Publications

Ruwolt M., He Y, Lima D.B., Barshop W., Broichhagen J., Huguet R., Viner R., Liu F. Real-time library search increases cross-link identification depth across all levels of sample complexity. (bioRxiv, DOI: 10.1101/2022.11.16.516769)

Zhu Y., Akkaya K.C., Lima D.B., Wang C., Lehmann M., Liu F. Cross-link assisted spatial proteomics to map sub-organelle proteomes and membrane protein topology. (bioRxiv, DOI: 10.1101/2022.05.05.490733)

Bogdanow B.#, Gruska I., Mühlberg L., Protze J., Hohensee S., Vetter B., Lehmann M., Wiebusch L.#, Liu F#. Spatial, Quantitative and Functional Deconstruction of Virus and Host Protein Interactions Inside Intact Cytomegalovirus Particles. (bioRxiv , DOI: 10.1101/2022.05.02.490278)

Bogdanow B., Katsimani N., Liu F., Selbach M. Combining metabolic pulse labeling and quantitative proteomics to monitor protein synthesis upon viral infection. Virus-Host Interactions: Methods and Protocols. (DOI: 10.1007/978-1-0716-2895-9_13)

Jang W., Puchkov D., Samsó P., Liang Y., Nadler-Holly M., Sigrist S.J., Kintscher U., Liu F., Mamchaoui K., Mouly V., Haucke V., Endosomal lipid signaling reshapes the endoplasmic reticulum to control mitochondrial function. Science. (DOI: 10.1126/science.abq5209)

Clasen M.A., Kurt L.U., Santos M.D.M., Lima D.B., Liu F., Gozzo F.C., Barbosa V.C., Carvalho P.C. Increasing confidence in proteomic spectral deconvolution through mass defect. Bioinformatics. (DOI: 10.1093/bioinformatics/btac638)

Ayala Mariscal S.M., Pigazzini M.L., Richter Y., Özel M., Grothaus I.L., Protze J., Ziege K., Kulke M., ElBediwi M., Vermaas J.V., Colombi Ciacchi L., Köppen S., Liu F. & Kirstein J., Identification of a HTT-specific binding motif in DNAJB1 essential for suppression and disaggregation of HTT. Nat Commun. (DOI: s41467-022-32370-5)

Lo W., Zhang Y, Vadas O., Roske Y., Gulluni F., Santis M.C.D., Zagar A.V., Stephanowitz H., Hirsch E., Liu F., Daumke O., Kudryashev M., Haucke V. Structural basis of phosphatidylinositol 3-kinase C2α function. Nat Struct Mol Biol. (DOI: 10.1038/s41594-022-00730-w)

Ashok Y., Vela-Rodríguez C., Yang C., Alanen H.I., Liu F., Paschal B.M., Lehtiö L. Reconstitution of the DTX3L-PARP9 complex reveals determinants for high-affinity heterodimerization and multimeric assembly. Biochem J. (DOI: 10.1042/BCJ20210722)

Ruwolt M., Schnirch L., Lima D.B., Nadler-Holly M., Viner R., Liu F. Optimized TMT-based quantitative cross-linking mass spectrometry strategy for large-scale interactomic studies. Anal Chem. (DOI: 10.1021/acs.analchem.1c04812)

Phan QV, Bogdanow B, Wyler E, Landthaler M, Liu F, Hagemeier C, Wiebusch L. Engineering, decoding and systems-level characterization of chimpanzee cytomegalovirus. PLoS Pathog. (DOI: 10.1371/journal.ppat.1010193)

Jiang P.L, Wang C., Diehl A., Viner R., Etienne C., Nandhikonda P., Foster L., Bomgarden R., Liu F. A Membrane-Permeable and Immobilized Metal Affinity Chromatography (IMAC)-Enrichable Cross-Linking Reagent to Advance In Vivo Cross-Linking Mass Spectrometry. Angew Chem Int Ed Engl. (DOI: 10.1002/anie.202113937)

Schoppe J, Schubert E, Apelbaum A, Yavavli E, Birkholz O, Stephanowitz H, Han Y, Perz A, Hofnagel O, Liu F, Piehler J, Raunser S, Ungermann C. Flexible open conformation of the AP-3 complex explains its role in cargo recruitment at the Golgi. J Biol Chem. (DOI: 10.1016/j.jbc.2021.101334)

Liang Y., Piao C., Beuschel C.B., Toppe D., Kollipara L., Bogdanow B., Maglione M., Lützkendorf J., See J.C.K., Huang S., Conrad T.O.F., Kintscher U., Madeo F., Liu F., Sickmann A., Sigrist S.J. eIF5A hypusination, boosted by dietary spermidine, protects from premature brain aging and mitochondrial dysfunction. Cell Rep. (DOI: 10.1016/j.celrep.2021.108941)

Lima D.B.,# Zhu Y., Liu F.# XlinkCyNET: A Cytoscape Application for Visualization of Protein Interaction Networks Based on Cross-Linking Mass Spectrometry Identifications. J. Proteome Res. (DOI: 10.1021/acs.jproteome.0c00957)

Gallrein C., Iburg M., Michelberger T., Koçak A., Puchkov D., Liu F., Ayala Mariscal S.M., Nayak T., Kaminski Schierle G.S., Kirstein J. Novel amyloid-beta pathology C. elegans model reveals distinct neurons as seeds of pathogenicity. Prog Neurobiol. (DOI: 10.1016/j.pneurobio.2020.101907)

Rabouw HH, Visser LJ, Passchier TC, Langereis MA, Liu F, Giansanti P, van Vliet, ALW, Dekker JG, van der Grein, SG, Saucedo JG, Anand AA, Trellet ME, Bonvin, AMJJ, Walter, P, Heck, AJR, de Groot RJ, van Kuppeveld, FJM. Inhibition of the integrated stress response by viral proteins that block p-eIF2–eIF2B association. Nat Microbiol (DOI: 10.1038/s41564-020-0759-0)

Schnirch L, Nadler-Holly M, Siao S, Frese CK, Viner R, and Liu F. Expanding the depth and sensitivity of cross-link identification by differential ion mobility using FAIMS. Anal Chem (DOI: 10.1101/2020.04.23.057091)

Petzoldt A, Götz T, Driller J, Lützkendorf J, Reddy-Alla S, Matkovic-Rachid T, Liu S, Knoche E, Mertel S, Ugorets V, Lehmann M, Ramesh N, Beuschel C, Kuropka B, Freund C, Stelzl U, Loll B, Liu F, Wahl M, and Sigrist S. RIM-Binding protein couples synaptic vesicle recruitment to release sites. JCB (DOI:10.1083/jcb.201902059)

Gonzalez-Lozano MA, Koopmans F, Sullivan PF, Protze J, Krause G, Verhage M, Li KW#, Liu F#, Smit AB#. Stitching the synapse: Cross-linking mass spectrometry into resolving synaptic protein interactions. Sci Adv (DOI: 10.1126/sciadv.aax5783)

Laezer I, Palma-Vera SE, Liu F, Frank M, Trakooljul N, Vernunft A, Schoen J, ChenS. Dynamic profile of EVs in porcine oviductal fluid during the periovulatory period. Reproduction (DOI: 10.1530/REP-19-0219)

Pavulraj S, Kamel M, Stephanowitz H, Liu F, Plendl J, Osterrieder N, Azab W. Equine Herpesvirus Type 1 Modulates Cytokine and Chemokine Profiles of Mononuclear Cells for Efficient Dissemination to Target Organs. Viruses (DOI: 10.3390/v12090999)

Iacobucci C, Piotrowski C, Aebersold R, Amaral BC, Andrews P, Bernfur K, Borchers C, Brodie NI, Bruce JE, Cao Y, Chaignepain S, Chavez JD, Claverol S, Cox J, Davis T, Degliesposti G, Dong MQ, Edinger N, Emanuelsson C, Gay M, Götze M, Gomes-Neto F, Gozzo FC, Gutierrez C, Haupt C, Heck AJR, Herzog F, Huang L, Hoopmann MR, Kalisman N, Klykov O, Kukacka Z, Liu F, et al. First community-wide, comparative cross-linking mass spectrometry study. Analytical Chemistry (DOI: 10.1021/acs.analchem.9b00658)

Liu F. Analysis of Synaptic Protein–Protein Interaction by Cross-linking Mass Spectrometry. Neuroproteomics (in the Springer book series Neuromethods) (DOI: 10.1007/978-1-4939-9662-9_9)

Wang C, Richter-Dennerlein R, Pacheu-Grau D, Liu F, Zhu Y, Dennerlein S, Rehling P. MITRAC15/COA1 promotes mitochondrial translation in a ND2 ribosome-nascent chain complex. EMBO Reports (DOI: 10.15252/embr.201948833)

2018

Liu F*, Lössl P*, Rabbitts BM*, Balaban RS#, Heck AJ#. The interactome of intact mitochondria by cross-linking mass spectrometry provides evidence for co-existing respiratory supercomplexes. Molecular and Cellular Proteomics (DOI: 10.1074/mcp.RA117.000470)

2017

Liu Q, Remmelzwaal S, Heck AJ, Akhmanova A#,Liu F#. Facilitating identification of minimal protein binding domains by cross-linking mass spectrometry. Scientific Reports (DOI: 10.1038/s41598-017-13663-y)

Liu F#*, Lossl P*, Scheltema R, Viner R, Heck AJ#. Optimized fragmentation schemes and data analysis strategies for proteome-wide cross-link identification. Nature Communications (DOI: 10.1038/ncomms15473)

2016

Yang Y*, Liu F*, Franc V*, Halim LA, Schellekens H, Heck AJ. Hybrid mass spectrometry approaches in glycoprotein analysis and their usage in scoring biosimilarity. Nature Communications (DOI: 10.1038/ncomms13397)

Liu Q, Liu F, Yu KL, Tas R, Grigoriev I, Remmelzwaal S, Serra-Marques A, Kapitein LC, Heck AJR, Akhmanova A. MICAL3 Flavoprotein Monooxygenase Forms a Complex with Centralspindlin and Regulates Cytokinesis. Journal of Biological Chemistry (DOI: 10.1074/jbc.M116.748186)

Lössl P, Brunner AM, Liu F, Leney AC, Yamashita M, Scheltema RA, Heck AJ. Deciphering the Interplay among Multisite Phosphorylation, Interaction Dynamics, and Conformational Transitions in a Tripartite Protein System. ACS Central Science (DOI: 10.1021/acscentsci.6b00053)

2015

Liu F, Rijkers DT, Post H, Heck AJ. Proteome-wide profiling of protein assemblies by cross-linking mass spectrometry. Nature Methods (DOI: 10.1038/nmeth.3603)

Liu F, Heck AJ. Interrogating the architecture of protein assemblies and protein interaction networks by cross-linking mass spectrometry. Current Opinion in Structural Biology (DOI: 10.1016/j.sbi.2015.10.006)

Glas M, van den Berg van Saparoea HB, McLaughlin SH, Roseboom W, Liu F, Koningstein GM, Fish A, den Blaauwen T, Heck AJ, de Jong L, Bitter W, de Esch IJ, Luirink J. The Soluble Periplasmic Domains of Escherichia coli Cell Division Proteins FtsQ/FtsB/FtsL Form a Trimeric Complex with Submicromolar Affinity. Journal of Biological Chemistry (DOI: 10.1074/jbc.M115.654756)

Argo AS, Shi C, Liu F, Goshe MB. Performing protein crosslinking using gas-phase cleavable chemical crosslinkers and liquid chromatography-tandem mass spectrometry. Methods (DOI: 10.1016/j.ymeth.2015.06.011)

Brunner AM, Lössl P, Liu F, Huguet R, Mullen C, Yamashita M, Zabrouskov V, Makarov A, Altelaar AF, Heck AJ. Benchmarking multiple fragmentation methods on an Orbitrap Fusion for top-down phospho-proteoform characterization. Analytical Chemistry (DOI: 10.1021/acs.analchem.5b00162)

2014

Liu F, van Breukelen B, Heck AJ. Facilitating protein disulfide mapping by a combination of pepsin digestion, electron transfer higher energy dissociation (EThcD), and a dedicated search algorithm SlinkS. Molecular and Cellular Proteomics (DOI: 10.1074/mcp.O114.039057)

2010-2013

Olson AL*, Liu F*, Tucker AT, Goshe MB, Cavanagh J. Chemical crosslinking and LC/MS analysis to determine protein domain orientation: application to AbrB. Biochemical and biophysical research communications (DOI: 10.1016/j.bbrc.2012.12.124)

Liu F*, Wu C*, Sweedler JV, Goshe MB. An enhanced protein crosslink identification strategy using CID-cleavable chemical crosslinkers and LC/MS(n) analysis. Proteomics (DOI: 10.1002/pmic.201100352)

Liu F, Goshe MB. Combinatorial electrostatic collision-induced dissociative chemical cross-linking reagents for probing protein surface topology. Analytical Chemistry (DOI: 10.1021/ac101030w)