List of Publications

C. W. Combe, M. Sivade, H. Hermjakob, J. Heimbach, B. H. Meldal, G. Micklem, S. Orchard, et al. 2017. ComplexViewer: visualization of curated macromolecular complexes. Bioinformatics. 33, 22 (Nov 15 2017), 3673-3675. DOI=10.1093/bioinformatics/btx497.

A. Belsom, G. Mudd, S. Giese, M. Auer and J. Rappsilber 2017. Complementary Benzophenone Cross-Linking/Mass Spectrometry Photochemistry. Analytical Chemistry. 89, 10 (May 16 2017), 5319-5324. DOI=10.1021/acs.analchem.6b04938.

L. Kolbowski, M. L. Mendes and J. Rappsilber 2017. Optimizing the parameters governing the fragmentation of cross-linked peptides in a tribrid mass spectrometer. Analytical Chemistry. 89, 10 (May 16 2017), 5311-5318. DOI=10.1021/acs.analchem.6b04935.

L. Fischer and J. Rappsilber 2017. Quirks of Error Estimation in Cross-Linking/Mass Spectrometry. Analytical Chemistry. 89, 7 (Apr 04 2017), 3829-3833. DOI=10.1021/acs.analchem.6b03745.

G. Kustatscher, P. Grabowski and J. Rappsilber 2017. Pervasive coexpression of spatially proximal genes is buffered at the protein level. Molecular systems biology. 13, 8 (2017), 937.

M. Schneider, A. Belsom, J. Rappsilber and O. Brock 2016. Blind testing of cross‐linking/mass spectrometry hybrid methods in CASP11. Proteins: Structure, Function, and Bioinformatics. 84, S1 (Sep 2016), 152-163. DOI=10.1002/prot.25028.

G. Kustatscher and J. Rappsilber 2016. Compositional dynamics: defining the fuzzy cell. Trends in cell biology. 26, 11 (Nov 2016), 800-803. DOI=10.1016/j.tcb.2016.08.012.

A. Belsom, M. Schneider, L. Fischer, O. Brock and J. Rappsilber 2016. Serum albumin domain structures in human blood serum by mass spectrometry and computational biology. Molecular & Cellular Proteomics. 15, 3 (Mar 2016), 1105-1116. DOI=10.1074/mcp.M115.048504.

S. H. Giese, L. Fischer and J. Rappsilber 2016. A Study into the Collision-induced Dissociation (CID) Behavior of Cross-Linked Peptides. Molecular & Cellular Proteomics. 15, 3 (Mar 2016), 1094-1104. DOI=10.1074/mcp.M115.049296.

A. Belsom, M. Schneider, O. Brock and J. Rappsilber 2016. Blind Evaluation of Hybrid Protein Structure Analysis Methods based on Cross-Linking. Trends in biochemical sciences. 41, 7 (Jul 2016), 564-567. DOI=10.1016/j.tibs.2016.05.005.

G. Kustatscher, P. Grabowski and J. Rappsilber 2016. Multiclassifier combinatorial proteomics of organelle shadows at the example of mitochondria in chromatin data. Proteomics. 16, 3 (Feb 2016), 393-401. DOI=10.1002/pmic.201500267.

A. Belsom, M. Schneider, L. Fischer, M. Mabrouk, K. Stahl, O. Brock and J. Rappsilber 2016. Blind testing cross-linking/mass spectrometry under the auspices of the 11th critical assessment of methods of protein structure prediction (CASP11). Wellcome open research. 1 (Dec 09 2016), 24. DOI=10.12688/wellcomeopenres.10046.1.

S. H. Giese, A. Belsom and J. Rappsilber 2016. Optimized Fragmentation Regime for Diazirine Photo-Cross-Linked Peptides. Analytical chemistry. 88, 16 (Aug 16 2016), 8239-8247. DOI=10.1021/acs.analchem.6b02082.

Z. A. Chen, L. Fischer, J. Cox and J. Rappsilber 2016. Quantitative cross-linking/mass spectrometry using isotope-labeled cross-linkers and MaxQuant. Molecular & Cellular Proteomics. 15, 8 (Aug 2016), 2769-2778. DOI=10.1074/mcp.M115.056481.

Z. A. Chen, R. Pellarin, L. Fischer, A. Sali, M. Nilges, P. N. Barlow and J. Rappsilber 2016. Structure of complement C3 (H2O) revealed by quantitative cross-linking/mass spectrometry and modeling. Molecular & Cellular Proteomics. 15, 8 (Aug 2016), 2730-2743. DOI=10.1074/mcp.M115.056473.

Z. Chen, L. Fischer, S. Tahir, J.-C. Bukowski-Wills, P. Barlow and J. Rappsilber 2016. Quantitative cross-linking/mass spectrometry reveals subtle protein conformational changes. Wellcome open research. 1 (2016), 5. DOI=10.12688/wellcomeopenres.9896.1.

C. W. Combe, L. Fischer and J. Rappsilber 2015. xiNET: cross-link network maps with residue resolution. Molecular & Cellular Proteomics. 14, 4 (Apr 2015), 1137-1147. DOI=10.1074/mcp.O114.042259.

G. Kustatscher, K. L. Wills, C. Furlan and J. Rappsilber 2014. Chromatin enrichment for proteomics. Nature protocols. 9, 9 (Sep 2014), 2090-2099. DOI=10.1038/nprot.2014.142.

G. Kustatscher, N. Hégarat, K. L. Wills, C. Furlan, J. C. Bukowski‐Wills, H. Hochegger and J. Rappsilber 2014. Proteomics of a fuzzy organelle: interphase chromatin. The EMBO journal. 33, 6 (Mar 18 2014), 648-664. DOI=10.1002/embj.201387614.

C. Alabert, J.-C. Bukowski-Wills, S.-B. Lee, G. Kustatscher, K. Nakamura, F. de Lima Alves, P. Menard, et al. 2014. Nascent chromatin capture proteomics determines chromatin dynamics during DNA replication and identifies unknown fork components. Nature cell biology. 16, 3 (Mar 2014), 281-291. DOI=10.1038/ncb2918.

L. Fischer, Z. A. Chen and J. Rappsilber 2013. Quantitative cross-linking/mass spectrometry using isotope-labelled cross-linkers. Journal of proteomics. 88 (Aug 2 2013), 120-128. DOI=10.1016/j.jprot.2013.03.005.

J. Rappsilber 2012. Cross-linking/mass spectrometry as a new field and the proteomics information mountain of tomorrow. Expert review of proteomics. 9, 5 (Oct 2012), 485-487. DOI=10.1586/Epr.12.44.

J. Rappsilber 2011. The beginning of a beautiful friendship: cross-linking/mass spectrometry and modelling of proteins and multi-protein complexes. Journal of structural biology. 173, 3 (Mar 2011), 530-540. DOI=10.1016/j.jsb.2010.10.014.

S. Ohta, J.-C. Bukowski-Wills, L. Sanchez-Pulido, F. de Lima Alves, L. Wood, Z. A. Chen, M. Platani, et al. 2010. The protein composition of mitotic chromosomes determined using multiclassifier combinatorial proteomics. Cell. 142, 5 (Sep 3 2010), 810-821. DOI=10.1016/j.cell.2010.07.047.

Z. A. Chen, A. Jawhari, L. Fischer, C. Buchen, S. Tahir, T. Kamenski, M. Rasmussen, et al. 2010. Architecture of the RNA polymerase II–TFIIF complex revealed by cross‐linking and mass spectrometry. The EMBO journal. 29, 4 (Feb 17 2010), 717-726. DOI=10.1038/emboj.2009.401.

L. Sennels, J.-C. Bukowski-Wills and J. Rappsilber 2009. Improved results in proteomics by use of local and peptide-class specific false discovery rates. BMC bioinformatics. 10, 1 (Jun 12 2009), 179. DOI=Artn 179
10.1186/1471-2105-10-179
.

J. Rappsilber and M. Mann 2007. Analysis of the topology of protein complexes using cross-linking and mass spectrometry. Cold Spring Harbor Protocols. 2007, 2 (2007), pdb. prot4594.

J. Rappsilber, M. Mann and Y. Ishihama 2007. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nature protocols. 2, 8 (2007), 1896-1906. DOI=10.1038/nprot.2007.261.

J. Rappsilber, M. Moniatte, M. L. Nielsen, A. V. Podtelejnikov and M. Mann 2003. Experiences and perspectives of MALDI MS and MS/MS in proteomic research. International Journal of Mass Spectrometry. 226, 1 (Mar 15 2003), 223-237. DOI=Pii S1387-3806(02)00976-4
Doi 10.1016/S1387-3806(02)00976-4
.

J. Rappsilber, W. J. Friesen, S. Paushkin, G. Dreyfuss and M. Mann 2003. Detection of arginine dimethylated peptides by parallel precursor ion scanning mass spectrometry in positive ion mode. Analytical chemistry. 75, 13 (Jul 01 2003), 3107-3114.

J. Rappsilber, Y. Ishihama and M. Mann 2003. Stop and go extraction tips for matrix-assisted laser desorption/ionization, nanoelectrospray, and LC/MS sample pretreatment in proteomics. Analytical chemistry. 75, 3 (Feb 01 2003), 663-670.

J. Rappsilber, U. Ryder, A. I. Lamond and M. Mann 2002. Large-scale proteomic analysis of the human spliceosome. Genome research. 12, 8 (Aug 2002), 1231-1245. DOI=10.1101/gr.473902.

J. Rappsilber and M. Mann 2002. Is mass spectrometry ready for proteome-wide protein expression analysis? Genome biology. 3, 8 (2002), comment2008. 1.

J. Rappsilber and M. Mann 2002. What does it mean to identify a protein in proteomics? Trends in biochemical sciences. 27, 2 (2002), 74-78.

J. Rappsilber, H. Steen and M. Mann 2001. Labile sulfogroup allows differentiation of sulfotyrosine and phosphotyrosine in peptides. Journal of Mass Spectrometry. 36, 7 (Jul 2001), 832-833. DOI=10.1002/jms.195.

J. Rappsilber, P. Ajuh, A. I. Lamond and M. Mann 2001. SPF30 is an essential human splicing factor required for assembly of the U4/U5/U6 tri-small nuclear ribonucleoprotein into the spliceosome. Journal of Biological Chemistry. 276, 33 (Aug 17 2001), 31142-31150. DOI=DOI 10.1074/jbc.M103620200.

J. Rappsilber, S. Siniossoglou, E. C. Hurt and M. Mann 2000. A generic strategy to analyze the spatial organization of multi-protein complexes by cross-linking and mass spectrometry. Analytical chemistry. 72, 2 (Jan 15 2000), 267-275.