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2. Initial recommendations for performing, benchmarking, and reporting single-cell proteomics experiments

Author

Gatto, Laurent, Aebersold, Ruedi, Cox, Juergen, Demichev, Vadim, Derks, Jason, Emmott, Edward, Franks, Alexander M., Ivanov, Alexander R., Kelly, Ryan T., Khoury, Luke, Leduc, Andrew, MacCoss, Michael J., Nemes, Peter, Perlman, David H., Petelski, Aleksandra A., Rose, Christopher M., Schoof, Erwin M., Van Eyk, Jennifer, Vanderaa, Christophe, Yates III, John R., and Slavov, Nikolai

Subjects
Quantitative Biology - Other Quantitative Biology
Abstract

Analyzing proteins from single cells by tandem mass spectrometry (MS) has become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and reproducibility of the results may be undermined by numerous factors affecting experimental design, sample preparation, data acquisition, and data analysis. Broadly accepted community guidelines and standardized metrics will enhance rigor, data quality, and alignment between laboratories. Here we propose best practices, quality controls, and data reporting recommendations to assist in the broad adoption of reliable quantitative workflows for single-cell proteomics., Comment: Supporting website: https://single-cell.net/guidelines

Published
2022
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4. Towards Increased Reliability, Transparency and Accessibility in Crosslinking Mass Spectrometry

Author

Leitner, Alexander, Bonvin, Alexandre M. J. J., Borchers, Christoph H., Chalkley, Robert J., Chamot-Rooke, Julia, Combe, Colin W., Cox, Jürgen, Dong, Meng-Qiu, Fischer, Lutz, Götze, Michael, Gozzo, Fabio C., Heck, Albert J. R., Hoopmann, Michael R., Huang, Lan, Ishihama, Yasushi, Jones, Andrew R., Kalisman, Nir, Kohlbacher, Oliver, Mechtler, Karl, Moritz, Robert L., Netz, Eugen, Novak, Petr, Petrotchenko, Evgeniy, Sali, Andrej, Scheltema, Richard A., Schmidt, Carla, Schriemer, David, Sinz, Andrea, Sobott, Frank, Stengel, Florian, Thalassinos, Konstantinos, Urlaub, Henning, Viner, Rosa, Vizcaino, Juan A., Wilkins, Marc R., and Rappsilber, Juri

Subjects
Quantitative Biology - Other Quantitative Biology
Abstract

Crosslinking mass spectrometry (Crosslinking MS) has substantially matured as a method over the last two decades through parallel development in multiple labs, demonstrating its applicability for protein structure determination, conformation analysis and mapping protein interactions in complex mixtures. Crosslinking MS has become a much-appreciated and routinely applied tool especially in structural biology. Therefore, it is timely that the community commits to the development of methodological and reporting standards. This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Crosslinking MS for which guidelines should be developed as part of a Crosslinking MS standards initiative., Comment: 26 pages, 1 figure

Published
2020

6. 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

10. The ER membrane protein complex interacts cotranslationally to enable biogenesis of multipass membrane proteins.

Author

Shurtleff, Matthew J, Itzhak, Daniel N, Hussmann, Jeffrey A, Schirle Oakdale, Nicole T, Costa, Elizabeth A, Jonikas, Martin, Weibezahn, Jimena, Popova, Katerina D, Jan, Calvin H, Sinitcyn, Pavel, Vembar, Shruthi S, Hernandez, Hilda, Cox, Jürgen, Burlingame, Alma L, Brodsky, Jeffrey L, Frost, Adam, Borner, Georg Hh, and Weissman, Jonathan S

Subjects
Endoplasmic Reticulum, Ribosomes, Humans, Saccharomyces cerevisiae, Multiprotein Complexes, Membrane Proteins, Molecular Chaperones, Proteomics, Protein Biosynthesis, Protein Transport, EMC, cell biology, endoplasmic reticulum, human, ion channel, transmembrane, transporter, Biochemistry and Cell Biology
Abstract

The endoplasmic reticulum (ER) supports biosynthesis of proteins with diverse transmembrane domain (TMD) lengths and hydrophobicity. Features in transmembrane domains such as charged residues in ion channels are often functionally important, but could pose a challenge during cotranslational membrane insertion and folding. Our systematic proteomic approaches in both yeast and human cells revealed that the ER membrane protein complex (EMC) binds to and promotes the biogenesis of a range of multipass transmembrane proteins, with a particular enrichment for transporters. Proximity-specific ribosome profiling demonstrates that the EMC engages clients cotranslationally and immediately following clusters of TMDs enriched for charged residues. The EMC can remain associated after completion of translation, which both protects clients from premature degradation and allows recruitment of substrate-specific and general chaperones. Thus, the EMC broadly enables the biogenesis of multipass transmembrane proteins containing destabilizing features, thereby mitigating the trade-off between function and stability.

Published
2018

14. The dental proteome of Homo antecessor

Author

Welker, Frido, Ramos-Madrigal, Jazmín, Gutenbrunner, Petra, Mackie, Meaghan, Tiwary, Shivani, Rakownikow Jersie-Christensen, Rosa, Chiva, Cristina, Dickinson, Marc R., Kuhlwilm, Martin, de Manuel, Marc, Gelabert, Pere, Martinón-Torres, María, Margvelashvili, Ann, Arsuaga, Juan Luis, Carbonell, Eudald, Marques-Bonet, Tomas, Penkman, Kirsty, Sabidó, Eduard, Cox, Jürgen, Olsen, Jesper V., Lordkipanidze, David, Racimo, Fernando, Lalueza-Fox, Carles, Bermúdez de Castro, José María, Willerslev, Eske, and Cappellini, Enrico

Published
2020
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15. Enamel proteome shows that Gigantopithecus was an early diverging pongine

Author

Welker, Frido, Ramos-Madrigal, Jazmín, Kuhlwilm, Martin, Liao, Wei, Gutenbrunner, Petra, de Manuel, Marc, Samodova, Diana, Mackie, Meaghan, Allentoft, Morten E., Bacon, Anne-Marie, Collins, Matthew J., Cox, Jürgen, Lalueza-Fox, Carles, Olsen, Jesper V., Demeter, Fabrice, Wang, Wei, Marques-Bonet, Tomas, and Cappellini, Enrico

Published
2019
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16. Multicenter Collaborative Study to Optimize Mass Spectrometry Workflows of Clinical Specimens

Author

Kardell, Oliver, primary, von Toerne, Christine, additional, Merl-Pham, Juliane, additional, König, Ann-Christine, additional, Blindert, Marcel, additional, Barth, Teresa K., additional, Mergner, Julia, additional, Ludwig, Christina, additional, Tüshaus, Johanna, additional, Eckert, Stephan, additional, Müller, Stephan A., additional, Breimann, Stephan, additional, Giesbertz, Pieter, additional, Bernhardt, Alexander M., additional, Schweizer, Lisa, additional, Albrecht, Vincent, additional, Teupser, Daniel, additional, Imhof, Axel, additional, Kuster, Bernhard, additional, Lichtenthaler, Stefan F., additional, Mann, Matthias, additional, Cox, Jürgen, additional, and Hauck, Stefanie M., additional

Published
2023
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18. Enamel proteins reveal biological sex and genetic variability within southern AfricanParanthropus

Author

Madupe, Palesa P., primary, Koenig, Claire, additional, Patramanis, Ioannis, additional, Rüther, Patrick L., additional, Hlazo, Nomawethu, additional, Mackie, Meaghan, additional, Tawane, Mirriam, additional, Krueger, Johanna, additional, Taurozzi, Alberto J., additional, Troché, Gaudry, additional, Kibii, Job, additional, Pickering, Robyn, additional, Dickinson, Marc, additional, Sahle, Yonatan, additional, Kgotleng, Dipuo, additional, Musiba, Charles, additional, Manthi, Fredrick, additional, Bell, Liam, additional, DuPlessis, Michelle, additional, Gilbert, Catherine, additional, Zipfel, Bernhard, additional, Kuderna, Lukas F. K., additional, Lizano, Esther, additional, Welker, Frido, additional, Kyriakidou, Pelagia, additional, Cox, Jürgen, additional, Mollereau, Catherine, additional, Tokarski, Caroline, additional, Blackburn, Jonathan, additional, Ramos-Madrigal, Jazmín, additional, Marques-Bonet, Tomas, additional, Penkman, Kirsty, additional, Zanolli, Clément, additional, Schroeder, Lauren, additional, Racimo, Fernando, additional, Olsen, Jesper V., additional, Ackermann, Rebecca R., additional, and Cappellini, Enrico, additional

Published
2023
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20. Suppl FigS3 from The Proteome of Prostate Cancer Bone Metastasis Reveals Heterogeneity with Prognostic Implications

Author

Iglesias-Gato, Diego, primary, Thysell, Elin, primary, Tyanova, Stefka, primary, Crnalic, Sead, primary, Santos, Alberto, primary, Lima, Thiago S., primary, Geiger, Tamar, primary, Cox, Jürgen, primary, Widmark, Anders, primary, Bergh, Anders, primary, Mann, Matthias, primary, Flores-Morales, Amilcar, primary, and Wikström, Pernilla, primary

Published
2023
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21. Table S3 from The Proteome of Prostate Cancer Bone Metastasis Reveals Heterogeneity with Prognostic Implications

Author

Iglesias-Gato, Diego, primary, Thysell, Elin, primary, Tyanova, Stefka, primary, Crnalic, Sead, primary, Santos, Alberto, primary, Lima, Thiago S., primary, Geiger, Tamar, primary, Cox, Jürgen, primary, Widmark, Anders, primary, Bergh, Anders, primary, Mann, Matthias, primary, Flores-Morales, Amilcar, primary, and Wikström, Pernilla, primary

Published
2023
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22. Accurate and Automated High-Coverage Identification of Chemically Cross-Linked Peptides with MaxLynx

Author

Yılmaz, Şule, Busch, Florian, Nagaraj, Nagarjuna, and Cox, Jürgen

Subjects
Cross-Linking Reagents, Drosophila melanogaster, Proteome, Animals, Peptides, Article, Mass Spectrometry, Software, Analytical Chemistry
Abstract

Cross-linking combined with mass spectrometry (XL-MS) provides a wealth of information about the three-dimensional (3D) structure of proteins and their interactions. We introduce MaxLynx, a novel computational proteomics workflow for XL-MS integrated into the MaxQuant environment. It is applicable to noncleavable and MS-cleavable cross-linkers. For both, we have generalized the Andromeda peptide database search engine to efficiently identify cross-linked peptides. For noncleavable peptides, we implemented a novel dipeptide Andromeda score, which is the basis for a computationally efficient N-squared search engine. Additionally, partial scores summarize the evidence for the two constituents of the dipeptide individually. A posterior error probability (PEP) based on total and partial scores is used to control false discovery rates (FDRs). For MS-cleavable cross-linkers, a score of signature peaks is combined with the conventional Andromeda score on the cleavage products. The MaxQuant 3D peak detection was improved to ensure more accurate determination of the monoisotopic peak of isotope patterns for heavy molecules, which cross-linked peptides typically are. A wide selection of filtering parameters can replace the manual filtering of identifications, which is often necessary when using other pipelines. On benchmark data sets of synthetic peptides, MaxLynx outperforms all other tested software on data for both types of cross-linkers and on a proteome-wide data set of cross-linked Drosophila melanogaster cell lysate. The workflow also supports ion mobility-enhanced MS data. MaxLynx runs on Windows and Linux, contains an interactive viewer for displaying annotated cross-linked spectra, and is freely available at https://www.maxquant.org/. publishedVersion

Published
2022

25. Author Correction: The dental proteome of Homo antecessor

Author

Welker, Frido, Ramos-Madrigal, Jazmín, Gutenbrunner, Petra, Mackie, Meaghan, Tiwary, Shivani, Jersie-Christensen, Rosa Rakownikow, Chiva, Cristina, Dickinson, Marc R., Kuhlwilm, Martin, de Manuel, Marc, Gelabert, Pere, Martinón-Torres, María, Margvelashvili, Ann, Arsuaga, Juan Luis, Carbonell, Eudald, Marques-Bonet, Tomas, Penkman, Kirsty, Sabidó, Eduard, Cox, Jürgen, Olsen, Jesper V., Lordkipanidze, David, Racimo, Fernando, Lalueza-Fox, Carles, de Castro, José María Bermúdez, Willerslev, Eske, and Cappellini, Enrico

Published
2020
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30. Prioritized single-cell proteomics reveals molecular and functional polarization across primary macrophages

Author

Huffman, R Gray, primary, Leduc, Andrew, additional, Wichmann, Christoph, additional, di Gioia, Marco, additional, Borriello, Francesco, additional, Specht, Harrison, additional, Derks, Jason, additional, Khan, Saad, additional, Khoury, Luke, additional, Emmott, Edward, additional, Petelski, Aleksandra A., additional, Perlman, David H, additional, Cox, Jürgen, additional, Zanoni, Ivan, additional, and Slavov, Nikolai, additional

Published
2022
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31. The proteogenomic subtypes of acute myeloid leukemia

Author

Jayavelu, Ashok Kumar, primary, Wolf, Sebastian, additional, Buettner, Florian, additional, Alexe, Gabriela, additional, Häupl, Björn, additional, Comoglio, Federico, additional, Schneider, Constanze, additional, Doebele, Carmen, additional, Fuhrmann, Dominik C., additional, Wagner, Sebastian, additional, Donato, Elisa, additional, Andresen, Carolin, additional, Wilke, Anne C., additional, Zindel, Alena, additional, Jahn, Dominique, additional, Splettstoesser, Bianca, additional, Plessmann, Uwe, additional, Münch, Silvia, additional, Abou-El-Ardat, Khali, additional, Makowka, Philipp, additional, Acker, Fabian, additional, Enssle, Julius C., additional, Cremer, Anjali, additional, Schnütgen, Frank, additional, Kurrle, Nina, additional, Chapuy, Björn, additional, Löber, Jens, additional, Hartmann, Sylvia, additional, Wild, Peter J., additional, Wittig, Ilka, additional, Hübschmann, Daniel, additional, Kaderali, Lars, additional, Cox, Jürgen, additional, Brüne, Bernhard, additional, Röllig, Christoph, additional, Thiede, Christian, additional, Steffen, Björn, additional, Bornhäuser, Martin, additional, Trumpp, Andreas, additional, Urlaub, Henning, additional, Stegmaier, Kimberly, additional, Serve, Hubert, additional, Mann, Matthias, additional, and Oellerich, Thomas, additional

Published
2022
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37. MaxQuant goes Linux

Author

Sinitcyn, Pavel, Tiwary, Shivani, Rudolph, Jan, Gutenbrunner, Petra, Wichmann, Christoph, Yılmaz, Şule, Hamzeiy, Hamid, Salinas, Favio, and Cox, Jürgen

Published
2018
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45. Meeting Report

Author

Leitner, Alexander, Bonvin, Alexandre M J J, Borchers, Christoph H, Chalkley, Robert J, Chamot-Rooke, Julia, Combe, Colin W, Cox, Jürgen, Dong, Meng-Qiu, Fischer, Lutz, Götze, Michael, Gozzo, Fabio C, Heck, Albert J R, Hoopmann, Michael R, Huang, Lan, Ishihama, Yasushi, Jones, Andrew R, Kalisman, Nir, Kohlbacher, Oliver, Mechtler, Karl, Moritz, Robert L, Netz, Eugen, Novak, Petr, Petrotchenko, Evgeniy, Sali, Andrej, Scheltema, Richard A, Schmidt, Carla, Schriemer, David, Sinz, Andrea, Sobott, Frank, Stengel, Florian, Thalassinos, Konstantinos, Urlaub, Henning, Viner, Rosa, Vizcaíno, Juan A, Wilkins, Marc R, Rappsilber, Juri, Sub NMR Spectroscopy, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, NMR Spectroscopy, Eidgenössische Technische Hochschule - Swiss Federal Institute of Technology [Zürich] (ETH Zürich), Utrecht University [Utrecht], University of Victoria [Canada] (UVIC), Lady Davis Institute for Medical Research [Montréal], McGill University = Université McGill [Montréal, Canada]-Jewish General Hospital, Skolkovo Institute of Science and Technology [Moscow] (Skoltech), University of California [San Francisco] (UCSF), University of California, Spectrométrie de Masse pour la Biologie – Mass Spectrometry for Biology (UTechS MSBio), Institut Pasteur [Paris]-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), University of Edinburgh, Max Planck Institute of Biochemistry (MPIB), Max-Planck-Gesellschaft, National Institute of Biological Sciences [Beijing, China] (Number 7 Science Park Road), Zhongguancun Life Science Park [Beijing, China], Technische Universität Berlin (TU), University of Campinas [Campinas] (UNICAMP), Institute for Systems Biology [Seattle] (ISB), University of California [Irvine] (UCI), Kyoto University [Kyoto], University of Liverpool, The Hebrew University of Jerusalem (HUJ), University of Tübingen, Max Planck Institute for Developmental Biology, Research Institute of Molecular Pathology (IMP), Charles University [Prague] (CU), Martin-Luther-University Halle-Wittenberg, University of Calgary, University of Leeds, University of Antwerp (UA), University of Konstanz, Birkbeck College [University of London], University College of London [London] (UCL), Max-Planck-Institut für Biophysikalische Chemie - Max Planck Institute for Biophysical Chemistry [Göttingen], Thermo Fisher Scientific (Bremen) GmbH, European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg, University of New South Wales [Sydney] (UNSW), This work was supported by the Wellcome Trust through a Senior Research Fellowship to J.R. (103139) and the Deutsche Forschungsgemeinschaft (DFG, German Research Foundation, project 329673113). Funded by the DFG under Germany's Excellence Strategy, EXC 2008/1-390540038. The Wellcome Centre for Cell Biology is supported by core funding from the Wellcome Trust (203149)., We thank the participants of the meetings mentioned throughout the text for their many different contributions. Although we made an effort to include all labs that may feel a belonging to the field of Cross-linking MS, we apologize to all those that we missed. Developing standards in Cross-linking MS is to be viewed as an inclusive activity, so please feel warmly invited to join our efforts, University of California [San Francisco] (UC San Francisco), University of California (UC), Institut Pasteur [Paris] (IP)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS), Max-Planck-Institut für Biochemie = Max Planck Institute of Biochemistry (MPIB), Technical University of Berlin / Technische Universität Berlin (TU), Universidade Estadual de Campinas = University of Campinas (UNICAMP), University of California [Irvine] (UC Irvine), Kyoto University, Sub NMR Spectroscopy, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, and NMR Spectroscopy

Subjects
0303 health sciences, Computer science, Physics, 030302 biochemistry & molecular biology, Mass spectrometry, Other Quantitative Biology (q-bio.OT), Data science, Quantitative Biology - Other Quantitative Biology, 03 medical and health sciences, Chemistry, White paper, Structural Biology, Transparency (graphic), FOS: Biological sciences, ddc:570, [SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology, Human medicine, Molecular Biology, Biology, Reliability (statistics), 030304 developmental biology
Abstract

Crosslinking mass spectrometry (Crosslinking MS) has substantially matured as a method over the last two decades through parallel development in multiple labs, demonstrating its applicability for protein structure determination, conformation analysis and mapping protein interactions in complex mixtures. Crosslinking MS has become a much-appreciated and routinely applied tool especially in structural biology. Therefore, it is timely that the community commits to the development of methodological and reporting standards. This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Crosslinking MS for which guidelines should be developed as part of a Crosslinking MS standards initiative., Comment: 26 pages, 1 figure

Published
2020

46. Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry

Author

Leitner, Alexander, Bonvin, Alexandre M J J, Borchers, Christoph H, Chalkley, Robert J, Chamot-Rooke, Julia, Combe, Colin W, Cox, Jürgen, Dong, Meng-Qiu, Fischer, Lutz, Götze, Michael, Gozzo, Fabio C, Heck, Albert J R, Hoopmann, Michael R, Huang, Lan, Ishihama, Yasushi, Jones, Andrew R, Kalisman, Nir, Kohlbacher, Oliver, Mechtler, Karl, Moritz, Robert L, Netz, Eugen, Novak, Petr, Petrotchenko, Evgeniy, Sali, Andrej, Scheltema, Richard A, Schmidt, Carla, Schriemer, David, Sinz, Andrea, Sobott, Frank, Stengel, Florian, Thalassinos, Konstantinos, Urlaub, Henning, Viner, Rosa, Vizcaíno, Juan A, Wilkins, Marc R, Rappsilber, Juri, Leitner, Alexander, Bonvin, Alexandre M J J, Borchers, Christoph H, Chalkley, Robert J, Chamot-Rooke, Julia, Combe, Colin W, Cox, Jürgen, Dong, Meng-Qiu, Fischer, Lutz, Götze, Michael, Gozzo, Fabio C, Heck, Albert J R, Hoopmann, Michael R, Huang, Lan, Ishihama, Yasushi, Jones, Andrew R, Kalisman, Nir, Kohlbacher, Oliver, Mechtler, Karl, Moritz, Robert L, Netz, Eugen, Novak, Petr, Petrotchenko, Evgeniy, Sali, Andrej, Scheltema, Richard A, Schmidt, Carla, Schriemer, David, Sinz, Andrea, Sobott, Frank, Stengel, Florian, Thalassinos, Konstantinos, Urlaub, Henning, Viner, Rosa, Vizcaíno, Juan A, Wilkins, Marc R, and Rappsilber, Juri

Abstract

Cross-linking mass spectrometry (MS) has substantially matured as a method over the past 2 decades through parallel development in multiple labs, demonstrating its applicability to protein structure determination, conformation analysis, and mapping protein interactions in complex mixtures. Cross-linking MS has become a much-appreciated and routinely applied tool, especially in structural biology. Therefore, it is timely that the community commits to the development of methodological and reporting standards. This white paper builds on an open process comprising a number of events at community conferences since 2015 and identifies aspects of Cross-linking MS for which guidelines should be developed as part of a Cross-linking MS standards initiative.

Published
2020

47. Toward Increased Reliability, Transparency, and Accessibility in Cross-linking Mass Spectrometry

Author

Sub NMR Spectroscopy, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, NMR Spectroscopy, Leitner, Alexander, Bonvin, Alexandre M J J, Borchers, Christoph H, Chalkley, Robert J, Chamot-Rooke, Julia, Combe, Colin W, Cox, Jürgen, Dong, Meng-Qiu, Fischer, Lutz, Götze, Michael, Gozzo, Fabio C, Heck, Albert J R, Hoopmann, Michael R, Huang, Lan, Ishihama, Yasushi, Jones, Andrew R, Kalisman, Nir, Kohlbacher, Oliver, Mechtler, Karl, Moritz, Robert L, Netz, Eugen, Novak, Petr, Petrotchenko, Evgeniy, Sali, Andrej, Scheltema, Richard A, Schmidt, Carla, Schriemer, David, Sinz, Andrea, Sobott, Frank, Stengel, Florian, Thalassinos, Konstantinos, Urlaub, Henning, Viner, Rosa, Vizcaíno, Juan A, Wilkins, Marc R, Rappsilber, Juri, Sub NMR Spectroscopy, Afd Biomol.Mass Spect. and Proteomics, Sub Biomol.Mass Spectrometry & Proteom., Biomolecular Mass Spectrometry and Proteomics, NMR Spectroscopy, Leitner, Alexander, Bonvin, Alexandre M J J, Borchers, Christoph H, Chalkley, Robert J, Chamot-Rooke, Julia, Combe, Colin W, Cox, Jürgen, Dong, Meng-Qiu, Fischer, Lutz, Götze, Michael, Gozzo, Fabio C, Heck, Albert J R, Hoopmann, Michael R, Huang, Lan, Ishihama, Yasushi, Jones, Andrew R, Kalisman, Nir, Kohlbacher, Oliver, Mechtler, Karl, Moritz, Robert L, Netz, Eugen, Novak, Petr, Petrotchenko, Evgeniy, Sali, Andrej, Scheltema, Richard A, Schmidt, Carla, Schriemer, David, Sinz, Andrea, Sobott, Frank, Stengel, Florian, Thalassinos, Konstantinos, Urlaub, Henning, Viner, Rosa, Vizcaíno, Juan A, Wilkins, Marc R, and Rappsilber, Juri

Published
2020

48. Tissue-specific gene (and protein) expression and its effects on protein-protein interaction networks in cancer and other complex diseases.

Author

Frishman, Dmitrij (Prof. Dr.), Cox, Jürgen (Prof., Ph.D.), Kataka, Evans, Frishman, Dmitrij (Prof. Dr.), Cox, Jürgen (Prof., Ph.D.), and Kataka, Evans

Abstract

The use of high throughput next-generation sequencing data advanced our understanding of cancer. Omics data integration with network data (protein-protein interaction networks, PPINs) is a novel way of studying diseases to find biomarkers. PPINs are vital in our understanding of the behavior of diseases and in the development of new therapies. This thesis aimed at identifying how differential isoform expression between cancer and healthy states may result in edgetic perturbations in cancer., Als neuartige Methode zur Untersuchung komplexer Krankheiten wurde die Integration von Sequenzierungsdaten der nächsten Generation und Omics Daten mit Protein-Protein-Interatkionsnetzwerken (PPINs) vorgeschlagen Biomarker zu identifizieren. PPINs spielen eine entscheidende Rolle für unser Verständnis Krankheiten, sowie bei der Entwicklung neuer Therapien. Diese Arbeit zielte darauf ab, herauszufinden wie unterschiedliche Isoformausprägungen zu randständigen Störungen bei Krebs führen können.

Published
2020

49. The dental proteome of Homo antecessor:{with Author Correction]

Author

Welker, Frido, Ramos-Madrigal, Jazmín, Gutenbrunner, Petra, Mackie, Meaghan, Tiwary, Shivani, Rakownikow Jersie-Christensen, Rosa, Chiva, Cristina, Dickinson, Marc R, Kuhlwilm, Martin, de Manuel, Marc, Gelabert, Pere, Martinón-Torres, María, Margvelashvili, Ann, Arsuaga, Juan Luis, Carbonell, Eudald, Marques-Bonet, Tomas, Penkman, Kirsty, Sabidó, Eduard, Cox, Jürgen, Olsen, Jesper V, Lordkipanidze, David, Racimo, Fernando, Lalueza-Fox, Carles, Bermúdez de Castro, José María, Willerslev, Eske, Cappellini, Enrico, Welker, Frido, Ramos-Madrigal, Jazmín, Gutenbrunner, Petra, Mackie, Meaghan, Tiwary, Shivani, Rakownikow Jersie-Christensen, Rosa, Chiva, Cristina, Dickinson, Marc R, Kuhlwilm, Martin, de Manuel, Marc, Gelabert, Pere, Martinón-Torres, María, Margvelashvili, Ann, Arsuaga, Juan Luis, Carbonell, Eudald, Marques-Bonet, Tomas, Penkman, Kirsty, Sabidó, Eduard, Cox, Jürgen, Olsen, Jesper V, Lordkipanidze, David, Racimo, Fernando, Lalueza-Fox, Carles, Bermúdez de Castro, José María, Willerslev, Eske, and Cappellini, Enrico

Abstract

The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated1-5. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge6-8. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain)9,10 and Homo erectus from Dmanisi (Georgia)1, two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor-that is, similar to that of modern humans-may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.

Published
2020

50. The dental proteome of Homo antecessor

Author

European Commission, Lundbeck Foundation, Danish National Research Foundation, Novo Nordisk Foundation, Carlsberg Foundation, Wellcome Trust, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Junta de Castilla y León, Fundación Atapuerca, Leakey Foundation, Howard Hughes Medical Institute, Fundación la Caixa, Generalitat de Catalunya, Instituto de Salud Carlos III, John Templeton Foundation, Shota Rustaveli National Science Foundation, Welker, Frido, Ramos-Madrigal, Jazmín, Gutenbrunner, Petra, Mackie, Meaghan, Tiwary, Shivani, Rakownikow Jersie-Christensen, Rosa, Chiva, Cristina, Dickinson, Mark R., Kuhlwilm, Martin, Manuel, Marc de, Gelabert, Pere, Martinón-Torres, María, Margvelashvili, Ann, Arsuaga, Juan Luis, Carbonell, Eudald, Marqués-Bonet, Tomàs, Penkman, Kirsty, Sabidó, Eduard, Cox, Jürgen, Olsen, Jesper V., Lordkipanidze, David, Racimo, Fernando, Lalueza-Fox, Carles, Bermúdez de Castro, José María, Willerslev, Eske, Cappellini, Enrico, European Commission, Lundbeck Foundation, Danish National Research Foundation, Novo Nordisk Foundation, Carlsberg Foundation, Wellcome Trust, Ministerio de Ciencia, Innovación y Universidades (España), Agencia Estatal de Investigación (España), Junta de Castilla y León, Fundación Atapuerca, Leakey Foundation, Howard Hughes Medical Institute, Fundación la Caixa, Generalitat de Catalunya, Instituto de Salud Carlos III, John Templeton Foundation, Shota Rustaveli National Science Foundation, Welker, Frido, Ramos-Madrigal, Jazmín, Gutenbrunner, Petra, Mackie, Meaghan, Tiwary, Shivani, Rakownikow Jersie-Christensen, Rosa, Chiva, Cristina, Dickinson, Mark R., Kuhlwilm, Martin, Manuel, Marc de, Gelabert, Pere, Martinón-Torres, María, Margvelashvili, Ann, Arsuaga, Juan Luis, Carbonell, Eudald, Marqués-Bonet, Tomàs, Penkman, Kirsty, Sabidó, Eduard, Cox, Jürgen, Olsen, Jesper V., Lordkipanidze, David, Racimo, Fernando, Lalueza-Fox, Carles, Bermúdez de Castro, José María, Willerslev, Eske, and Cappellini, Enrico

Abstract

The phylogenetic relationships between hominins of the Early Pleistocene epoch in Eurasia, such as Homo antecessor, and hominins that appear later in the fossil record during the Middle Pleistocene epoch, such as Homo sapiens, are highly debated. For the oldest remains, the molecular study of these relationships is hindered by the degradation of ancient DNA. However, recent research has demonstrated that the analysis of ancient proteins can address this challenge. Here we present the dental enamel proteomes of H. antecessor from Atapuerca (Spain) and Homo erectus from Dmanisi (Georgia), two key fossil assemblages that have a central role in models of Pleistocene hominin morphology, dispersal and divergence. We provide evidence that H. antecessor is a close sister lineage to subsequent Middle and Late Pleistocene hominins, including modern humans, Neanderthals and Denisovans. This placement implies that the modern-like face of H. antecessor—that is, similar to that of modern humans—may have a considerably deep ancestry in the genus Homo, and that the cranial morphology of Neanderthals represents a derived form. By recovering AMELY-specific peptide sequences, we also conclude that the H. antecessor molar fragment from Atapuerca that we analysed belonged to a male individual. Finally, these H. antecessor and H. erectus fossils preserve evidence of enamel proteome phosphorylation and proteolytic digestion that occurred in vivo during tooth formation. Our results provide important insights into the evolutionary relationships between H. antecessor and other hominin groups, and pave the way for future studies using enamel proteomes to investigate hominin biology across the existence of the genus Homo.

Published
2020

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