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3. First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study

Author

Iacobucci, Claudio, Piotrowski, Christine, Aebersold, Ruedi, Amaral, Bruno C, Andrews, Philip, Bernfur, Katja, Borchers, Christoph, Brodie, Nicolas I, Bruce, James E, Cao, Yong, Chaignepain, Stéphane, Chavez, Juan D, Claverol, Stéphane, Cox, Jürgen, Davis, Trisha, Degliesposti, Gianluca, Dong, Meng-Qiu, Edinger, Nufar, Emanuelsson, Cecilia, Gay, Marina, Götze, Michael, Gomes-Neto, Francisco, Gozzo, Fabio C, Gutierrez, Craig, Haupt, Caroline, Heck, Albert JR, Herzog, Franz, Huang, Lan, Hoopmann, Michael R, Kalisman, Nir, Klykov, Oleg, Kukačka, Zdeněk, Liu, Fan, MacCoss, Michael J, Mechtler, Karl, Mesika, Ravit, Moritz, Robert L, Nagaraj, Nagarjuna, Nesati, Victor, Neves-Ferreira, Ana GC, Ninnis, Robert, Novák, Petr, O’Reilly, Francis J, Pelzing, Matthias, Petrotchenko, Evgeniy, Piersimoni, Lolita, Plasencia, Manolo, Pukala, Tara, Rand, Kasper D, Rappsilber, Juri, Reichmann, Dana, Sailer, Carolin, Sarnowski, Chris P, Scheltema, Richard A, Schmidt, Carla, Schriemer, David C, Shi, Yi, Skehel, J Mark, Slavin, Moriya, Sobott, Frank, Solis-Mezarino, Victor, Stephanowitz, Heike, Stengel, Florian, Stieger, Christian E, Trabjerg, Esben, Trnka, Michael, Vilaseca, Marta, Viner, Rosa, Xiang, Yufei, Yilmaz, Sule, Zelter, Alex, Ziemianowicz, Daniel, Leitner, Alexander, and Sinz, Andrea

Subjects
Generic health relevance, Cross-Linking Reagents, Laboratories, Mass Spectrometry, Reproducibility of Results, Serum Albumin, Bovine, Analytical Chemistry, Other Chemical Sciences
Abstract

The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

Published
2019

21. An anti-HER2 nanobody binds to its antigen HER2 via two independent paratopes

Author

Ubbiali, Daniele, primary, Orlando, Marco, additional, Kovačič, Matic, additional, Iacobucci, Claudio, additional, Semrau, Marta S., additional, Bajc, Gregor, additional, Fortuna, Sara, additional, Ilc, Gregor, additional, Medagli, Barbara, additional, Oloketuyi, Sandra, additional, Storici, Paola, additional, Sinz, Andrea, additional, Grandori, Rita, additional, and de Marco, Ario, additional

Published
2021
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30. The First Community-Wide, Comparative Cross-linking Mass Spectrometry Study

Author

Iacobucci, Claudio, Piotrowski, Christine, Aebersold, Ruedi, Amaral, Bruno C, Andrews, Philip C, Bernfur, Katja, Borchers, Christoph H, Brodie, Nicholas I, Bruce, James E, Cao, Yong, Chaignepain, Stéphane, Chavez, Juan D, Claverol, Stéphane, Cox, Jurgen, Davis, Trisha N, Degliesposti, Gianluca, Dong, Meng-Qiu, Edinger, Nufar, Emanuelsson, Cecilia, Gay, Marina, Götze, Michael, Gomes-Neto, Francisco, Gozzo, Fabio Cesar, Gutierrez, Craig B, Haupt, Caroline, Heck, Albert J R, Herzog, Frank, Huang, Lan, Hoopmann, Michael R, Kalisman, Nir, Klykov, Oleg, Kukačka, Zdeněk, Liu, Fan, MacCoss, Michael J, Mechtler, Karl, Mesika, Ravit, Moritz, Robert L, Nagaraj, Nagarjuna, Nesati, Victor, Neves-Fereira, Ana G C, Ninnis, Robert, Novák, Petr, O'Reilly, Francis J, Pelzing, Matthias, Petrotchenko, Evgeniy V, Piersimoni, Lolita, Plasencia, Manolo, Pukala, Tara L, Rand, Kasper D, Rappsilber, Juri, Reichman, Dana, Sailer, Carolin, Sarnowski, Chris P, Scheltema, Richard A, Schmidt, Carla, Schriemer, David C, Shi, Yi, Skehel, J Mark, Slavin, Moriya, Sobott, Frank, Solis-Mezarino, Victor, Stephanowitz, Heike, Stengel, Florian, Stieger, Christian E, Trabjerg, Esben, Trnka, Michael J, Vilaseca, Marta, Viner, Rosa, Xiang, Yufei, Yılmaz, Şule, Zelter, Alex, Ziemianowicz, Daniel S, Leitner, Alexander, Sinz, Andrea, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., and Biomolecular Mass Spectrometry and Proteomics

Abstract

The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein-protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines for conducting cross-linking experiments, performing data analysis, and reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

Published
2019

31. Anal. Chem

Author

Iacobucci, Claudio, Piotrowski, Christine, Aebersold, Ruedi, Amaral, Bruno C, Andrews, Philip C, Bernfur, Katja, Borchers, Christoph H, Brodie, Nicholas I, Bruce, James E, Cao, Yong, Chaignepain, Stéphane, Chavez, Juan D, Claverol, Stéphane, Cox, Jurgen, Davis, Trisha N, Degliesposti, Gianluca, Dong, Meng-Qiu, Edinger, Nufar, Emanuelsson, Cecilia, Gay, Marina, Götze, Michael, Gomes-Neto, Francisco, Gozzo, Fabio Cesar, Gutierrez, Craig B, Haupt, Caroline, Heck, Albert J R, Herzog, Frank, Huang, Lan, Hoopmann, Michael R, Kalisman, Nir, Klykov, Oleg, Kukačka, Zdeněk, Liu, Fan, MacCoss, Michael J, Mechtler, Karl, Mesika, Ravit, Moritz, Robert L, Nagaraj, Nagarjuna, Nesati, Victor, Neves-Fereira, Ana G C, Ninnis, Robert, Novák, Petr, O'Reilly, Francis J, Pelzing, Matthias, Petrotchenko, Evgeniy V, Piersimoni, Lolita, Plasencia, Manolo, Pukala, Tara L, Rand, Kasper D, Rappsilber, Juri, Reichman, Dana, Sailer, Carolin, Sarnowski, Chris P, Scheltema, Richard A, Schmidt, Carla, Schriemer, David C, Shi, Yi, Skehel, J Mark, Slavin, Moriya, Sobott, Frank, Solis-Mezarino, Victor, Stephanowitz, Heike, Stengel, Florian, Stieger, Christian E, Trabjerg, Esben, Trnka, Michael J, Vilaseca, Marta, Viner, Rosa, Xiang, Yufei, Yılmaz, Şule, Zelter, Alex, Ziemianowicz, Daniel S, Leitner, Alexander, Sinz, Andrea, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, Univ Bordeaux, CNRS UMR 5248, Inst Chim & Biol Membranes & Nanoobjets, INP Bordeaux, Université de Bordeaux (UB)-Institut Polytechnique de Bordeaux (Bordeaux INP)-Centre National de la Recherche Scientifique (CNRS), Plateforme Métabolome-Fluxome du Centre de Génomique Fonctionnelle de Bordeaux, Institut National de la Recherche Agronomique (INRA), Chimie et Biologie des Membranes et des Nanoobjets (CBMN), and École Nationale d'Ingénieurs des Travaux Agricoles - Bordeaux (ENITAB)-Institut de Chimie du CNRS (INC)-Université de Bordeaux (UB)-Centre National de la Recherche Scientifique (CNRS)

Subjects
Proteomics, Status quo, Group method of data handling, media_common.quotation_subject, Best practice, Harmonization, Peptides and proteins, 010402 general chemistry, 01 natural sciences, Field (computer science), Article, Mass Spectrometry, Analytical Chemistry, Serum Albumin, media_common, Community based, Chemistry, 010401 analytical chemistry, Monomers, Information analysis, Reproducibility of Results, Serum Albumin, Bovine, [CHIM.MATE]Chemical Sciences/Material chemistry, Bovine, Data science, 0104 chemical sciences, Nucleic acid structure Software, Cross-Linking Reagents, Multicenter study, Generic health relevance, Laboratories, Other Chemical Sciences
Abstract

The number of publications in the field of chemical cross-linking combined with mass spectrometry (XL-MS) to derive constraints for protein three-dimensional structure modeling and to probe protein protein interactions has increased during the last years. As the technique is now becoming routine for in vitro and in vivo applications in proteomics and structural biology there is a pressing need to define protocols as well as data analysis and reporting formats. Such consensus formats should become accepted in the field and be shown to lead to reproducible results. This first, community-based harmonization study on XL-MS is based on the results of 32 groups participating worldwide. The aim of this paper is to summarize the status quo of XL-MS and to compare and evaluate existing cross-linking strategies. Our study therefore builds the framework for establishing best practice guidelines to conduct cross-linking experiments, perform data analysis, and define reporting formats with the ultimate goal of assisting scientists to generate accurate and reproducible XL-MS results.

Published
2019

33. Flexibility of intrinsically disordered degrons in AUX/IAA proteins reinforces auxin co-receptor assemblies

Author

Niemeyer, Michael, primary, Castillo, Elena Moreno, additional, Ihling, Christian H., additional, Iacobucci, Claudio, additional, Wilde, Verona, additional, Hellmuth, Antje, additional, Hoehenwarter, Wolfgang, additional, Samodelov, Sophia L., additional, Zurbriggen, Matias D., additional, Kastritis, Panagiotis L., additional, Sinz, Andrea, additional, and Calderón Villalobos, Luz Irina A., additional

Published
2019
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35. Instrumentation

Author

Iacobucci, Claudio, primary, Suder, Piotr, additional, Bodzon‐Kulakowska, Anna, additional, Antolak, Anna, additional, Silberring, Jerzy, additional, Smoluch, Marek, additional, Mielczarek, Przemyslaw, additional, Grasso, Giuseppe, additional, Pawlaczyk, Aleksandra, additional, Szynkowska, Małgorzata Iwona, additional, Tuccitto, Nunzio, additional, Stefanowicz, Piotr, additional, Szewczuk, Zbigniew, additional, and Natale, Giuseppe, additional

Published
2019
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37. Carboxyl-Photo-Reactive MS-Cleavable Cross-Linkers: Unveiling a Hidden Aspect of Diazirine-Based Reagents

Author

Iacobucci, Claudio, Götze, Michael, Piotrowski, Christine, Arlt, Christian, Rehkamp, Anne, Ihling, Christian, Hage, Christoph, and Sinz, Andrea

Abstract

A major challenge in cross-linking/mass spectrometry (MS) is targeting carboxyl functions in proteins under physiological conditions that do not disturb the protein’s conformation. Cross-linking of glutamic acid and aspartic acid residues in proteins will greatly expand the scope of structural mass spectrometry. We discovered that carboxyl-reactive cross-linkers have already been employed for many years in cross-linking/MS studies, yet in a completely different context. Diazirine-based cross-linkers, such as photomethionine and succinimidyldiazirine cross-linkers, are currently considered to react nonspecifically upon UV-A photoactivation with all 20 proteinogenic amino acids through a reactive carbene that inserts mainly into C–H bonds. We discovered that the cross-linking capability of diazirines based on X–H (X = C, N, O) insertion is in fact only the tip of the iceberg. Diazirines isomerize to linear diazo compounds that can react with carboxylic acids to yield esters. On top of that, the resulting cross-linked products are MS-cleavable allowing an automated analysis of cross-links via customized software tools. Therefore, diazirines open an entirely new route for photo-cross-linking of carboxylic acids. Previous cross-linking studies using diazirines have to be revisited in the light of these findings.

Published
2024
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38. Evaluating Imide-Based Mass Spectrometry-Cleavable Cross-Linkers for Structural Proteomics Studies

Author

Ianni, Alessio Di, Ihling, Christian H., Vranka, Tomáš, Matoušek, Václav, Sinz, Andrea, and Iacobucci, Claudio

Abstract

Disuccinimidyl dibutyric urea (DSBU) is a mass spectrometry (MS)-cleavable cross-linker that has multiple applications in structural biology, ranging from isolated protein complexes to comprehensive system-wide interactomics. DSBU facilitates a rapid and reliable identification of cross-links through the dissociation of its urea group in the gas phase. In this study, we further advance the structural capabilities of DSBU by remodeling the urea group into an imide, thus introducing a novel class of cross-linkers. This modification preserves the MS cleavability of the amide bond, granted by the two acyl groups of the imide function. The central nitrogen atom enables the introduction of affinity purification tags. Here, we introduce disuccinimidyl disuccinic imide (DSSI) as a prototype of this class of cross-linkers. It features a phosphonate handle for immobilized metal ion affinity chromatography enrichment. We detail DSSI synthesis and describe its behavior in solution and in the gas phase while cross-linking isolated proteins and human cell lysates. DSSI and DSBU cross-links are compared at the same enrichment depth to bridge these two cross-linker classes. We validate DSSI cross-links by mapping them in high-resolution structures of large protein assemblies. The cross-links observed yield insights into the morphology of intrinsically disordered proteins and their complexes. The DSSI linker might spearhead a novel class of MS-cleavable and enrichable cross-linkers.

Published
2024
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39. Cross-linking/Mass Spectrometry: A Community-Wide, Comparative Study Towards Establishing Best Practice Guidelines

Author

Iacobucci, Claudio, primary, Piotrowski, Christine, additional, Aebersold, Ruedi, additional, Amaral, Bruno C., additional, Andrews, Philip, additional, Borchers, Christoph, additional, Brodie, Nicolas I., additional, Bruce, James E., additional, Chaignepain, Stéphane, additional, Chavez, Juan D., additional, Claverol, Stéphane, additional, Cox, Jürgen, additional, Degliesposti, Gianluca, additional, Dong, Meng-Qiu, additional, Edinger, Nufar, additional, Emanuelsson, Cecilia, additional, Gay, Marina, additional, Götze, Michael, additional, Gozzo, Fabio C., additional, Gutierrez, Craig, additional, Haupt, Caroline, additional, Heck, Albert J. R., additional, Herzog, Franz, additional, Huang, Lan, additional, Hoopmann, Michael R., additional, Kalisman, Nir, additional, Klykov, Oleg, additional, Kukačka, Zdeněk, additional, Liu, Fan, additional, MacCoss, Michael J., additional, Mechtler, Karl, additional, Mesika, Ravit, additional, Moritz, Robert L., additional, Nagaraj, Nagarjuna, additional, Nesati, Victor, additional, Ninnis, Robert, additional, Novák, Petr, additional, O’Reilly, Francis J, additional, Pelzing, Matthias, additional, Petrotchenko, Evgeniy, additional, Piersimoni, Lolita, additional, Plasencia, Manolo, additional, Pukala, Tara, additional, Rand, Kasper D., additional, Rappsilber, Juri, additional, Reichmann, Dana, additional, Sailer, Caroline, additional, Sarnowski, Chris P., additional, Scheltema, Richard A., additional, Schmidt, Carla, additional, Schriemer, David C., additional, Shi, Yi, additional, Skehel, J. Mark, additional, Slavin, Moriya, additional, Sobott, Frank, additional, Solis-Mezarino, Victor, additional, Stephanowitz, Heike, additional, Stengel, Florian, additional, Stieger, Christian E., additional, Trnka, Michael, additional, Vilaseca, Marta, additional, Viner, Rosa, additional, Xiang, Yufei, additional, Yilmaz, Sule, additional, Zelter, Alex, additional, Ziemianowicz, Daniel, additional, Leitner, Alexander, additional, and Sinz, Andrea, additional

Published
2018
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45. Gating the electron transfer at a monocopper centre through the supramolecular coordination of water molecules within a protein chamber mimic

Author

Le Poul, Nicolas, primary, Colasson, Benoit, additional, Thiabaud, Grégory, additional, Dit Fouque, Dany Jeanne, additional, Iacobucci, Claudio, additional, Memboeuf, Antony, additional, Douziech, Bénédicte, additional, Řezáč, Jan, additional, Prangé, Thierry, additional, Lande, Aurélien de la, additional, Reinaud, Olivia, additional, and Le Mest, Yves, additional

Published
2018
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50. Free radical‐initiated peptide sequencing (FRIPS)‐based cross‐linkers for improved peptide and protein structure analysis.

Author

Iacobucci, Claudio, Schäfer, Mathias, and Sinz, Andrea

Subjects
*FREE radicals, *AMINO acid sequence, *PROTEIN structure, *CHARGE exchange, *CROSSLINKING (Polymerization)
Abstract

Free radical‐initiated peptide sequencing (FRIPS) has recently been introduced as an analytical strategy to create peptide radical ions in a predictable and effective way by collisional activation of specifically modified peptides ions. FRIPS is based on the unimolecular dissociation of open‐shell ions and yields fragments that resemble those obtained by electron capture dissociation (ECD) or electron transfer dissociation (ETD). In this review article, we describe the fundamentals of FRIPS and highlight its fruitful combination with chemical cross‐linking/mass spectrometry (MS) as a highly promising option to derive complementary structural information of peptides and proteins. FRIPS does not only yield exhaustive sequence information of cross‐linked peptides, but also defines the exact cross‐linking sites of the connected peptides. The development of more advanced FRIPS cross‐linkers that extend the FRIPS‐based cross‐linking/MS approach to the study of large protein assemblies and protein interaction networks can be eagerly anticipated. [ABSTRACT FROM AUTHOR]

Published
2019
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