2023

Bogdanow B.#*, Mühlberg L.*, Gruska I., Vetter B., Ruta J., Elofsson A., Wiebusch L.#, Liu F.# Structural Host-Virus Interactome Profiling of Intact Infected Cells. bioRxiv. (DOI: 10.1101/2023.12.03.569778)

Clasen MA.*, Ruwolt M.*, Kurt LU., Gozzo FC., Wang S., Chen T., Carvalho PC.#, Lima DB.#, Liu F.# Proteome-scale recombinant standards and a robust high-speed search engine to advance cross-linking MS-based interactomics. bioRxiv. (DOI: 10.1101/2023.11.30.569448)

Bogdanow B.#, Gruska I., Mühlberg L., Protze J., Hohensee S., Vetter B., Bosse JB., Lehmann M., Sadeghi M.#, Wiebusch L.#, Liu F#. Spatially resolved protein map of intact human cytomegalovirus virions. Nat Microbiol. (DOI: 10.1038/s41564-023-01433-8)

Ramesh N, Escher M, Turrel O, Lützkendorf J, Matkovic T, Liu F, Sigrist SJ. An antagonism between Spinophilin and Syd-1 operates upstream of memory-promoting presynaptic long-term plasticity. Elife. (DOI: 10.7554/eLife.86084)

Lučić I, Héluin L, Jiang PL, Castro Scalise AG, Wang C, Franz A, Heyd F, Wahl M, Liu F, Plested AJR. CaMKII autophosphorylation can occur between holoenzymes without subunit exchange. Elife. (DOI: 10.7554/eLife.86090)

Bogdanow B., Wang C., Ruwolt M., Ruta J., Mühlberg L., Zeng W., Elofsson A., Liu F. Enhancing Inter-link Coverage in Cross-Linking Mass Spectrometry through Context-Sensitive Subgrouping and Decoy Fusion. bioRxiv. (DOI: 10.1101/2023.07.19.549678)

Ruwolt M., Piazza I.#, Liu F.# The potential of cross-linking mass spectrometry in the development of protein-protein interaction modulators. Curr Opin Struct Biol. (DOI: 10.1016/j.sbi.2023.102648)

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. Anal Chem. (DOI: 10.1021/acs.analchem.2c05141)

2022

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)

2021

Jiang P.*, 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)

2020

Rabouw H.H., Visser L.J., Passchier T.C., Langereis M.A., Liu F., Giansanti P., van Vliet A.L.W., Dekker J.G., van der Grein S.G., Saucedo J.G., Anand A.A., Trellet M.E., Bonvin, A.M.J.J., Walter P., Heck A.J.R., de Groot R.J., van Kuppeveld F.J.M. 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 C.K., 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 M.A., Koopmans F., Sullivan P.F., Protze J., Krause G., Verhage M., Li K.W.,# Liu F.,# Smit AB#. Stitching the synapse: Cross-linking mass spectrometry into resolving synaptic protein interactions. Sci Adv (DOI: 10.1126/sciadv.aax5783)

2019

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)

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)

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)

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)