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

Stamatiou, K, Huguet, F, Serapinas, LV, Spanos, C, Rappsilber, J, Vagnarelli, P et al.. Ki-67 is necessary during DNA replication for fork protection and genome stability. Genome Biol. 2024;25 (1):105. doi: 10.1186/s13059-024-03243-5. PubMed PMID:38649976 PubMed Central PMC11034166.
Dendooven, T, Yatskevich, S, Burt, A, Chen, ZA, Bellini, D, Rappsilber, J et al.. Structure of the native γ-tubulin ring complex capping spindle microtubules. Nat Struct Mol Biol. 2024; :. doi: 10.1038/s41594-024-01281-y. PubMed PMID:38609662 .
Cayla, M, Spanos, C, McWilliam, K, Waskett, E, Rappsilber, J, Matthews, KR et al.. Differentiation granules, a dynamic regulator of T. brucei development. Nat Commun. 2024;15 (1):2972. doi: 10.1038/s41467-024-47309-1. PubMed PMID:38582942 PubMed Central PMC10998879.
Webster, MW, Chauvier, A, Rahil, H, Graziadei, A, Charles, K, Takacs, M et al.. Molecular basis of mRNA delivery to the bacterial ribosome. bioRxiv. 2024; :. doi: 10.1101/2024.03.19.585789. PubMed PMID:38562847 PubMed Central PMC10983998.
Vallat, B, Webb, BM, Westbrook, JD, Goddard, TD, Hanke, CA, Graziadei, A et al.. IHMCIF: An Extension of the PDBx/mmCIF Data Standard for Integrative Structure Determination Methods. J Mol Biol. 2024; :168546. doi: 10.1016/j.jmb.2024.168546. PubMed PMID:38508301 .
Zoch, A, Konieczny, G, Auchynnikava, T, Stallmeyer, B, Rotte, N, Heep, M et al.. C19ORF84 connects piRNA and DNA methylation machineries to defend the mammalian germ line. Mol Cell. 2024;84 (6):1021-1035.e11. doi: 10.1016/j.molcel.2024.01.014. PubMed PMID:38359823 PubMed Central PMC10960678.
Rappsilber, J. A dive into the unknome. Trends Genet. 2024;40 (1):15-16. doi: 10.1016/j.tig.2023.10.011. PubMed PMID:37968205 .
Tang, M, Pobegalov, G, Tanizawa, H, Chen, ZA, Rappsilber, J, Molodtsov, M et al.. Establishment of dsDNA-dsDNA interactions by the condensin complex. Mol Cell. 2023;83 (21):3787-3800.e9. doi: 10.1016/j.molcel.2023.09.019. PubMed PMID:37820734 PubMed Central PMC10842940.
Kolbowski, L, Fischer, L, Rappsilber, J. Cleavable Cross-Linkers Redefined by a Novel MS³-Trigger Algorithm. Anal Chem. 2023;95 (42):15461-15464. doi: 10.1021/acs.analchem.3c01673. PubMed PMID:37816155 PubMed Central PMC10603603.
Hempelmann, P, Lolicato, F, Graziadei, A, Brown, RDR, Spiegel, S, Rappsilber, J et al.. The sterol transporter STARD3 transports sphingosine at ER-lysosome contact sites. bioRxiv. 2023; :. doi: 10.1101/2023.09.18.557036. PubMed PMID:37790546 PubMed Central PMC10542139.