07963-3. PubMed PMID:39294378 PubMed Central PMC11499256.
Pinto, MBC, Schmidt, FL, Chen, Z, Rappsilber, J, Gibson, B, Wietstock, PC et al.. The Influence of Barley Proteome on Hop Bitter Acid Yield during Brewing. J Agric Food Chem. 2024;72 (38):21166-21180. doi: 10.1021/acs.jafc.4c04396. PubMed PMID:39285157 PubMed Central PMC11440504.
Stahl, K, Warneke, R, Demann, L, Bremenkamp, R, Hormes, B, Brock, O et al.. Modelling protein complexes with crosslinking mass spectrometry and deep learning. Nat Commun. 2024;15 (1):7866. doi: 10.1038/s41467-024-51771-2. PubMed PMID:39251624 PubMed Central PMC11383924.
Combe, CW, Graham, M, Kolbowski, L, Fischer, L, Rappsilber, J. xiVIEW: Visualisation of Crosslinking Mass Spectrometry Data. J Mol Biol. 2024;436 (17):168656. doi: 10.1016/j.jmb.2024.168656. PubMed PMID:39237202 .
Parashara, P, Medina-Pritchard, B, Abad, MA, Sotelo-Parrilla, P, Thamkachy, R, Grundei, D et al.. PLK1-mediated phosphorylation cascade activates Mis18 complex to ensure centromere inheritance. Science. 2024;385 (6713):1098-1104. doi: 10.1126/science.ado8270. PubMed PMID:39236175 .
Li, C, Moro, S, Shostak, K, O'Reilly, FJ, Donzeau, M, Graziadei, A et al.. Molecular mechanism of IKK catalytic dimer docking to NF-κB substrates. Nat Commun. 2024;15 (1):7692. doi: 10.1038/s41467-024-52076-0. PubMed PMID:39227404 PubMed Central PMC11371828.
Fischer, L, Rappsilber, J. Rescuing error control in crosslinking mass spectrometry. Mol Syst Biol. 2024;20 (9):1076-1084. doi: 10.1038/s44320-024-00057-2. PubMed PMID:39095427 PubMed Central PMC11368935.