List of Publications

  1. Müller, F, Graziadei, A, Rappsilber, J. Quantitative Photo-crosslinking Mass Spectrometry Revealing Protein Structure Response to Environmental Changes. Anal. Chem. 2019;91 (14):9041-9048. doi: 10.1021/acs.analchem.9b01339. PubMed PMID:31274288 PubMed Central PMC6639777.
  2. Dau, T, Gupta, K, Berger, I, Rappsilber, J. Sequential Digestion with Trypsin and Elastase in Cross-Linking Mass Spectrometry. Anal. Chem. 2019;91 (7):4472-4478. doi: 10.1021/acs.analchem.8b05222. PubMed PMID:30817130 PubMed Central PMC6458965.
  3. Müller, F, Kolbowski, L, Bernhardt, OM, Reiter, L, Rappsilber, J. Data-independent Acquisition Improves Quantitative Cross-linking Mass Spectrometry. Mol. Cell Proteomics. 2019;18 (4):786-795. doi: 10.1074/mcp.TIR118.001276. PubMed PMID:30651306 PubMed Central PMC6442367.
  4. Giese, SH, Belsom, A, Sinn, L, Fischer, L, Rappsilber, J. Noncovalently Associated Peptides Observed during Liquid Chromatography-Mass Spectrometry and Their Effect on Cross-Link Analyses. Anal. Chem. 2019;91 (4):2678-2685. doi: 10.1021/acs.analchem.8b04037. PubMed PMID:30649854 PubMed Central PMC6396951.
  5. Grabowski, P, Hesse, S, Hollizeck, S, Rohlfs, M, Behrends, U, Sherkat, R et al.. Proteome Analysis of Human Neutrophil Granulocytes From Patients With Monogenic Disease Using Data-independent Acquisition. Mol. Cell Proteomics. 2019;18 (4):760-772. doi: 10.1074/mcp.RA118.001141. PubMed PMID:30630937 PubMed Central PMC6442368.
  6. Chen, ZA, Rappsilber, J. Quantitative cross-linking/mass spectrometry to elucidate structural changes in proteins and their complexes. Nat Protoc. 2019;14 (1):171-201. doi: 10.1038/s41596-018-0089-3. PubMed PMID:30559374 .
  7. Grabowski, P, Rappsilber, J. A Primer on Data Analytics in Functional Genomics: How to Move from Data to Insight?. Trends Biochem. Sci. 2019;44 (1):21-32. doi: 10.1016/j.tibs.2018.10.010. PubMed PMID:30522862 PubMed Central PMC6318833.
  8. O'Reilly, FJ, Rappsilber, J. Cross-linking mass spectrometry: methods and applications in structural, molecular and systems biology. Nat. Struct. Mol. Biol. 2018;25 (11):1000-1008. doi: 10.1038/s41594-018-0147-0. PubMed PMID:30374081 .
  9. Chen, ZA, Rappsilber, J. Protein Dynamics in Solution by Quantitative Crosslinking/Mass Spectrometry. Trends Biochem. Sci. 2018;43 (11):908-920. doi: 10.1016/j.tibs.2018.09.003. PubMed PMID:30318267 PubMed Central PMC6240160.
  10. Lenz, S, Giese, SH, Fischer, L, Rappsilber, J. In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides. J. Proteome Res. 2018;17 (11):3923-3931. doi: 10.1021/acs.jproteome.8b00600. PubMed PMID:30293428 PubMed Central PMC6279313.
  11. Grabowski, P, Kustatscher, G, Rappsilber, J. Epigenetic Variability Confounds Transcriptome but Not Proteome Profiling for Coexpression-based Gene Function Prediction. Mol. Cell Proteomics. 2018;17 (11):2082-2090. doi: 10.1074/mcp.RA118.000935. PubMed PMID:30042154 PubMed Central PMC6210221.
  12. Fischer, L, Rappsilber, J. False discovery rate estimation and heterobifunctional cross-linkers. PLoS ONE. 2018;13 (5):e0196672. doi: 10.1371/journal.pone.0196672. PubMed PMID:29746514 PubMed Central PMC5944926.
  13. Kolbowski, L, Combe, C, Rappsilber, J. xiSPEC: web-based visualization, analysis and sharing of proteomics data. Nucleic Acids Res. 2018;46 (W1):W473-W478. doi: 10.1093/nar/gky353. PubMed PMID:29741719 PubMed Central PMC6030980.
  14. Giese, SH, Ishihama, Y, Rappsilber, J. Peptide Retention in Hydrophilic Strong Anion Exchange Chromatography Is Driven by Charged and Aromatic Residues. Anal. Chem. 2018;90 (7):4635-4640. doi: 10.1021/acs.analchem.7b05157. PubMed PMID:29528219 PubMed Central PMC5937359.
  15. Schneider, M, Belsom, A, Rappsilber, J. Protein Tertiary Structure by Crosslinking/Mass Spectrometry. Trends Biochem. Sci. 2018;43 (3):157-169. doi: 10.1016/j.tibs.2017.12.006. PubMed PMID:29395654 PubMed Central PMC5854373.
  16. Müller, F, Fischer, L, Chen, ZA, Auchynnikava, T, Rappsilber, J. On the Reproducibility of Label-Free Quantitative Cross-Linking/Mass Spectrometry. J. Am. Soc. Mass Spectrom. 2018;29 (2):405-412. doi: 10.1007/s13361-017-1837-2. PubMed PMID:29256016 PubMed Central PMC5814520.
  17. Combe, CW, Sivade, MD, Hermjakob, H, Heimbach, J, Meldal, BHM, Micklem, G et al.. ComplexViewer: visualization of curated macromolecular complexes. Bioinformatics. 2017;33 (22):3673-3675. doi: 10.1093/bioinformatics/btx497. PubMed PMID:29036573 PubMed Central PMC5870653.
  18. Kustatscher, G, Grabowski, P, Rappsilber, J. Pervasive coexpression of spatially proximal genes is buffered at the protein level. Mol. Syst. Biol. 2017;13 (8):937. doi: 10.15252/msb.20177548. PubMed PMID:28835372 PubMed Central PMC5572396.
  19. Kolbowski, L, Mendes, ML, Rappsilber, J. Optimizing the Parameters Governing the Fragmentation of Cross-Linked Peptides in a Tribrid Mass Spectrometer. Anal. Chem. 2017;89 (10):5311-5318. doi: 10.1021/acs.analchem.6b04935. PubMed PMID:28402676 PubMed Central PMC5436099.
  20. Chen, JWC, Chen, ZA, Rogala, KB, Metz, J, Deane, CM, Rappsilber, J et al.. Cross-linking mass spectrometry identifies new interfaces of Augmin required to localise the γ-tubulin ring complex to the mitotic spindle. Biol Open. 2017;6 (5):654-663. doi: 10.1242/bio.022905. PubMed PMID:28351835 PubMed Central PMC5450317.
  21. Fischer, L, Rappsilber, J. Quirks of Error Estimation in Cross-Linking/Mass Spectrometry. Anal. Chem. 2017;89 (7):3829-3833. doi: 10.1021/acs.analchem.6b03745. PubMed PMID:28267312 PubMed Central PMC5423704.
  22. Giese, SH, Belsom, A, Rappsilber, J. Correction to Optimized Fragmentation Regime for Diazirine Photo-Cross-Linked Peptides. Anal. Chem. 2017;89 (6):3802-3803. doi: 10.1021/acs.analchem.7b00046. PubMed PMID:28245109 PubMed Central PMC5423702.
  23. Chen, Z, Fischer, L, Tahir, S, Bukowski-Wills, JC, Barlow, P, Rappsilber, J et al.. Quantitative cross-linking/mass spectrometry reveals subtle protein conformational changes. Wellcome Open Res. 2016;1 :5. doi: 10.12688/wellcomeopenres.9896.1. PubMed PMID:27976756 PubMed Central PMC5140025.
  24. Kustatscher, G, Rappsilber, J. Compositional Dynamics: Defining the Fuzzy Cell. Trends Cell Biol. 2016;26 (11):800-803. doi: 10.1016/j.tcb.2016.08.012. PubMed PMID:27651031 PubMed Central PMC5080450.
  25. Giese, SH, Belsom, A, Rappsilber, J. Optimized Fragmentation Regime for Diazirine Photo-Cross-Linked Peptides. Anal. Chem. 2016;88 (16):8239-47. doi: 10.1021/acs.analchem.6b02082. PubMed PMID:27454319 PubMed Central PMC5047652.
  26. Chen, ZA, Fischer, L, Cox, J, Rappsilber, J. Quantitative Cross-linking/Mass Spectrometry Using Isotope-labeled Cross-linkers and MaxQuant. Mol. Cell Proteomics. 2016;15 (8):2769-78. doi: 10.1074/mcp.M115.056481. PubMed PMID:27302889 PubMed Central PMC4974350.
  27. Chen, ZA, Pellarin, R, Fischer, L, Sali, A, Nilges, M, Barlow, PN et al.. Structure of Complement C3(H2O) Revealed By Quantitative Cross-Linking/Mass Spectrometry And Modeling. Mol. Cell Proteomics. 2016;15 (8):2730-43. doi: 10.1074/mcp.M115.056473. PubMed PMID:27250206 PubMed Central PMC4974347.
  28. Schneider, M, Belsom, A, Rappsilber, J, Brock, O. Blind testing of cross-linking/mass spectrometry hybrid methods in CASP11. Proteins. 2016;84 Suppl 1 :152-63. doi: 10.1002/prot.25028. PubMed PMID:26945814 PubMed Central PMC5042049.
  29. Giese, SH, Fischer, L, Rappsilber, J. A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides. Mol. Cell Proteomics. 2016;15 (3):1094-104. doi: 10.1074/mcp.M115.049296. PubMed PMID:26719564 PubMed Central PMC4813691.
  30. Kustatscher, G, Grabowski, P, Rappsilber, J. Multiclassifier combinatorial proteomics of organelle shadows at the example of mitochondria in chromatin data. Proteomics. 2016;16 (3):393-401. doi: 10.1002/pmic.201500267. PubMed PMID:26510496 PubMed Central PMC4862026.
  31. Combe, CW, Fischer, L, Rappsilber, J. xiNET: cross-link network maps with residue resolution. Mol. Cell Proteomics. 2015;14 (4):1137-47. doi: 10.1074/mcp.O114.042259. PubMed PMID:25648531 PubMed Central PMC4390258.
  32. Kustatscher, G, Wills, KL, Furlan, C, Rappsilber, J. Chromatin enrichment for proteomics. Nat Protoc. 2014;9 (9):2090-9. doi: 10.1038/nprot.2014.142. PubMed PMID:25101823 PubMed Central PMC4300392.
  33. Kustatscher, G, Hégarat, N, Wills, KL, Furlan, C, Bukowski-Wills, JC, Hochegger, H et al.. Proteomics of a fuzzy organelle: interphase chromatin. EMBO J. 2014;33 (6):648-64. doi: 10.1002/embj.201387614. PubMed PMID:24534090 PubMed Central PMC3983682.
  34. Fischer, L, Chen, ZA, Rappsilber, J. Quantitative cross-linking/mass spectrometry using isotope-labelled cross-linkers. J Proteomics. 2013;88 :120-8. doi: 10.1016/j.jprot.2013.03.005. PubMed PMID:23541715 PubMed Central PMC3714596.
  35. Rappsilber, J. Cross-linking/mass spectrometry as a new field and the proteomics information mountain of tomorrow. Expert Rev Proteomics. 2012;9 (5):485-7. doi: 10.1586/epr.12.44. PubMed PMID:23194264 PubMed Central PMC3926187.
  36. Rappsilber, J. The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. J. Struct. Biol. 2011;173 (3):530-40. doi: 10.1016/j.jsb.2010.10.014. PubMed PMID:21029779 PubMed Central PMC3043253.
  37. Chen, ZA, Jawhari, A, Fischer, L, Buchen, C, Tahir, S, Kamenski, T et al.. Architecture of the RNA polymerase II-TFIIF complex revealed by cross-linking and mass spectrometry. EMBO J. 2010;29 (4):717-26. doi: 10.1038/emboj.2009.401. PubMed PMID:20094031 PubMed Central PMC2810376.
  38. Rappsilber, J, Mann, M, Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat Protoc. 2007;2 (8):1896-906. doi: 10.1038/nprot.2007.261. PubMed PMID:17703201 .
  39. Rappsilber, J, Mann, M. Analysis of the topology of protein complexes using cross-linking and mass spectrometry. CSH Protoc. 2007;2007 :pdb.prot4594. doi: 10.1101/pdb.prot4594. PubMed PMID:21357017 .
  40. Rappsilber, J, Friesen, WJ, Paushkin, S, Dreyfuss, G, Mann, M. Detection of arginine dimethylated peptides by parallel precursor ion scanning mass spectrometry in positive ion mode. Anal. Chem. 2003;75 (13):3107-14. doi: 10.1021/ac026283q. PubMed PMID:12964758 .
  41. Rappsilber, J, Ishihama, Y, Mann, M. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Anal. Chem. 2003;75 (3):663-70. doi: 10.1021/ac026117i. PubMed PMID:12585499 .
  42. Rappsilber, J, Mann, M. Is mass spectrometry ready for proteome-wide protein expression analysis?. Genome Biol. 2002;3 (8):COMMENT2008. doi: 10.1186/gb-2002-3-8-comment2008. PubMed PMID:12186637 PubMed Central PMC139390.
  43. Rappsilber, J, Ryder, U, Lamond, AI, Mann, M. Large-scale proteomic analysis of the human spliceosome. Genome Res. 2002;12 (8):1231-45. doi: 10.1101/gr.473902. PubMed PMID:12176931 PubMed Central PMC186633.
  44. Rappsilber, J, Mann, M. What does it mean to identify a protein in proteomics?. Trends Biochem. Sci. 2002;27 (2):74-8. . PubMed PMID:11852244 .
  45. Chen, J, Rappsilber, J, Chiang, YC, Russell, P, Mann, M, Denis, CL et al.. Purification and characterization of the 1.0 MDa CCR4-NOT complex identifies two novel components of the complex. J. Mol. Biol. 2001;314 (4):683-94. doi: 10.1006/jmbi.2001.5162. PubMed PMID:11733989 .
  46. Rappsilber, J, Steen, H, Mann, M. Labile sulfogroup allows differentiation of sulfotyrosine and phosphotyrosine in peptides. J Mass Spectrom. 2001;36 (7):832-3. doi: 10.1002/jms.195. PubMed PMID:11473407 .
  47. Rappsilber, J, Ajuh, P, Lamond, AI, Mann, M. SPF30 is an essential human splicing factor required for assembly of the U4/U5/U6 tri-small nuclear ribonucleoprotein into the spliceosome. J. Biol. Chem. 2001;276 (33):31142-50. doi: 10.1074/jbc.M103620200. PubMed PMID:11331295 .
  48. Rappsilber, J, Siniossoglou, S, Hurt, EC, Mann, M. A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry. Anal. Chem. 2000;72 (2):267-75. doi: 10.1021/ac991081o. PubMed PMID:10658319 .
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