Novel MS/MS-Cleavable Cross-Linkers: Synthesis, Evaluation of Fragmentation Behavior, and Application for Protein Structure Analysis

• Applicants: Professor Dr. Mathias Schäfer; Professorin Dr. Andrea Sinz
• Subject Area: Analytical Chemistry
• Term: from 2011 to 2020
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 196601425

• Final Report Year: 2020

Final Report Abstract

Chemical cross-linking in combination with mass spectrometry (XL-MS) has evolved into an alternative strategy for elucidating three-dimensional protein structures and for mapping protein interfaces. In the DFG-funded projects novel collision-induced dissociation (CID)-MS/MS labile cross-linkers were designed, synthesized, and successfully applied to address important biological questions. Our most prominent cross-linker containing a CID-labile urea group (disuccinimidyl dibutyric urea, DSBU, formerly BuUrBu) has become commercially available and is currently in use for conducting XL-MS studies by a number of groups worldwide. The projects have been extraordinarily successful and ultimately resulted in a fully automated analytical workflow that for conducting XL-MS of whole proteomes. This workflow, published in Nature Protocols (2018) and Anal. Chem. (2019), has gained great interest within the community of structural biologists to map protein-protein interaction networks and to determine protein conformations in the complex cellular environment.

Publications

• Automated assignment of MS/MS cleavable cross-links in protein 3D-structure analysis. J Am Soc Mass Spectrom. 2015 Jan;26(1):83-97
  Götze M, Pettelkau J, Fritzsche R, Ihling CH, Schäfer M, Sinz A
  (See online at https://doi.org/10.1007/s13361-014-1001-1)
• Dissociation behavior of a bifunctional tempo-active ester reagent for peptide structure analysis by free radical initiated peptide sequencing (FRIPS) mass spectrometry. J Mass Spectrom. 2015 Feb;50(2):396-406
  Ihling C, Falvo F, Kratochvil I, Sinz A, Schäfer M
  (See online at https://doi.org/10.1002/jms.3543)
• Integrated Workflow for Structural Proteomics Studies Based on Cross-Linking/Mass Spectrometry with an MS/MS Cleavable Cross-Linker. Anal Chem. 2016 Aug 16;88(16):7930-7
  Arlt C, Götze M, Ihling CH, Hage C, Schäfer M, Sinz A
  (See online at https://doi.org/10.1021/acs.analchem.5b04853)
• A Novel MS-Cleavable Azo Cross- Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS). J Am Soc Mass Spectrom. 2017 Oct;28(10):2039-2053
  Iacobucci C, Hage C, Schäfer M, Sinz A
  (See online at https://doi.org/10.1007/s13361-017-1744-6)
• An Integrated Mass Spectrometry Based Approach to Probe the Structure of the Full-Length Wild-Type Tetrameric p53 Tumor Suppressor. Angew Chem Int Ed Engl. 2017 Jan 2;56(1):275-279
  Arlt C, Flegler V, Ihling CH, Schäfer M, Thondorf I, Sinz A
  (See online at https://doi.org/10.1002/ange.201609826)
• Dissociation Behavior of a TEMPO-Active Ester Cross-Linker for Peptide Structure Analysis by Free Radical Initiated Peptide Sequencing (FRIPS) in Negative ESI-MS. J Am Soc Mass Spectrom. 2017 Jan;28(1):56-68
  Hage C, Ihling CH, Götze M, Schäfer M, Sinz A
  (See online at https://doi.org/10.1007/s13361-016-1426-9)
• Novel Concepts of MS-Cleavable Crosslinkers for Improved Peptide Structure Analysis. J Am Soc Mass Spectrom. 2017 Oct;28(10):2022-2038
  Hage C, Falvo F, Schäfer M, Sinz A
  (See online at https://doi.org/10.1007/s13361-017-1712-1)
• The First Zero-Length Mass Spectrometry-Cleavable Cross-Linker for Protein Structure Analysis. Angew Chem Int Ed Engl. 2017 Nov 13;56(46):14551-14555
  Hage C, Iacobucci C, Rehkamp A, Arlt C, Sinz A
  (See online at https://doi.org/10.1002/anie.201708273)
• A cross-linking/mass spectrometry workflow based on MS-cleavable cross-linkers and the MeroX software for studying protein structures and protein-protein interactions. Nat Protoc. 2018 Dec;13(12):2864-2889
  Iacobucci C, Götze M, Ihling CH, Piotrowski C, Arlt C, Schäfer M, Hage C, Schmidt R, Sinz A
  (See online at https://doi.org/10.1038/s41596-018-0068-8)
• Carboxyl-Photo-Reactive MS-Cleavable Cross-Linkers: Unveiling a Hidden Aspect of Diazirine-Based Reagents. Anal Chem. 2018 Feb 20;90(4):2805-2809
  acobucci C, Götze M, Piotrowski C, Arlt C, Rehkamp A, Ihling C, Hage C, Sinz A
  (See online at https://doi.org/10.1021/acs.analchem.7b04915)
• Molecular Details of Retinal Guanylyl Cyclase 1/GCAP-2 Interaction. Front Mol Neurosci. 2018 Sep 19;11:330
  Rehkamp A, Tänzler D, Iacobucci C, Golbik RP, Ihling CH, Sinz A
  (See online at https://doi.org/10.3389/fnmol.2018.00330)
• A biuret-derived, MS-cleavable crosslinking reagent for protein structural analysis: A proof-of-principle study. J Mass Spectrom. 2019 Dec 9
  Hage C, Iacobucci C, Götze M, Sinz A
  (See online at https://doi.org/10.1002/jms.4449)
• A Simple Cross-Linking/Mass Spectrometry Workflow for Studying System-wide Protein Interactions. Anal Chem. 2019 Aug 6;91(15):10236-10244
  Götze M, Iacobucci C, Ihling CH, Sinz A
  (See online at https://doi.org/10.1021/acs.analchem.9b02372)
• Cross-linking/mass spectrometry to get a closer view on protein interaction networks. Curr Opin Biotechnol. 2019 Dec 28;63:48-53
  Iacobucci C, Götze M, Sinz A
  (See online at https://doi.org/10.1016/j.copbio.2019.12.009)
• Free radical-initiated peptide sequencing (FRIPS)-based cross-linkers for improved peptide and protein structure analysis. Mass Spectrom Rev. 2019 Mar;38(2):187-201
  Iacobucci C, Schäfer M, Sinz A
  (See online at https://doi.org/10.1002/mas.21568)
• Olefinic reagents tested for peptide derivatization with switchable properties: stable upon Collision Induced Dissociation and cleavable by In-Source Paternò-Büchi Reactions. J Mass Spectrom 54, 2019, 976- 986
  Esch P, Fischer M, Heiles S, Schäfer M
  (See online at https://doi.org/10.1002/jms.4474)
• The First MS- Cleavable, Photo-Thiol-Reactive Cross-Linker for Protein Structural Studies. J Am Soc Mass Spectrom. 2019 Jan;30(1):139-148
  Iacobucci C, Piotrowski C, Rehkamp A, Ihling CH, Sinz A
  (See online at https://doi.org/10.1007/s13361-018-1952-8)
• The Isotope-Labeled, MS-Cleavable Cross-Linker Disuccinimidyl Dibutyric Urea (DSBU) for Improved Cross-Linking/Mass Spectrometry Studies. J Am Soc Mass Spectrom, 30, 2019
  Ihling C, Springorum P, Iacobucci C, Hage C, Götze M, Schäfer M, Sinz A
  (See online at https://doi.org/10.1021/jasms.9b00008)