1
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Cirri E, Knaudt H, Di Fraia D, Pömpner N, Rahnis N, Heinze I, Ori A, Dau T. Optimized Automated Workflow for BioID Improves Reproducibility and Identification of Protein-Protein Interactions. J Proteome Res 2024; 23:4359-4368. [PMID: 39231529 PMCID: PMC11460324 DOI: 10.1021/acs.jproteome.4c00308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2024] [Revised: 07/11/2024] [Accepted: 07/18/2024] [Indexed: 09/06/2024]
Abstract
Proximity-dependent biotinylation is an important method to study protein-protein interactions in cells, for which an expanding number of applications has been proposed. The laborious and time-consuming sample processing has limited project sizes so far. Here, we introduce an automated workflow on a liquid handler to process up to 96 samples at a time. The automation not only allows higher sample numbers to be processed in parallel but also improves reproducibility and lowers the minimal sample input. Furthermore, we combined automated sample processing with shorter liquid chromatography gradients and data-independent acquisition to increase the analysis throughput and enable reproducible protein quantitation across a large number of samples. We successfully applied this workflow to optimize the detection of proteasome substrates by proximity-dependent labeling.
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Affiliation(s)
- Emilio Cirri
- Leibniz Institute on Aging—Fritz
Lipmann Institute (FLI), 07745 Jena, Germany
| | - Hannah Knaudt
- Leibniz Institute on Aging—Fritz
Lipmann Institute (FLI), 07745 Jena, Germany
| | - Domenico Di Fraia
- Leibniz Institute on Aging—Fritz
Lipmann Institute (FLI), 07745 Jena, Germany
| | - Nadine Pömpner
- Leibniz Institute on Aging—Fritz
Lipmann Institute (FLI), 07745 Jena, Germany
| | - Norman Rahnis
- Leibniz Institute on Aging—Fritz
Lipmann Institute (FLI), 07745 Jena, Germany
| | - Ivonne Heinze
- Leibniz Institute on Aging—Fritz
Lipmann Institute (FLI), 07745 Jena, Germany
| | - Alessandro Ori
- Leibniz Institute on Aging—Fritz
Lipmann Institute (FLI), 07745 Jena, Germany
| | - Therese Dau
- Leibniz Institute on Aging—Fritz
Lipmann Institute (FLI), 07745 Jena, Germany
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2
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Schreiber KJ, Kadijk E, Youn JY. Exploring Options for Proximity-Dependent Biotinylation Experiments: Comparative Analysis of Labeling Enzymes and Affinity Purification Resins. J Proteome Res 2024; 23:1531-1543. [PMID: 38507741 PMCID: PMC11002925 DOI: 10.1021/acs.jproteome.3c00908] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 03/05/2024] [Accepted: 03/07/2024] [Indexed: 03/22/2024]
Abstract
Proximity-dependent biotinylation (PDB) techniques provide information about the molecular neighborhood of a protein of interest, yielding insights into its function and localization. Here, we assessed how different labeling enzymes and streptavidin resins influence PDB results. We compared the high-confidence interactors of the DNA/RNA-binding protein transactive response DNA-binding protein 43 kDa (TDP-43) identified using either miniTurbo (biotin ligase) or APEX2 (peroxidase) enzymes. We also evaluated two commercial affinity resins for purification of biotinylated proteins: conventional streptavidin sepharose versus a new trypsin-resistant streptavidin conjugated to magnetic resin, which significantly reduces the level of contamination by streptavidin peptides following on-bead trypsin digestion. Downstream analyses involved liquid chromatography coupled to mass spectrometry in data-dependent acquisition mode, database searching, and statistical analysis of high-confidence interactors using SAINTexpress. The APEX2-TDP-43 experiment identified more interactors than miniTurbo-TDP-43, although miniTurbo provided greater overlap with previously documented TDP-43 interactors. Purifications on sepharose resin yielded more interactors than magnetic resin in small-scale experiments using a range of magnetic resin volumes. We suggest that resin-specific background protein binding profiles and different lysate-to-resin ratios cumulatively affect the distributions of prey protein abundance in experimental and control samples, which impact statistical confidence scores. Overall, we highlight key experimental variables to consider for the empirical optimization of PDB experiments.
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Affiliation(s)
- Karl J. Schreiber
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
| | - Eileigh Kadijk
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
| | - Ji-Young Youn
- Program
in Molecular Medicine, The Hospital for
Sick Children, Toronto, ON M5G 0A4, Canada
- Department
of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
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3
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Hollenstein D, Maurer-Granofszky M, Reiter W, Anrather D, Gossenreiter T, Babic R, Hartl N, Kraft C, Hartl M. Chemical Acetylation of Ligands and Two-Step Digestion Protocol for Reducing Codigestion in Affinity Purification-Mass Spectrometry. J Proteome Res 2023; 22:3383-3391. [PMID: 37712406 PMCID: PMC10563155 DOI: 10.1021/acs.jproteome.3c00424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Indexed: 09/16/2023]
Abstract
We present an effective, fast, and user-friendly method to reduce codigestion of bead-bound ligands, such as antibodies or streptavidin, in affinity purification-mass spectrometry experiments. A short preincubation of beads with Sulfo-NHS-Acetate leads to chemical acetylation of lysine residues, making ligands insusceptible to Lys-C-mediated proteolysis. In contrast to similar approaches, our procedure offers the advantage of exclusively using nontoxic chemicals and employing mild chemical reaction conditions. After binding of bait proteins to Sulfo-NHS-Acetate treated beads, we employ a two-step digestion protocol with the sequential use of Lys-C protease for on-bead digestion followed by in-solution digestion of the released proteins with trypsin. The implementation of this protocol results in a strong reduction of contaminating ligand peptides, which allows significantly higher amounts of sample to be subjected to LC-MS analysis, improving sensitivity and quantitative accuracy.
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Affiliation(s)
- David
M. Hollenstein
- Department
for Biochemistry and Cell Biology, University
of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, Vienna 1030, Austria
- Mass
Spectrometry Facility, Max Perutz Laboratories, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna 1030, Austria
| | | | - Wolfgang Reiter
- Mass
Spectrometry Facility, Max Perutz Laboratories, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna 1030, Austria
| | - Dorothea Anrather
- Mass
Spectrometry Facility, Max Perutz Laboratories, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna 1030, Austria
| | - Thomas Gossenreiter
- Mass
Spectrometry Facility, Max Perutz Laboratories, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna 1030, Austria
| | - Riccardo Babic
- Institute
of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
- Faculty
of Biology, University of Freiburg, Freiburg 79104, Germany
- Spemann Graduate
School of Biology and Medicine (SGBM), University
of Freiburg, Freiburg 79104, Germany
| | - Natascha Hartl
- Department
for Biochemistry and Cell Biology, University
of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, Vienna 1030, Austria
- Mass
Spectrometry Facility, Max Perutz Laboratories, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna 1030, Austria
| | - Claudine Kraft
- Institute
of Biochemistry and Molecular Biology, ZBMZ, Faculty of Medicine, University of Freiburg, Freiburg 79104, Germany
- CIBSS
- Centre for Integrative Biological Signalling Studies, University of Freiburg, Freiburg 79104, Germany
| | - Markus Hartl
- Department
for Biochemistry and Cell Biology, University
of Vienna, Center for Molecular Biology, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 9, Vienna 1030, Austria
- Mass
Spectrometry Facility, Max Perutz Laboratories, Vienna Biocenter Campus (VBC), Dr. Bohr-Gasse 7, Vienna 1030, Austria
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4
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Studying the ubiquitin code through biotin-based labelling methods. Semin Cell Dev Biol 2022; 132:109-119. [PMID: 35181195 DOI: 10.1016/j.semcdb.2022.02.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 02/03/2022] [Accepted: 02/05/2022] [Indexed: 12/15/2022]
Abstract
Post-translational modifications of cellular substrates by members of the ubiquitin (Ub) and ubiquitin-like (UbL) family are crucial for regulating protein homeostasis in organisms. The term "ubiquitin code" encapsulates how this diverse family of modifications, via adding single UbLs or different types of UbL chains, leads to specific fates for substrates. Cancer, neurodegeneration and other conditions are sometimes linked to underlying errors in this code. Studying these modifications in cells is particularly challenging since they are usually transient, scarce, and compartment-specific. Advances in the use of biotin-based methods to label modified proteins, as well as their proximally-located interactors, facilitate isolation and identification of substrates, modification sites, and the enzymes responsible for writing and erasing these modifications, as well as factors recruited as a consequence of the substrate being modified. In this review, we discuss site-specific and proximity biotinylation approaches being currently applied for studying modifications by UbLs, highlighting the pros and cons, with mention of complementary methods when possible. Future improvements may come from bioengineering and chemical biology but even now, biotin-based technology is uncovering new substrates and regulators, expanding potential therapeutic targets to manipulate the Ub code.
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5
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Pauwels J, Fijałkowska D, Eyckerman S, Gevaert K. Mass spectrometry and the cellular surfaceome. MASS SPECTROMETRY REVIEWS 2022; 41:804-841. [PMID: 33655572 DOI: 10.1002/mas.21690] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 02/05/2021] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
The collection of exposed plasma membrane proteins, collectively termed the surfaceome, is involved in multiple vital cellular processes, such as the communication of cells with their surroundings and the regulation of transport across the lipid bilayer. The surfaceome also plays key roles in the immune system by recognizing and presenting antigens, with its possible malfunctioning linked to disease. Surface proteins have long been explored as potential cell markers, disease biomarkers, and therapeutic drug targets. Despite its importance, a detailed study of the surfaceome continues to pose major challenges for mass spectrometry-driven proteomics due to the inherent biophysical characteristics of surface proteins. Their inefficient extraction from hydrophobic membranes to an aqueous medium and their lower abundance compared to intracellular proteins hamper the analysis of surface proteins, which are therefore usually underrepresented in proteomic datasets. To tackle such problems, several innovative analytical methodologies have been developed. This review aims at providing an extensive overview of the different methods for surfaceome analysis, with respective considerations for downstream mass spectrometry-based proteomics.
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Affiliation(s)
- Jarne Pauwels
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Sven Eyckerman
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Kris Gevaert
- VIB Center for Medical Biotechnology, VIB, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
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6
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Kramer MC, Kim HJ, Palos KR, Garcia BA, Lyons E, Beilstein MA, Nelson ADL, Gregory BD. A Conserved Long Intergenic Non-coding RNA Containing snoRNA Sequences, lncCOBRA1, Affects Arabidopsis Germination and Development. FRONTIERS IN PLANT SCIENCE 2022; 13:906603. [PMID: 35693169 PMCID: PMC9175010 DOI: 10.3389/fpls.2022.906603] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 05/04/2022] [Indexed: 05/04/2023]
Abstract
Long non-coding RNAs (lncRNAs) are an increasingly studied group of non-protein coding transcripts with a wide variety of molecular functions gaining attention for their roles in numerous biological processes. Nearly 6,000 lncRNAs have been identified in Arabidopsis thaliana but many have yet to be studied. Here, we examine a class of previously uncharacterized lncRNAs termed CONSERVED IN BRASSICA RAPA (lncCOBRA) transcripts that were previously identified for their high level of sequence conservation in the related crop species Brassica rapa, their nuclear-localization and protein-bound nature. In particular, we focus on lncCOBRA1 and demonstrate that its abundance is highly tissue and developmental specific, with particularly high levels early in germination. lncCOBRA1 contains two snoRNAs domains within it, making it the first sno-lincRNA example in a non-mammalian system. However, we find that it is processed differently than its mammalian counterparts. We further show that plants lacking lncCOBRA1 display patterns of delayed germination and are overall smaller than wild-type plants. Lastly, we identify the proteins that interact with lncCOBRA1 and propose a novel mechanism of lincRNA action in which it may act as a scaffold with the RACK1A protein to regulate germination and development, possibly through a role in ribosome biogenesis.
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Affiliation(s)
- Marianne C. Kramer
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Hee Jong Kim
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Biochemistry and Molecular Biophysics Graduate Group, University of Pennsylvania, Philadelphia, PA, United States
| | - Kyle R. Palos
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | - Benjamin A. Garcia
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
| | - Eric Lyons
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
- CyVerse Inc., Tucson, AZ, United States
| | - Mark A. Beilstein
- School of Plant Sciences, University of Arizona, Tucson, AZ, United States
| | | | - Brian D. Gregory
- Department of Biology, University of Pennsylvania, Philadelphia, PA, United States
- Cell and Molecular Biology Graduate Group, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, United States
- *Correspondence: Brian D. Gregory,
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7
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Niinae T, Ishihama Y, Imami K. Biotinylation-based proximity labeling proteomics: Basics, applications, and technical considerations. J Biochem 2021; 170:569-576. [PMID: 34752609 DOI: 10.1093/jb/mvab123] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2021] [Accepted: 11/07/2021] [Indexed: 11/13/2022] Open
Abstract
Recent advances in biotinylation-based proximity labeling (PL) have opened up new avenues for mapping the protein composition of cellular compartments and protein complexes in living cells at high spatiotemporal resolution. In particular, PL combined with mass spectrometry-based proteomics has been successfully applied to defining protein-protein interactions, protein-nucleic acid interactions, (membraneless) organelle proteomes, and secretomes in various systems ranging from cultured cells to whole animals. In this review, we first summarize the basics and recent biological applications of PL proteomics, and then highlight recent developments in enrichment techniques for biotinylated proteins and peptides, focusing on the advantages of PL and technical considerations.
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Affiliation(s)
- Tomoya Niinae
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan
| | - Yasushi Ishihama
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,Laboratory of Clinical and Analytical Chemistry, National Institute of Biomedical Innovation, Health and Nutrition, Ibaraki, Osaka 567-0085, Japan
| | - Koshi Imami
- Department of Molecular and Cellular BioAnalysis, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.,PRESTO, Japan Science and Technology Agency (JST), 5-3 Yonban-cho, Chiyoda-ku, Tokyo, 102-0075, Japan
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8
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St-Germain JR, Samavarchi Tehrani P, Wong C, Larsen B, Gingras AC, Raught B. Variability in Streptavidin-Sepharose Matrix Quality Can Significantly Affect Proximity-Dependent Biotinylation (BioID) Data. J Proteome Res 2020; 19:3554-3561. [PMID: 32628020 DOI: 10.1021/acs.jproteome.0c00117] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Due to their ease of use and high binding affinity, streptavidin-based purification tools have become widely used for isolating biotinylated compounds from complex mixtures. We and others routinely use streptavidin-sepharose matrices to isolate biotinylated polypeptides generated in proximity-dependent biotinylation approaches, such as BioID or APEX. However, we noted sporadic, substantial variation in the quality of BioID experiments performed in the same laboratories over time, using seemingly identical protocols. Identifying the source of this problem, here, we highlight considerable variability in streptavidin contamination derived from different production lots of streptavidin-sepharose beads from the same manufacturer and demonstrate that high levels of streptavidin peptide contamination can have detrimental effects on BioID data. We also describe two simple, rapid approaches to assess the degree of streptavidin "shedding" from individual lots of the sepharose matrix before use to avoid the use of lower quality reagent.
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Affiliation(s)
- Jonathan R St-Germain
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada
| | - Payman Samavarchi Tehrani
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Cassandra Wong
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Brett Larsen
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada
| | - Anne-Claude Gingras
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, and Department of Molecular Genetics, University of Toronto, 600 University Avenue, Toronto, ON M5G 1X5, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Brian Raught
- Princess Margaret Cancer Centre, University Health Network, University of Toronto, 101 College Street, Toronto, ON M5G 1L7, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, ON M5G 1L7, Canada
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9
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Rafiee M, Sigismondo G, Kalxdorf M, Förster L, Brügger B, Béthune J, Krijgsveld J. Protease-resistant streptavidin for interaction proteomics. Mol Syst Biol 2020; 16:e9370. [PMID: 32400114 PMCID: PMC7218406 DOI: 10.15252/msb.20199370] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Revised: 04/09/2020] [Accepted: 04/14/2020] [Indexed: 11/12/2022] Open
Abstract
Streptavidin-mediated enrichment is a powerful strategy to identify biotinylated biomolecules and their interaction partners; however, intense streptavidin-derived peptides impede protein identification by mass spectrometry. Here, we present an approach to chemically modify streptavidin, thus rendering it resistant to proteolysis by trypsin and LysC. This modification results in over 100-fold reduction of streptavidin contamination and in better coverage of proteins interacting with various biotinylated bait molecules (DNA, protein, and lipid) in an overall simplified workflow.
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Affiliation(s)
- Mahmoud‐Reza Rafiee
- Division of Proteomics of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Medical FacultyHeidelberg UniversityHeidelbergGermany
- Present address:
The Francis Crick InstituteLondonUK
| | - Gianluca Sigismondo
- Division of Proteomics of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Medical FacultyHeidelberg UniversityHeidelbergGermany
| | - Mathias Kalxdorf
- Division of Proteomics of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Medical FacultyHeidelberg UniversityHeidelbergGermany
| | - Laura Förster
- Heidelberg University Biochemistry Center (BZH)HeidelbergGermany
| | - Britta Brügger
- Heidelberg University Biochemistry Center (BZH)HeidelbergGermany
| | - Julien Béthune
- Heidelberg University Biochemistry Center (BZH)HeidelbergGermany
| | - Jeroen Krijgsveld
- Division of Proteomics of Stem Cells and CancerGerman Cancer Research Center (DKFZ)HeidelbergGermany
- Medical FacultyHeidelberg UniversityHeidelbergGermany
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