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Proteomics Core Facility

This facility provides a full proteomics infrastructure for the identification and characterisation of proteins.

Publications

Drug target identification in tissues by thermal proteome profiling.

Mateus A, Kurzawa N, Perrin J, Bergamini G, Savitski MM

Annual review of pharmacology and toxicology 2021

doi:10.1146/annurev-pharmtox-052120-013205.

Bioaccumulation of therapeutic drugs by human gut bacteria.

Klünemann M, Andrejev S, Blasche S, Mateus A, Phapale P, Devendran S, Vappiani J, Simon B, Scott TA, Kafkia E, Konstantinidis D, Zirngibl K, Mastrorilli E, Banzhaf M, Mackmull MT, Hövelmann F, Nesme L, Brochado AR, Maier L, Bock T, Periwal V, Kumar M, Kim Y, Tramontano M, Schultz C, Beck M, Hennig J, Zimmermann M, Sévin DC, Cabreiro F, Savitski MM, Bork P, Typas A, Patil KR

Nature 2021

doi:10.1038/s41586-021-03891-8.

Transcriptional and post-transcriptional polar effects in bacterial gene deletion libraries.

Mateus A, Shah M, Hevler J, Kurzawa N, Bobonis J, Typas A, Savitski MM

mSystems 2021

doi:10.1128/mSystems.00813-21.

Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif.

Lorenzo R, Defelipe LA, Aliperti L, Niebling S, Custódio TF, Löw C, Schwarz JJ, Remans K, Craig PO, Otero LH, Klinke S, García-Alai M, Sánchez IE, Alonso LG

The Journal of biological chemistry 2021

doi:10.1016/j.jbc.2021.101175.

The rise of proteome-wide biophysics.

Mateus A, Savitski MM, Piazza I

Molecular systems biology 2021

doi:10.15252/msb.202110442.

Structure and dynamics of the quaternary hunchback mRNA translation repression complex.

Macošek J, Simon B, Linse JB, Jagtap PKA, Winter SL, Foot J, Lapouge K, Perez K, Rettel M, Ivanović MT, Masiewicz P, Murciano B, Savitski MM, Loedige I, Hub JS, Gabel F, Hennig J

Nucleic acids research 2021

doi:10.1093/nar/gkab635.

P38α-MAPK phosphorylates Snapin and reduces Snapin-mediated BACE1 transportation in APP-transgenic mice.

Schnöder L, Tomic I, Schwindt L, Helm D, Rettel M, Schulz-Schaeffer W, Krause E, Rettig J, Fassbender K, Liu Y

FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2021

doi:10.1096/fj.202100017R.

SETD7-mediated monomethylation is enriched on soluble Tau in Alzheimer's disease.

Bichmann M, Prat Oriol N, Ercan-Herbst E, Schöndorf DC, Gomez Ramos B, Schwärzler V, Neu M, Schlüter A, Wang X, Jin L, Hu C, Tian Y, Ried JS, Haberkant P, Gasparini L, Ehrnhoefer DE

Molecular neurodegeneration 2021

doi:10.1186/s13024-021-00468-x.

Structure of the mycobacterial ESX-5 type VII secretion system pore complex.

Beckham KSH, Ritter C, Chojnowski G, Ziemianowicz DS, Mullapudi E, Rettel M, Savitski MM, Mortensen SA, Kosinski J, Wilmanns M

Science advances 2021

doi:10.1126/sciadv.abg9923.

Increased levels of mitochondrial import factor Mia40 prevent the aggregation of polyQ proteins in the cytosol.

Schlagowski AM, Knöringer K, Morlot S, Sánchez Vicente A, Flohr T, Krämer L, Boos F, Khalid N, Ahmed S, Schramm J, Murschall LM, Haberkant P, Stein F, Riemer J, Westermann B, Braun RJ, Winklhofer KF, Charvin G, Herrmann JM

The EMBO journal 2021

doi:10.15252/embj.2021107913.

Impact of phosphorylation on thermal stability of proteins.

Potel CM, Kurzawa N, Becher I, Typas A, Mateus A, Savitski MM

Nature methods 2021

doi:10.1038/s41592-021-01177-5.

Quality standards in proteomics research facilities: common standards and quality procedures are essential for proteomics facilities and their users.

Chiva C, Mendes Maia T, Panse C, Stejskal K, Douché T, Matondo M, Loew D, Helm D, Rettel M, Mechtler K, Impens F, Nanni P, Shevchenko A, Sabidó E

EMBO reports 2021

doi:10.15252/embr.202152626.

Identification of dynamic RNA-binding proteins uncovers a Cpeb4-controlled regulatory cascade during pathological cell growth of cardiomyocytes.

Riechert E, Kmietczyk V, Stein F, Schwarzl T, Sekaran T, Jürgensen L, Kamuf-Schenk V, Varma E, Hofmann C, Rettel M, Gür K, Ölschläger J, Kühl F, Martin J, Ramirez-Pedraza M, Fernandez M, Doroudgar S, Méndez R, Katus HA, Hentze MW, Völkers M

Cell reports 2021

doi:10.1016/j.celrep.2021.109100.

Global mapping of Salmonella enterica-host protein-protein interactions during infection.

Walch P, Selkrig J, Knodler LA, Rettel M, Stein F, Fernandez K, Viéitez C, Potel CM, Scholzen K, Geyer M, Rottner K, Steele-Mortimer O, Savitski MM, Holden DW, Typas A

2021

doi:10.1016/j.chom.2021.06.004.

NMD inhibition by 5-azacytidine augments presentation of immunogenic frameshift-derived neoepitopes.

Becker JP, Helm D, Rettel M, Stein F, Hernandez-Sanchez A, Urban K, Gebert J, Kloor M, Neu-Yilik G, von Knebel Doeberitz M, Hentze MW, Kulozik AE

iScience 2021

doi:10.1016/j.isci.2021.102389.

SARS-CoV-2 infection remodels the host protein thermal stability landscape.

Selkrig J, Stanifer M, Mateus A, Mitosch K, Barrio-Hernandez I, Rettel M, Kim H, Voogdt CGP, Walch P, Kee C, Kurzawa N, Stein F, Potel C, Jarzab A, Kuster B, Bartenschlager R, Boulant S, Beltrao P, Typas A, Savitski MM

Molecular systems biology 2021

doi:10.15252/msb.202010188.

Cell surface thermal proteome profiling tracks perturbations and drug targets on the plasma membrane.

Kalxdorf M, Günthner I, Becher I, Kurzawa N, Knecht S, Savitski MM, Eberl HC, Bantscheff M

Nature methods 2021

doi:10.1038/s41592-020-01022-1.

Extensive OMICS resource for Sf21 and Tni cell lines.

Galik B, Landry JM, Kirkpatrick J, Fritz M, Baying B, Blake J, Haase B, Collier PG, Hercog R, Pavlinic D, Stolt-Bergner P, Besir H, Remans K, Gyenesei A, Benes V

2021

doi:10.1101/2021.04.06.438574.

The central role of salivary metalloproteases in host acquired resistance to tick feeding.

Perner J, Helm D, Haberkant P, Hatalova T, Kropackova S, Ribeiro JM, Kopacek P

Frontiers in cellular and infection microbiology 2020

doi:10.3389/fcimb.2020.563349.

An integrated multiomic and quantitative label-free microscopy-based approach to study pro-fibrotic signalling in ex vivo human precision-cut lung slices.

Khan MM, Poeckel D, Halavatyi A, Zukowska-Kasprzyk J, Stein F, Vappiani J, Sevin DC, Tischer C, Zinn N, Eley JD, Gudmann NS, Muley T, Winter H, Fisher AJ, Nanthakumar CB, Bergamini G, Pepperkok R

The European respiratory journal 2020

doi:10.1183/13993003.00221-2020.

Stroma transcriptomic and proteomic profile of prostate cancer metastasis xenograft models reveals prognostic value of stroma signatures.

Karkampouna S, De Filippo MR, Ng CKY, Klima I, Zoni E, Spahn M, Stein F, Haberkant P, Thalmann GN, Kruithof de Julio M

Cancers 2020

doi:10.3390/cancers12123786.

A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles.

Kurzawa N, Becher I, Sridharan S, Franken H, Mateus A, Anders S, Bantscheff M, Huber W, Savitski MM

Nature communications 2020

doi:10.1038/s41467-020-19529-8.

The functional proteome landscape of Escherichia coli.

Mateus A, Hevler J, Bobonis J, Kurzawa N, Shah M, Mitosch K, Goemans CV, Helm D, Stein F, Typas A, Savitski MM

Nature 2020

doi:10.1038/s41586-020-3002-5.

Aggregation and disaggregation features of the human proteome.

Määttä TA, Rettel M, Sridharan S, Helm D, Kurzawa N, Stein F, Savitski MM

Molecular systems biology 2020

doi:10.15252/msb.20209500.

Rtpca: an R package for differential thermal proximity coaggregation analysis.

Kurzawa N, Mateus A, Savitski MM

Bioinformatics (Oxford, England) 2020

doi:10.1093/bioinformatics/btaa682.

Pseudo-RNA-binding domains mediate RNA structure specificity in Upstream of N-Ras.

Hollmann NM, Jagtap PKA, Masiewicz P, Guitart T, Simon B, Provaznik J, Stein F, Haberkant P, Sweetapple LJ, Villacorta L, Moojiman D, Benes V, Savitski MM, Gebauer F, Hennig J

2020

doi:10.1016/j.celrep.2020.107930.

Dissecting the sequence determinants for dephosphorylation by the catalytic subunits of phosphatases PP1 and PP2A.

Hoermann B, Kokot T, Helm D, Heinzlmeir S, Chojnacki JE, Schubert T, Ludwig C, Berteotti A, Kurzawa N, Kuster B, Savitski MM, Köhn M

Nature communications 2020

doi:10.1038/s41467-020-17334-x.

Bacterial retrons encode tripartite toxin/antitoxin systems.

Bobonis J, Mateus A, Pfalz B, Garcia-Santamarina S, Galardini M, Kobayashi C, Stein F, Savitski MM, Elfenbein JR, Andrews-Poymenis H, Typas A

2020

doi:10.1101/2020.06.22.160168.

Spatiotemporal proteomics uncovers cathepsin-dependent macrophage cell death during Salmonella infection.

Selkrig J, Li N, Hausmann A, Mangan MSJ, Zietek M, Mateus A, Bobonis J, Sueki A, Imamura H, El Debs B, Sigismondo G, Florea BI, Overkleeft HS, Kopitar-Jerala N, Turk B, Beltrao P, Savitski MM, Latz E, Hardt WD, Krijgsveld J, Typas A

Nature microbiology 2020

doi:10.1038/s41564-020-0736-7.

ACLY is the novel signaling target of PIP 2/PIP 3 and Lyn in acute myeloid leukemia.

Basappa J, Citir M, Zhang Q, Wang HY, Liu X, Melnikov O, Yahya H, Stein F, Muller R, Traynor-Kaplan A, Schultz C, Wasik MA, Ptasznik A

Heliyon 2020

doi:10.1016/j.heliyon.2020.e03910.

Phage proteins block and trigger retron toxin/antitoxin systems.

Bobonis J, Mitosch K, Mateus A, Kritikos G, Elfenbein JR, Savitski MM, Andrews-Polymenis H, Typas A

2020

doi:10.1101/2020.06.22.160242.

A dual-mechanism antibiotic kills gram-negative bacteria and avoids drug resistance.

Martin JK, Sheehan JP, Bratton BP, Moore GM, Mateus A, Li SH, Kim H, Rabinowitz JD, Typas A, Savitski MM, Wilson MZ, Gitai Z

Cell 2020

doi:10.1016/j.cell.2020.05.005.

Plasticity of nuclear and cytoplasmic stress responses of RNA-binding proteins.

Backlund M, Stein F, Rettel M, Schwarzl T, Perez-Perri JI, Brosig A, Zhou Y, Neu-Yilik G, Hentze MW, Kulozik AE

Nucleic acids research 2020

doi:10.1093/nar/gkaa256.

Meltome atlas-thermal proteome stability across the tree of life.

Jarzab A, Kurzawa N, Hopf T, Moerch M, Zecha J, Leijten N, Bian Y, Musiol E, Maschberger M, Stoehr G, Becher I, Daly C, Samaras P, Mergner J, Spanier B, Werner T, Angelov A, Wilhelm M, Bantscheff M, Lemeer S, Klingenspor M, Hahne H, Liebl W, Kuster B, Savitski MM

Nature methods 2020

doi:10.1038/s41592-020-0801-4.

Thermal proteome profiling for interrogating protein interactions.

Mateus A, Kurzawa N, Becher I, Sridharan S, Helm D, Stein F, Typas A, Savitski MM

Molecular systems biology 2020

doi:10.15252/msb.20199232.

Systematic localization of Escherichia coli membrane proteins.

Sueki A, Stein F, Savitski MM, Selkrig J, Typas A

mSystems 2020

doi:10.1128/mSystems.00808-19.

Human mast cell proteome reveals unique lineage, putative functions, and structural basis for cell ablation.

Plum T, Wang X, Rettel M, Krijgsveld J, Feyerabend TB, Rodewald HR

Immunity 2020

doi:10.1016/j.immuni.2020.01.012.

A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress.

Viéitez C, Martínez-Cebrián G, Solé C, Böttcher R, Potel CM, Savitski MM, Onnebo S, Fabregat M, Shilatifard A, Posas F, de Nadal E

Nucleic acids research 2020

doi:10.1093/nar/gkaa081.

Outer membrane lipoprotein NlpI scaffolds peptidoglycan hydrolases within multi-enzyme complexes in Escherichia coli.

Banzhaf M, Yau HC, Verheul J, Lodge A, Kritikos G, Mateus A, Cordier B, Hov AK, Stein F, Wartel M, Pazos M, Solovyova AS, Breukink E, van Teeffelen S, Savitski MM, den Blaauwen T, Typas A, Vollmer W

The EMBO journal 2020

doi:10.15252/embj.2019102246.

A misprocessed form of Apolipoprotein A-I is specifically associated with recurrent focal segmental glomerulosclerosis.

Jacobs-Cachá C, Puig-Gay N, Helm D, Rettel M, Sellarès J, Meseguer A, Savitski MM, Moreso FJ, Soler MJ, Seron D, Lopez-Hellin J

Scientific reports 2020

doi:10.1038/s41598-020-58197-y.

Identifying drug targets in tissues and whole blood with thermal-shift profiling.

Perrin J, Werner T, Kurzawa N, Rutkowska A, Childs DD, Kalxdorf M, Poeckel D, Stonehouse E, Strohmer K, Heller B, Thomson DW, Krause J, Becher I, Eberl HC, Vappiani J, Rau CE, Sevin DC, Huber W, Franken H, Savitski MM, Faelth-Savitski M, Bergamini G, Bantscheff M

Nature biotechnology 2020

doi:10.1038/s41587-019-0388-4.

Impact of phosphorylation on thermal stability of proteins.

Potel CM, Kurzawa N, Becher I, Typas A, Mateus A, Savitski MM

2020

doi:10.1101/2020.01.14.903849.

Towards a systematic map of the functional role of protein phosphorylation.

Viéitez​ C​, Busby​ BP, Ochoa​ D​, Mateus​ A​, Galardini​ M​, Jawed​ A​, Memon​ D​, Potel​ CM​, Vonesch SC​, Tu​ CS, Shahraz​ M​, Stein​ F​, Steinmetz​ LM, Savitski​ MM, Typas A, Beltrao​ P

2019

doi:10.1101/872770.

The functional landscape of the human phosphoproteome.

Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, Beltrao P

Nature biotechnology 2019

doi:10.1038/s41587-019-0344-3.

A new antibiotic selectively kills Gram-negative pathogens.

Imai Y, Meyer KJ, Iinishi A, Favre-Godal Q, Green R, Manuse S, Caboni M, Mori M, Niles S, Ghiglieri M, Honrao C, Ma X, Guo J, Makriyannis A, Linares-Otoya L, Wuisan ZG, Böhringer N, Wu R, Kaur H, Typas A, Mateus A, Espinoza JL, Savitski MM, Nelson KE, O'Rourke A, Noinaj N, Hiller S, D'Onofrio A, Schäberle TF, Lewis K

Nature 2019

doi:10.1038/s41586-019-1791-1.

Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins.

Childs D, Bach K, Franken H, Anders S, Kurzawa N, Bantscheff M, Savitski M, Huber W

Molecular & cellular proteomics : MCP 2019

doi:10.1074/mcp.TIR119.001481.

Target discovery using thermal proteome profiling.

Sridharan S, Günthner I, Becher I, Savitski M, Bantscheff M

2019

doi:10.1002/9781118970195.ch11.

The Hsp90 isoforms from S. cerevisiae differ in structure, function and client range.

Girstmair H, Tippel F, Lopez A, Tych K, Stein F, Haberkant P, Schmid PWN, Helm D, Rief M, Sattler M, Buchner J

Nature communications 2019

doi:10.1038/s41467-019-11518-w.

Monitoring cell-type-specific gene expression using ribosome profiling in vivo during cardiac hemodynamic stress.

Doroudgar S, Hofmann C, Boileau E, Malone B, Riechert E, Gorska AA, Jakobi T, Sandmann C, Jürgensen L, Kmietczyk V, Malovrh E, Burghaus J, Rettel M, Stein F, Younesi F, Mauz V, Friedrich UA, Kramer G, Backs J, Dieterich C, Katus HA, Völkers M

Circulation research 2019

doi:10.1161/CIRCRESAHA.119.314817.

Asparagine endopeptidase cleaves tau at N167 after uptake into microglia.

Behrendt A, Bichmann M, Ercan-Herbst E, Haberkant P, Schöndorf DC, Wolf M, Fahim SA, Murolo E, Ehrnhoefer DE

Neurobiology of disease 2019

doi:10.1016/j.nbd.2019.104518.

Publisher Correction: Mitochondrial protein-induced stress triggers a global adaptive transcriptional programme.

Boos F, Krämer L, Groh C, Jung F, Haberkant P, Stein F, Wollweber F, Gackstatter A, Zöller E, van der Laan M, Savitski MM, Benes V, Herrmann JM

Nature cell biology 2019

doi:10.1038/s41556-019-0326-1.

Secretome profiling of heterotypic spheroids suggests a role of fibroblasts in HIF-1 pathway modulation and colorectal cancer photodynamic resistance.

Lamberti MJ, Rettel M, Krijgsveld J, Rivarola VA, Rumie Vittar NB

Cellular oncology (Dordrecht) 2019

doi:10.1007/s13402-018-00418-8.

Mitochondrial protein-induced stress triggers a global adaptive transcriptional programme.

Boos F, Krämer L, Groh C, Jung F, Haberkant P, Stein F, Wollweber F, Gackstatter A, Zöller E, van der Laan M, Savitski MM, Benes V, Herrmann JM

Nature cell biology 2019

doi:10.1038/s41556-019-0294-5.

Cytosolic glucosylceramide regulates endolysosomal function in Niemann-Pick type C disease.

Wheeler S, Haberkant P, Bhardwaj M, Tongue P, Ferraz MJ, Halter D, Sprong H, Schmid R, Aerts JMFG, Sullo N, Sillence DJ

Neurobiology of disease 2019

doi:10.1016/j.nbd.2019.03.005.

Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP.

Sridharan S, Kurzawa N, Werner T, Günthner I, Helm D, Huber W, Bantscheff M, Savitski MM

Nature communications 2019

doi:10.1038/s41467-019-09107-y.

Effect of Sec61 interaction with Mpd1 on endoplasmic reticulum-associated degradation.

Pereira F, Rettel M, Stein F, Savitski MM, Collinson I, Römisch K

PloS one 2019

doi:10.1371/journal.pone.0211180.

Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture.

Perez-Perri JI, Rogell B, Schwarzl T, Stein F, Zhou Y, Rettel M, Brosig A, Hentze MW

Nature communications 2018

doi:10.1038/s41467-018-06557-8.

A Bifunctional Noncanonical Amino Acid: Synthesis, Expression, and Residue-Specific Proteome-wide Incorporation.

Hoffmann JE, Dziuba D, Stein F, Schultz C

Biochemistry 2018

doi:10.1021/acs.biochem.8b00397.

Thermal proteome profiling in bacteria: probing protein state in vivo.

Mateus A, Bobonis J, Kurzawa N, Stein F, Helm D, Hevler J, Typas A, Savitski MM

Molecular systems biology 2018

doi:10.15252/msb.20188242.

Species-specific activity of antibacterial drug combinations.

Brochado AR, Telzerow A, Bobonis J, Banzhaf M, Mateus A, Selkrig J, Huth E, Bassler S, Zamarreño Beas J, Zietek M, Ng N, Foerster S, Ezraty B, Py B, Barras F, Bork P, Savitski MM, Göttig S, Typas A

Nature 2018

doi:10.1038/s41586-018-0278-9.

TRRAP is essential for regulating the accumulation of mutant and wild-type p53 in lymphoma.

Jethwa A, Słabicki M, Hüllein J, Jentzsch M, Dalal V, Rabe S, Wagner L, Walther T, Klapper W, Bohnenberger H, Rettel M, Lu J, Smits AH, Stein F, Savitski MM, Huber W, Aylon Y, Oren M, Zenz T

Blood 2018

doi:10.1182/blood-2017-09-806679.

Pervasive protein thermal stability variation during the cell cycle.

Becher I, Andrés-Pons A, Romanov N, Stein F, Schramm M, Baudin F, Helm D, Kurzawa N, Mateus A, Mackmull MT, Typas A, Müller CW, Bork P, Beck M, Savitski MM

Cell 2018

doi:10.1016/j.cell.2018.03.053.

Author Correction: Structural analysis of human ARS2 as a platform for co-transcriptional RNA sorting.

Schulze WM, Stein F, Rettel M, Nanao M, Cusack S

Nature communications 2018

doi:10.1038/s41467-018-04643-5.

Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.

Strucko T, Zirngibl K, Pereira F, Kafkia E, Mohamed ET, Rettel M, Stein F, Feist AM, Jouhten P, Patil KR, Forster J

Metabolic engineering 2018

doi:10.1016/j.ymben.2018.03.006.

Spatial tissue proteomics quantifies inter- and intra-tumor heterogeneity in hepatocellular carcinoma.

Buczak K, Ori A, Kirkpatrick JM, Holzer K, Dauch D, Roessler S, Endris V, Lasitschka F, Parca L, Schmidt A, Zender L, Schirmacher P, Krijgsveld J, Singer S, Beck M

Molecular & cellular proteomics : MCP 2018

doi:10.1074/mcp.RA117.000189.

Structural analysis of human ARS2 as a platform for co-transcriptional RNA sorting.

Schulze WM, Stein F, Rettel M, Nanao M, Cusack S

Nature communications 2018

doi:10.1038/s41467-018-04142-7.

Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis.

Savitski MM, Zinn N, Faelth-Savitski M, Poeckel D, Gade S, Becher I, Muelbaier M, Wagner AJ, Strohmer K, Werner T, Melchert S, Petretich M, Rutkowska A, Vappiani J, Franken H, Steidel M, Sweetman GM, Gilan O, Lam EYN, Dawson MA, Prinjha RK, Grandi P, Bergamini G, Bantscheff M

Cell 2018

doi:10.1016/j.cell.2018.02.030.

A search for ceramide binding proteins using bifunctional lipid analogs yields CERT-related protein StarD7.

Bockelmann S, Mina JGM, Korneev S, Hassan DG, Mueller D, Hilderink A, Vlieg HC, Raijmakers R, Heck AJR, Haberkant P, Holthuis JCM

Journal of lipid research 2018

doi:10.1194/jlr.M082354.

Systematic analysis of protein turnover in primary cells.

Mathieson T, Franken H, Kosinski J, Kurzawa N, Zinn N, Sweetman G, Poeckel D, Ratnu VS, Schramm M, Becher I, Steidel M, Noh KM, Bergamini G, Beck M, Bantscheff M, Savitski MM

Nature communications 2018

doi:10.1038/s41467-018-03106-1.

Leaderless secreted peptide signaling molecule alters global gene expression and increases virulence of a human bacterial pathogen.

Do H, Makthal N, VanderWal AR, Rettel M, Savitski MM, Peschek N, Papenfort K, Olsen RJ, Musser JM, Kumaraswami M

Proceedings of the National Academy of Sciences of the United States of America 2017

doi:10.1073/pnas.1705972114.

Specific RNP capture with antisense LNA/DNA mixmers.

Rogell BM, Fischer B, Rettel M, Krijgsveld J, Castello A, Hentze MW

RNA (New York, N.Y.) 2017

doi:10.1261/rna.060798.117.

Wilhelm et al. reply.

Wilhelm M, Hahne H, Savitski M, Marx H, Lemeer S, Bantscheff M, Kuster B

Nature 2017

doi:10.1038/nature22294.

A Ratiometric Sensor for Imaging Insulin Secretion in Single β Cells.

Schifferer M, Yushchenko DA, Stein F, Bolbat A, Schultz C

Cell chemical biology 2017

doi:10.1016/j.chembiol.2017.03.001.

Identification of a feedback loop involving beta-glucosidase 2 and its product sphingosine sheds light on the molecular mechanisms in Gaucher disease.

Schonauer S, Körschen HG, Penno A, Rennhack A, Breiden B, Sandhoff K, Gutbrod K, Dörmann P, Raju DN, Haberkant P, Gerl MJ, Brügger B, Zigdon H, Vardi A, Futerman AH, Thiele C, Wachten D

The Journal of biological chemistry 2017

doi:10.1074/jbc.m116.762831.

Structure of the mycobacterial ESX-5 type VII secretion system membrane complex by single-particle analysis.

Beckham KS, Ciccarelli L, Bunduc CM, Mertens HD, Ummels R, Lugmayr W, Mayr J, Rettel M, Savitski MM, Svergun DI, Bitter W, Wilmanns M, Marlovits TC, Parret AH, Houben EN

Nature microbiology 2017

doi:10.1038/nmicrobiol.2017.47.

Spatiotemporal Analysis of a Glycolytic Activity Gradient Linked to Mouse Embryo Mesoderm Development

Bulusu V, Prior N, Snaebjornsson MT, Kuehne A, Sonnen KF, Kress J, Stein F, Schultz C, Sauer U, Aulehla A

Developmental cell 2017

doi:10.1016/j.devcel.2017.01.015.

Trifunctional lipid probes for comprehensive studies of single lipid species in living cells.

Höglinger D, Nadler A, Haberkant P, Kirkpatrick J, Schifferer M, Stein F, Hauke S, Porter FD, Schultz C

Proceedings of the National Academy of Sciences of the United States of America 2017

doi:10.1073/pnas.1611096114.

High-Content Imaging Platform for Profiling Intracellular Signaling Network Activity in Living Cells.

Kuchenov D, Laketa V, Stein F, Salopiata F, Klingmüller U, Schultz C

Cell chemical biology 2016

doi:10.1016/j.chembiol.2016.11.008.

In planta determination of the mRNA-binding proteome of Arabidopsis etiolated seedlings.

Reichel M, Liao Y, Rettel M, Ragan C, Evers M, Alleaume AM, Horos R, Hentze MW, Preiss T, Millar AA

The Plant cell 2016

doi:10.1105/tpc.16.00562.

A standardized production pipeline for high profile targets from Mycobacterium tuberculosis.

Milewski MC, Broger T, Kirkpatrick J, Filomena A, Komadina D, Schneiderhan-Marra N, Wilmanns M, Parret AH

Proteomics. Clinical applications 2016

doi:10.1002/prca.201600033.

Comprehensive Identification of RNA-Binding Domains in Human Cells.

Castello A, Fischer B, Frese CK, Horos R, Alleaume AM, Foehr S, Curk T, Krijgsveld J, Hentze MW

MOLECULAR CELL 2016

doi:10.1016/j.molcel.2016.06.029.

Identification of RNA-binding proteins in macrophages by interactome capture.

Liepelt A, Naarmann-de Vries IS, Simons N, Eichelbaum K, Foehr S, Archer SK, Castello A, Usadel B, Krijgsveld J, Preiss T, Marx G, Hentze MW, Ostareck DH, Ostareck-Lederer A

Molecular & cellular proteomics : MCP 2016

doi:10.1074/mcp.M115.056564.

An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation.

Schur FK, Obr M, Hagen WJ, Wan W, Jakobi AJ, Kirkpatrick JM, Sachse C, Kräusslich HG, Briggs JA

Science (New York, N.Y.) 2016

doi:10.1126/science.aaf9620.

The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease

Liao Y, Castello A, Fischer B, Leicht S, Föehr S, Frese C, Ragan C, Kurscheid S, Pagler E, Yang H, Krijgsveld J, Hentze MW, Preiss T

Cell Reports 2016

doi:10.1016/j.celrep.2016.06.084.

Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in <i>Drosophila</i>.

Sysoev VO, Fischer B, Frese CK, Gupta I, Krijgsveld J, Hentze MW, Castello A, Ephrussi A

Nature communications 2016

doi:10.1038/ncomms12128.

Identification of maturation-specific proteins by single-cell proteomics of human oocytes.

Virant-Klun I, Leicht S, Hughes C, Krijgsveld J

Molecular & cellular proteomics : MCP 2016

doi:10.1074/mcp.M115.056887.

RhVI1 is a membrane-anchored vacuolar invertase highly expressed in Rosa hybrida L. petals.

Farci D, Collu G, Kirkpatrick J, Esposito F, Piano D

Journal of experimental botany 2016

doi:10.1093/jxb/erw148.

Crystal structure of the CTP1L endolysin reveals how its activity is regulated by a secondary translation product.

Dunne M, Leicht S, Krichel B, Mertens HD, Thompson A, Krijgsveld J, Svergun DI, Gómez-Torres N, Garde S, Uetrecht C, Narbad A, Mayer MJ, Meijers R

The Journal of biological chemistry 2015

doi:10.1074/jbc.M115.671172.

Proteomic analysis reveals branch-specific regulation of the unfolded protein response by nonsense-mediated mRNA decay.

Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE

Molecular & cellular proteomics : MCP 2016

doi:10.1074/mcp.M115.054056.

Isolation of Plant Photosystem II Complexes by Fractional Solubilization.

Haniewicz P, Floris D, Farci D, Kirkpatrick J, Loi MC, Büchel C, Bochtler M, Piano D

Frontiers in plant science 2015

doi:10.3389/fpls.2015.01100.

The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs.

Beckmann BM, Horos R, Fischer B, Castello A, Eichelbaum K, Alleaume AM, Schwarzl T, Curk T, Foehr S, Huber W, Krijgsveld J, Hentze MW

Nature communications 2015

doi:10.1038/ncomms10127.

Ataxin-10 is part of a cachexokine cocktail triggering cardiac metabolic dysfunction in cancer cachexia.

Schäfer M, Oeing CU, Rohm M, Baysal-Temel E, Lehmann LH, Bauer R, Volz HC, Boutros M, Sohn D, Sticht C, Gretz N, Eichelbaum K, Werner T, Hirt MN, Eschenhagen T, Müller-Decker K, Strobel O, Hackert T, Krijgsveld J, Katus HA, Berriel Diaz M, Backs J, Herzig S

Molecular Metabolism 2016

doi:10.1016/j.molmet.2015.11.004.

Transcription Factor 7 Limits Regulatory T Cell Generation in the Thymus.

Barra MM, Richards DM, Hansson J, Hofer AC, Delacher M, Hettinger J, Krijgsveld J, Feuerer M

Journal of immunology (Baltimore, Md. : 1950) 2015

doi:10.4049/jimmunol.1500821.

Inflammation-induced emergency megakaryopoiesis driven by hematopoietic stem cell-like megakaryocyte progenitors.

Haas S, Hansson J, Klimmeck D, Loeffler D, Velten L, Uckelmann H, Wurzer S, Prendergast ÁM, Schnell A, Hexel K, Santarella-Mellwig R, Blaszkiewicz S, Kuck A, Geiger H, Milsom MD, Steinmetz LM, Schroeder T, Trumpp A, Krijgsveld J, Essers MA

Cell stem cell 2015

doi:10.1016/j.stem.2015.07.007.

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell ST, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P

Nucleic acids research 2014

doi:10.1093/nar/gku1147.

5-azacytidine inhibits nonsense-mediated decay in a MYC-dependent fashion.

Bhuvanagiri M, Lewis J, Putzker K, Becker JP, Leicht S, Krijgsveld J, Batra R, Turnwald B, Jovanovic B, Hauer C, Sieber J, Hentze MW, Kulozik AE

EMBO molecular medicine 2014

doi:10.15252/emmm.201404461.

Quantitative proteomics reveals the dynamics of protein changes during Drosophila oocyte maturation and the oocyte-to-embryo transition.

Kronja I, Whitfield ZJ, Yuan B, Dzeyk K, Kirkpatrick J, Krijgsveld J, Orr-Weaver TL

Proceedings of the National Academy of Sciences of the United States of America 2014

doi:10.1073/pnas.1418657111.

Unnatural Amino Acid Mutagenesis Reveals Dimerization As a Negative Regulatory Mechanism of VHR's Phosphatase Activity

Pavic K, Rios P, Dzeyk K, Koehler C, Lemke EA, Köhn M

ACS chemical biology 2014

doi:10.1021/cb500240n.

New features of the cell wall of the radio-resistant bacterium Deinococcus radiodurans

Farci D, Bowler MW, Kirkpatrick J, McSweeney S, Tramontano E, Piano D

Biochimica et biophysica acta 2014

doi:10.1016/j.bbamem.2014.02.014.

Widespread Changes in the Posttranscriptional Landscape at the Drosophila Oocyte-to-Embryo Transition

Kronja I, Yuan B, Eichhorn SW, Dzeyk K, Krijgsveld J, Bartel DP, Orr-Weaver TL

Cell reports 2014

doi:10.1016/j.celrep.2014.05.002.

Src kinase modulates the apoptotic p53 pathway by altering HIPK2 localization

Polonio-Vallon T, Kirkpatrick J, Krijgsveld J, Hofmann TG

Cell cycle (Georgetown, Tex.) 2013

doi:10.4161/cc.26857.

Proteomes of animal oocytes: what can we learn for human oocytes in the in vitro fertilization programme?

Virant-Klun I, Krijgsveld J

BioMed Research International 2014

doi:10.1155/2014/856907.

Comprehensive histone phosphorylation analysis and identification of Pf14-3-3 protein as a histone H3 phosphorylation reader in malaria parasites

Dastidar EG, Dzeyk K, Krijgsveld J, Malmquist NA, Doerig C, Scherf A, Lopez-Rubio JJ

PloS one 2013

doi:10.1371/journal.pone.0053179.

Anticancer compound ABT-263 accelerates apoptosis in virus-infected cells and imbalances cytokine production and lowers survival rates of infected mice

Kakkola L, Denisova OV, Tynell J, Viiliäinen J, Ysenbaert T, Matos RC, Nagaraj A, Ohman T, Kuivanen S, Paavilainen H, Feng L, Yadav B, Julkunen I, Vapalahti O, Hukkanen V, Stenman J, Aittokallio T, Verschuren EW, Ojala PM, Nyman T, Saelens X, Dzeyk K, Kainov DE

Cell death & disease 2013

doi:10.1038/cddis.2013.267.

Developments in quantitative mass spectrometry for the analysis of proteome dynamics

Hughes C, Krijgsveld J

Trends in biotechnology 2012

doi:10.1016/j.tibtech.2012.09.007.

Immune response to seasonal influenza A virus infection: a proteomic approach

Teran LM, Rüggeberg S, Santiago J, Fuentes-Arenas F, Hernández JL, Montes-Vizuet AR, Xinping L, Franz T

Archives of medical research 2012

doi:10.1016/j.arcmed.2012.08.008.

Arginine deficiency leads to impaired cofilin dephosphorylation in activated human T lymphocytes

Feldmeyer N, Wabnitz G, Leicht S, Luckner-Minden C, Schiller M, Franz T, Conradi R, Kropf P, Müller I, Ho AD, Samstag Y, Munder M

International immunology 2012

doi:10.1093/intimm/dxs004.

MSQuant: a platform for stable isotope-based quantitative proteomics

Gouw JW, Krijgsveld J

Methods in molecular biology (Clifton, N.J.) 2012

doi:10.1007/978-1-61779-885-6_31.

The ecoresponsive genome of Daphnia pulex

Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL

Science (New York, N.Y.) 2011

doi:10.1126/science.1197761.

Metabolic labeling of model organisms using heavy nitrogen (15N)

Gouw JW, Tops BB, Krijgsveld J

Methods in molecular biology (Clifton, N.J.) 2011

doi:10.1007/978-1-61779-148-2_2.

Madin-Darby canine kidney cells are increased in aerobic glycolysis when cultured on flat and stiff collagen-coated surfaces rather than in physiological 3-D cultures

Pampaloni F, Stelzer EH, Leicht S, Marcello M

Proteomics 2010

doi:10.1002/pmic.201000236.

Microtubule motility on reconstituted meiotic chromatin

Bieling P, Kronja I, Surrey T

Current biology : CB 2010

doi:10.1016/j.cub.2010.02.067.

Molecular variability of FLT3/ITD mutants and their impact on the differentiation program of 32D cells: implications for the biological properties of AML blasts

Pekova S, Ivanek R, Dvorak M, Rueggeberg S, Leicht S, Li X, Franz T, Kozak T, Vrba J, Koza V, Karas M, Schwarz J, Cetkovsky P, Prucha M

Leukemia research 2009

doi:10.1016/j.leukres.2009.01.004.

XMAP215-EB1 interaction is required for proper spindle assembly and chromosome segregation in Xenopus egg extract

Kronja I, Kruljac-Letunic A, Caudron-Herger M, Bieling P, Karsenti E

Molecular biology of the cell 2009

doi:10.1091/mbc.e08-10-1051.

Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile

Reuter M, Chuma S, Tanaka T, Franz T, Stark A, Pillai RS

Nature structural & molecular biology 2009

doi:10.1038/nsmb.1615.

CaM kinase II initiates meiotic spindle depolymerization independently of APC/C activation

Reber S, Over S, Kronja I, Gruss OJ

The Journal of cell biology 2008

doi:10.1083/jcb.200807006.

Muscle RING-finger protein-1 (MuRF1) as a connector of muscle energy metabolism and protein synthesis

Koyama S, Hata S, Witt CC, Ono Y, Lerche S, Ojima K, Chiba T, Doi N, Kitamura F, Tanaka K, Abe K, Witt SH, Rybin V, Gasch A, Franz T, Labeit S, Sorimachi H

Journal of molecular biology 2008

doi:10.1016/j.jmb.2007.11.049.

Discrete states of a protein interaction network govern interphase and mitotic microtubule dynamics

Niethammer P, Kronja I, Kandels-Lewis S, Rybina S, Bastiaens P, Karsenti E

PLoS biology 2007

doi:10.1371/journal.pbio.0050029.

Silicone/graphite coating for on-target desalting and improved peptide mapping performance of matrix-assisted laser desorption/ionization-mass spectrometry targets in proteomic experiments

Li X, Wilm M, Franz T

Proteomics 2005

doi:10.1002/pmic.200401023.

Threshold values for detergents in protein and peptide samples for mass spectrometry

Funk J, Li X, Franz T

Rapid communications in mass spectrometry : RCM 2005

doi:10.1002/rcm.2142.

Characterization of an Escherichia coli elaC deletion mutant

Schilling O, Rüggeberg S, Vogel A, Rittner N, Weichert S, Schmidt S, Doig S, Franz T, Benes V, Andrews SC, Baum M, Meyer-Klaucke W

Biochemical and biophysical research communications 2004

doi:10.1016/j.bbrc.2004.05.227.

Structural basis of dynamic glycine receptor clustering by gephyrin

Sola M, Bavro VN, Timmins J, Franz T, Ricard-Blum S, Schoehn G, Ruigrok RW, Paarmann I, Saiyed T, O'Sullivan GA, Schmitt B, Betz H, Weissenhorn W

The EMBO journal 2004

doi:10.1038/sj.emboj.7600256.

Isolation and characterisation of the rabies virus N degrees-P complex produced in insect cells

Mavrakis M, Iseni F, Mazza C, Schoehn G, Ebel C, Gentzel M, Franz T, Ruigrok RW

Virology 2003

doi:10.1006/viro.2002.1748.


Drug target identification in tissues by thermal proteome profiling.

Mateus A, Kurzawa N, Perrin J, Bergamini G, Savitski MM

Annual review of pharmacology and toxicology 2021

doi:10.1146/annurev-pharmtox-052120-013205.

Bioaccumulation of therapeutic drugs by human gut bacteria.

Klünemann M, Andrejev S, Blasche S, Mateus A, Phapale P, Devendran S, Vappiani J, Simon B, Scott TA, Kafkia E, Konstantinidis D, Zirngibl K, Mastrorilli E, Banzhaf M, Mackmull MT, Hövelmann F, Nesme L, Brochado AR, Maier L, Bock T, Periwal V, Kumar M, Kim Y, Tramontano M, Schultz C, Beck M, Hennig J, Zimmermann M, Sévin DC, Cabreiro F, Savitski MM, Bork P, Typas A, Patil KR

Nature 2021

doi:10.1038/s41586-021-03891-8.

Transcriptional and post-transcriptional polar effects in bacterial gene deletion libraries.

Mateus A, Shah M, Hevler J, Kurzawa N, Bobonis J, Typas A, Savitski MM

mSystems 2021

doi:10.1128/mSystems.00813-21.

Deamidation drives molecular aging of the SARS-CoV-2 spike protein receptor-binding motif.

Lorenzo R, Defelipe LA, Aliperti L, Niebling S, Custódio TF, Löw C, Schwarz JJ, Remans K, Craig PO, Otero LH, Klinke S, García-Alai M, Sánchez IE, Alonso LG

The Journal of biological chemistry 2021

doi:10.1016/j.jbc.2021.101175.

The rise of proteome-wide biophysics.

Mateus A, Savitski MM, Piazza I

Molecular systems biology 2021

doi:10.15252/msb.202110442.

Structure and dynamics of the quaternary hunchback mRNA translation repression complex.

Macošek J, Simon B, Linse JB, Jagtap PKA, Winter SL, Foot J, Lapouge K, Perez K, Rettel M, Ivanović MT, Masiewicz P, Murciano B, Savitski MM, Loedige I, Hub JS, Gabel F, Hennig J

Nucleic acids research 2021

doi:10.1093/nar/gkab635.

P38α-MAPK phosphorylates Snapin and reduces Snapin-mediated BACE1 transportation in APP-transgenic mice.

Schnöder L, Tomic I, Schwindt L, Helm D, Rettel M, Schulz-Schaeffer W, Krause E, Rettig J, Fassbender K, Liu Y

FASEB journal : official publication of the Federation of American Societies for Experimental Biology 2021

doi:10.1096/fj.202100017R.

SETD7-mediated monomethylation is enriched on soluble Tau in Alzheimer's disease.

Bichmann M, Prat Oriol N, Ercan-Herbst E, Schöndorf DC, Gomez Ramos B, Schwärzler V, Neu M, Schlüter A, Wang X, Jin L, Hu C, Tian Y, Ried JS, Haberkant P, Gasparini L, Ehrnhoefer DE

Molecular neurodegeneration 2021

doi:10.1186/s13024-021-00468-x.

Structure of the mycobacterial ESX-5 type VII secretion system pore complex.

Beckham KSH, Ritter C, Chojnowski G, Ziemianowicz DS, Mullapudi E, Rettel M, Savitski MM, Mortensen SA, Kosinski J, Wilmanns M

Science advances 2021

doi:10.1126/sciadv.abg9923.

Increased levels of mitochondrial import factor Mia40 prevent the aggregation of polyQ proteins in the cytosol.

Schlagowski AM, Knöringer K, Morlot S, Sánchez Vicente A, Flohr T, Krämer L, Boos F, Khalid N, Ahmed S, Schramm J, Murschall LM, Haberkant P, Stein F, Riemer J, Westermann B, Braun RJ, Winklhofer KF, Charvin G, Herrmann JM

The EMBO journal 2021

doi:10.15252/embj.2021107913.

Impact of phosphorylation on thermal stability of proteins.

Potel CM, Kurzawa N, Becher I, Typas A, Mateus A, Savitski MM

Nature methods 2021

doi:10.1038/s41592-021-01177-5.

Quality standards in proteomics research facilities: common standards and quality procedures are essential for proteomics facilities and their users.

Chiva C, Mendes Maia T, Panse C, Stejskal K, Douché T, Matondo M, Loew D, Helm D, Rettel M, Mechtler K, Impens F, Nanni P, Shevchenko A, Sabidó E

EMBO reports 2021

doi:10.15252/embr.202152626.

Identification of dynamic RNA-binding proteins uncovers a Cpeb4-controlled regulatory cascade during pathological cell growth of cardiomyocytes.

Riechert E, Kmietczyk V, Stein F, Schwarzl T, Sekaran T, Jürgensen L, Kamuf-Schenk V, Varma E, Hofmann C, Rettel M, Gür K, Ölschläger J, Kühl F, Martin J, Ramirez-Pedraza M, Fernandez M, Doroudgar S, Méndez R, Katus HA, Hentze MW, Völkers M

Cell reports 2021

doi:10.1016/j.celrep.2021.109100.

Global mapping of Salmonella enterica-host protein-protein interactions during infection.

Walch P, Selkrig J, Knodler LA, Rettel M, Stein F, Fernandez K, Viéitez C, Potel CM, Scholzen K, Geyer M, Rottner K, Steele-Mortimer O, Savitski MM, Holden DW, Typas A

2021

doi:10.1016/j.chom.2021.06.004.

NMD inhibition by 5-azacytidine augments presentation of immunogenic frameshift-derived neoepitopes.

Becker JP, Helm D, Rettel M, Stein F, Hernandez-Sanchez A, Urban K, Gebert J, Kloor M, Neu-Yilik G, von Knebel Doeberitz M, Hentze MW, Kulozik AE

iScience 2021

doi:10.1016/j.isci.2021.102389.

SARS-CoV-2 infection remodels the host protein thermal stability landscape.

Selkrig J, Stanifer M, Mateus A, Mitosch K, Barrio-Hernandez I, Rettel M, Kim H, Voogdt CGP, Walch P, Kee C, Kurzawa N, Stein F, Potel C, Jarzab A, Kuster B, Bartenschlager R, Boulant S, Beltrao P, Typas A, Savitski MM

Molecular systems biology 2021

doi:10.15252/msb.202010188.

Cell surface thermal proteome profiling tracks perturbations and drug targets on the plasma membrane.

Kalxdorf M, Günthner I, Becher I, Kurzawa N, Knecht S, Savitski MM, Eberl HC, Bantscheff M

Nature methods 2021

doi:10.1038/s41592-020-01022-1.

Extensive OMICS resource for Sf21 and Tni cell lines.

Galik B, Landry JM, Kirkpatrick J, Fritz M, Baying B, Blake J, Haase B, Collier PG, Hercog R, Pavlinic D, Stolt-Bergner P, Besir H, Remans K, Gyenesei A, Benes V

2021

doi:10.1101/2021.04.06.438574.

The central role of salivary metalloproteases in host acquired resistance to tick feeding.

Perner J, Helm D, Haberkant P, Hatalova T, Kropackova S, Ribeiro JM, Kopacek P

Frontiers in cellular and infection microbiology 2020

doi:10.3389/fcimb.2020.563349.

An integrated multiomic and quantitative label-free microscopy-based approach to study pro-fibrotic signalling in ex vivo human precision-cut lung slices.

Khan MM, Poeckel D, Halavatyi A, Zukowska-Kasprzyk J, Stein F, Vappiani J, Sevin DC, Tischer C, Zinn N, Eley JD, Gudmann NS, Muley T, Winter H, Fisher AJ, Nanthakumar CB, Bergamini G, Pepperkok R

The European respiratory journal 2020

doi:10.1183/13993003.00221-2020.

Stroma transcriptomic and proteomic profile of prostate cancer metastasis xenograft models reveals prognostic value of stroma signatures.

Karkampouna S, De Filippo MR, Ng CKY, Klima I, Zoni E, Spahn M, Stein F, Haberkant P, Thalmann GN, Kruithof de Julio M

Cancers 2020

doi:10.3390/cancers12123786.

A computational method for detection of ligand-binding proteins from dose range thermal proteome profiles.

Kurzawa N, Becher I, Sridharan S, Franken H, Mateus A, Anders S, Bantscheff M, Huber W, Savitski MM

Nature communications 2020

doi:10.1038/s41467-020-19529-8.

The functional proteome landscape of Escherichia coli.

Mateus A, Hevler J, Bobonis J, Kurzawa N, Shah M, Mitosch K, Goemans CV, Helm D, Stein F, Typas A, Savitski MM

Nature 2020

doi:10.1038/s41586-020-3002-5.

Aggregation and disaggregation features of the human proteome.

Määttä TA, Rettel M, Sridharan S, Helm D, Kurzawa N, Stein F, Savitski MM

Molecular systems biology 2020

doi:10.15252/msb.20209500.

Rtpca: an R package for differential thermal proximity coaggregation analysis.

Kurzawa N, Mateus A, Savitski MM

Bioinformatics (Oxford, England) 2020

doi:10.1093/bioinformatics/btaa682.

Pseudo-RNA-binding domains mediate RNA structure specificity in Upstream of N-Ras.

Hollmann NM, Jagtap PKA, Masiewicz P, Guitart T, Simon B, Provaznik J, Stein F, Haberkant P, Sweetapple LJ, Villacorta L, Moojiman D, Benes V, Savitski MM, Gebauer F, Hennig J

2020

doi:10.1016/j.celrep.2020.107930.

Dissecting the sequence determinants for dephosphorylation by the catalytic subunits of phosphatases PP1 and PP2A.

Hoermann B, Kokot T, Helm D, Heinzlmeir S, Chojnacki JE, Schubert T, Ludwig C, Berteotti A, Kurzawa N, Kuster B, Savitski MM, Köhn M

Nature communications 2020

doi:10.1038/s41467-020-17334-x.

Bacterial retrons encode tripartite toxin/antitoxin systems.

Bobonis J, Mateus A, Pfalz B, Garcia-Santamarina S, Galardini M, Kobayashi C, Stein F, Savitski MM, Elfenbein JR, Andrews-Poymenis H, Typas A

2020

doi:10.1101/2020.06.22.160168.

Spatiotemporal proteomics uncovers cathepsin-dependent macrophage cell death during Salmonella infection.

Selkrig J, Li N, Hausmann A, Mangan MSJ, Zietek M, Mateus A, Bobonis J, Sueki A, Imamura H, El Debs B, Sigismondo G, Florea BI, Overkleeft HS, Kopitar-Jerala N, Turk B, Beltrao P, Savitski MM, Latz E, Hardt WD, Krijgsveld J, Typas A

Nature microbiology 2020

doi:10.1038/s41564-020-0736-7.

ACLY is the novel signaling target of PIP 2/PIP 3 and Lyn in acute myeloid leukemia.

Basappa J, Citir M, Zhang Q, Wang HY, Liu X, Melnikov O, Yahya H, Stein F, Muller R, Traynor-Kaplan A, Schultz C, Wasik MA, Ptasznik A

Heliyon 2020

doi:10.1016/j.heliyon.2020.e03910.

Phage proteins block and trigger retron toxin/antitoxin systems.

Bobonis J, Mitosch K, Mateus A, Kritikos G, Elfenbein JR, Savitski MM, Andrews-Polymenis H, Typas A

2020

doi:10.1101/2020.06.22.160242.

A dual-mechanism antibiotic kills gram-negative bacteria and avoids drug resistance.

Martin JK, Sheehan JP, Bratton BP, Moore GM, Mateus A, Li SH, Kim H, Rabinowitz JD, Typas A, Savitski MM, Wilson MZ, Gitai Z

Cell 2020

doi:10.1016/j.cell.2020.05.005.

Plasticity of nuclear and cytoplasmic stress responses of RNA-binding proteins.

Backlund M, Stein F, Rettel M, Schwarzl T, Perez-Perri JI, Brosig A, Zhou Y, Neu-Yilik G, Hentze MW, Kulozik AE

Nucleic acids research 2020

doi:10.1093/nar/gkaa256.

Meltome atlas-thermal proteome stability across the tree of life.

Jarzab A, Kurzawa N, Hopf T, Moerch M, Zecha J, Leijten N, Bian Y, Musiol E, Maschberger M, Stoehr G, Becher I, Daly C, Samaras P, Mergner J, Spanier B, Werner T, Angelov A, Wilhelm M, Bantscheff M, Lemeer S, Klingenspor M, Hahne H, Liebl W, Kuster B, Savitski MM

Nature methods 2020

doi:10.1038/s41592-020-0801-4.

Thermal proteome profiling for interrogating protein interactions.

Mateus A, Kurzawa N, Becher I, Sridharan S, Helm D, Stein F, Typas A, Savitski MM

Molecular systems biology 2020

doi:10.15252/msb.20199232.

Systematic localization of Escherichia coli membrane proteins.

Sueki A, Stein F, Savitski MM, Selkrig J, Typas A

mSystems 2020

doi:10.1128/mSystems.00808-19.

Human mast cell proteome reveals unique lineage, putative functions, and structural basis for cell ablation.

Plum T, Wang X, Rettel M, Krijgsveld J, Feyerabend TB, Rodewald HR

Immunity 2020

doi:10.1016/j.immuni.2020.01.012.

A genetic analysis reveals novel histone residues required for transcriptional reprogramming upon stress.

Viéitez C, Martínez-Cebrián G, Solé C, Böttcher R, Potel CM, Savitski MM, Onnebo S, Fabregat M, Shilatifard A, Posas F, de Nadal E

Nucleic acids research 2020

doi:10.1093/nar/gkaa081.

Outer membrane lipoprotein NlpI scaffolds peptidoglycan hydrolases within multi-enzyme complexes in Escherichia coli.

Banzhaf M, Yau HC, Verheul J, Lodge A, Kritikos G, Mateus A, Cordier B, Hov AK, Stein F, Wartel M, Pazos M, Solovyova AS, Breukink E, van Teeffelen S, Savitski MM, den Blaauwen T, Typas A, Vollmer W

The EMBO journal 2020

doi:10.15252/embj.2019102246.

A misprocessed form of Apolipoprotein A-I is specifically associated with recurrent focal segmental glomerulosclerosis.

Jacobs-Cachá C, Puig-Gay N, Helm D, Rettel M, Sellarès J, Meseguer A, Savitski MM, Moreso FJ, Soler MJ, Seron D, Lopez-Hellin J

Scientific reports 2020

doi:10.1038/s41598-020-58197-y.

Identifying drug targets in tissues and whole blood with thermal-shift profiling.

Perrin J, Werner T, Kurzawa N, Rutkowska A, Childs DD, Kalxdorf M, Poeckel D, Stonehouse E, Strohmer K, Heller B, Thomson DW, Krause J, Becher I, Eberl HC, Vappiani J, Rau CE, Sevin DC, Huber W, Franken H, Savitski MM, Faelth-Savitski M, Bergamini G, Bantscheff M

Nature biotechnology 2020

doi:10.1038/s41587-019-0388-4.

Impact of phosphorylation on thermal stability of proteins.

Potel CM, Kurzawa N, Becher I, Typas A, Mateus A, Savitski MM

2020

doi:10.1101/2020.01.14.903849.

Towards a systematic map of the functional role of protein phosphorylation.

Viéitez​ C​, Busby​ BP, Ochoa​ D​, Mateus​ A​, Galardini​ M​, Jawed​ A​, Memon​ D​, Potel​ CM​, Vonesch SC​, Tu​ CS, Shahraz​ M​, Stein​ F​, Steinmetz​ LM, Savitski​ MM, Typas A, Beltrao​ P

2019

doi:10.1101/872770.

The functional landscape of the human phosphoproteome.

Ochoa D, Jarnuczak AF, Viéitez C, Gehre M, Soucheray M, Mateus A, Kleefeldt AA, Hill A, Garcia-Alonso L, Stein F, Krogan NJ, Savitski MM, Swaney DL, Vizcaíno JA, Noh KM, Beltrao P

Nature biotechnology 2019

doi:10.1038/s41587-019-0344-3.

A new antibiotic selectively kills Gram-negative pathogens.

Imai Y, Meyer KJ, Iinishi A, Favre-Godal Q, Green R, Manuse S, Caboni M, Mori M, Niles S, Ghiglieri M, Honrao C, Ma X, Guo J, Makriyannis A, Linares-Otoya L, Wuisan ZG, Böhringer N, Wu R, Kaur H, Typas A, Mateus A, Espinoza JL, Savitski MM, Nelson KE, O'Rourke A, Noinaj N, Hiller S, D'Onofrio A, Schäberle TF, Lewis K

Nature 2019

doi:10.1038/s41586-019-1791-1.

Non-parametric analysis of thermal proteome profiles reveals novel drug-binding proteins.

Childs D, Bach K, Franken H, Anders S, Kurzawa N, Bantscheff M, Savitski M, Huber W

Molecular & cellular proteomics : MCP 2019

doi:10.1074/mcp.TIR119.001481.

Target discovery using thermal proteome profiling.

Sridharan S, Günthner I, Becher I, Savitski M, Bantscheff M

2019

doi:10.1002/9781118970195.ch11.

The Hsp90 isoforms from S. cerevisiae differ in structure, function and client range.

Girstmair H, Tippel F, Lopez A, Tych K, Stein F, Haberkant P, Schmid PWN, Helm D, Rief M, Sattler M, Buchner J

Nature communications 2019

doi:10.1038/s41467-019-11518-w.

Monitoring cell-type-specific gene expression using ribosome profiling in vivo during cardiac hemodynamic stress.

Doroudgar S, Hofmann C, Boileau E, Malone B, Riechert E, Gorska AA, Jakobi T, Sandmann C, Jürgensen L, Kmietczyk V, Malovrh E, Burghaus J, Rettel M, Stein F, Younesi F, Mauz V, Friedrich UA, Kramer G, Backs J, Dieterich C, Katus HA, Völkers M

Circulation research 2019

doi:10.1161/CIRCRESAHA.119.314817.

Asparagine endopeptidase cleaves tau at N167 after uptake into microglia.

Behrendt A, Bichmann M, Ercan-Herbst E, Haberkant P, Schöndorf DC, Wolf M, Fahim SA, Murolo E, Ehrnhoefer DE

Neurobiology of disease 2019

doi:10.1016/j.nbd.2019.104518.

Publisher Correction: Mitochondrial protein-induced stress triggers a global adaptive transcriptional programme.

Boos F, Krämer L, Groh C, Jung F, Haberkant P, Stein F, Wollweber F, Gackstatter A, Zöller E, van der Laan M, Savitski MM, Benes V, Herrmann JM

Nature cell biology 2019

doi:10.1038/s41556-019-0326-1.

Secretome profiling of heterotypic spheroids suggests a role of fibroblasts in HIF-1 pathway modulation and colorectal cancer photodynamic resistance.

Lamberti MJ, Rettel M, Krijgsveld J, Rivarola VA, Rumie Vittar NB

Cellular oncology (Dordrecht) 2019

doi:10.1007/s13402-018-00418-8.

Mitochondrial protein-induced stress triggers a global adaptive transcriptional programme.

Boos F, Krämer L, Groh C, Jung F, Haberkant P, Stein F, Wollweber F, Gackstatter A, Zöller E, van der Laan M, Savitski MM, Benes V, Herrmann JM

Nature cell biology 2019

doi:10.1038/s41556-019-0294-5.

Cytosolic glucosylceramide regulates endolysosomal function in Niemann-Pick type C disease.

Wheeler S, Haberkant P, Bhardwaj M, Tongue P, Ferraz MJ, Halter D, Sprong H, Schmid R, Aerts JMFG, Sullo N, Sillence DJ

Neurobiology of disease 2019

doi:10.1016/j.nbd.2019.03.005.

Proteome-wide solubility and thermal stability profiling reveals distinct regulatory roles for ATP.

Sridharan S, Kurzawa N, Werner T, Günthner I, Helm D, Huber W, Bantscheff M, Savitski MM

Nature communications 2019

doi:10.1038/s41467-019-09107-y.

Effect of Sec61 interaction with Mpd1 on endoplasmic reticulum-associated degradation.

Pereira F, Rettel M, Stein F, Savitski MM, Collinson I, Römisch K

PloS one 2019

doi:10.1371/journal.pone.0211180.

Discovery of RNA-binding proteins and characterization of their dynamic responses by enhanced RNA interactome capture.

Perez-Perri JI, Rogell B, Schwarzl T, Stein F, Zhou Y, Rettel M, Brosig A, Hentze MW

Nature communications 2018

doi:10.1038/s41467-018-06557-8.

A Bifunctional Noncanonical Amino Acid: Synthesis, Expression, and Residue-Specific Proteome-wide Incorporation.

Hoffmann JE, Dziuba D, Stein F, Schultz C

Biochemistry 2018

doi:10.1021/acs.biochem.8b00397.

Thermal proteome profiling in bacteria: probing protein state in vivo.

Mateus A, Bobonis J, Kurzawa N, Stein F, Helm D, Hevler J, Typas A, Savitski MM

Molecular systems biology 2018

doi:10.15252/msb.20188242.

Species-specific activity of antibacterial drug combinations.

Brochado AR, Telzerow A, Bobonis J, Banzhaf M, Mateus A, Selkrig J, Huth E, Bassler S, Zamarreño Beas J, Zietek M, Ng N, Foerster S, Ezraty B, Py B, Barras F, Bork P, Savitski MM, Göttig S, Typas A

Nature 2018

doi:10.1038/s41586-018-0278-9.

TRRAP is essential for regulating the accumulation of mutant and wild-type p53 in lymphoma.

Jethwa A, Słabicki M, Hüllein J, Jentzsch M, Dalal V, Rabe S, Wagner L, Walther T, Klapper W, Bohnenberger H, Rettel M, Lu J, Smits AH, Stein F, Savitski MM, Huber W, Aylon Y, Oren M, Zenz T

Blood 2018

doi:10.1182/blood-2017-09-806679.

Pervasive protein thermal stability variation during the cell cycle.

Becher I, Andrés-Pons A, Romanov N, Stein F, Schramm M, Baudin F, Helm D, Kurzawa N, Mateus A, Mackmull MT, Typas A, Müller CW, Bork P, Beck M, Savitski MM

Cell 2018

doi:10.1016/j.cell.2018.03.053.

Author Correction: Structural analysis of human ARS2 as a platform for co-transcriptional RNA sorting.

Schulze WM, Stein F, Rettel M, Nanao M, Cusack S

Nature communications 2018

doi:10.1038/s41467-018-04643-5.

Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.

Strucko T, Zirngibl K, Pereira F, Kafkia E, Mohamed ET, Rettel M, Stein F, Feist AM, Jouhten P, Patil KR, Forster J

Metabolic engineering 2018

doi:10.1016/j.ymben.2018.03.006.

Spatial tissue proteomics quantifies inter- and intra-tumor heterogeneity in hepatocellular carcinoma.

Buczak K, Ori A, Kirkpatrick JM, Holzer K, Dauch D, Roessler S, Endris V, Lasitschka F, Parca L, Schmidt A, Zender L, Schirmacher P, Krijgsveld J, Singer S, Beck M

Molecular & cellular proteomics : MCP 2018

doi:10.1074/mcp.RA117.000189.

Structural analysis of human ARS2 as a platform for co-transcriptional RNA sorting.

Schulze WM, Stein F, Rettel M, Nanao M, Cusack S

Nature communications 2018

doi:10.1038/s41467-018-04142-7.

Multiplexed Proteome Dynamics Profiling Reveals Mechanisms Controlling Protein Homeostasis.

Savitski MM, Zinn N, Faelth-Savitski M, Poeckel D, Gade S, Becher I, Muelbaier M, Wagner AJ, Strohmer K, Werner T, Melchert S, Petretich M, Rutkowska A, Vappiani J, Franken H, Steidel M, Sweetman GM, Gilan O, Lam EYN, Dawson MA, Prinjha RK, Grandi P, Bergamini G, Bantscheff M

Cell 2018

doi:10.1016/j.cell.2018.02.030.

A search for ceramide binding proteins using bifunctional lipid analogs yields CERT-related protein StarD7.

Bockelmann S, Mina JGM, Korneev S, Hassan DG, Mueller D, Hilderink A, Vlieg HC, Raijmakers R, Heck AJR, Haberkant P, Holthuis JCM

Journal of lipid research 2018

doi:10.1194/jlr.M082354.

Systematic analysis of protein turnover in primary cells.

Mathieson T, Franken H, Kosinski J, Kurzawa N, Zinn N, Sweetman G, Poeckel D, Ratnu VS, Schramm M, Becher I, Steidel M, Noh KM, Bergamini G, Beck M, Bantscheff M, Savitski MM

Nature communications 2018

doi:10.1038/s41467-018-03106-1.

Leaderless secreted peptide signaling molecule alters global gene expression and increases virulence of a human bacterial pathogen.

Do H, Makthal N, VanderWal AR, Rettel M, Savitski MM, Peschek N, Papenfort K, Olsen RJ, Musser JM, Kumaraswami M

Proceedings of the National Academy of Sciences of the United States of America 2017

doi:10.1073/pnas.1705972114.

Specific RNP capture with antisense LNA/DNA mixmers.

Rogell BM, Fischer B, Rettel M, Krijgsveld J, Castello A, Hentze MW

RNA (New York, N.Y.) 2017

doi:10.1261/rna.060798.117.

Wilhelm et al. reply.

Wilhelm M, Hahne H, Savitski M, Marx H, Lemeer S, Bantscheff M, Kuster B

Nature 2017

doi:10.1038/nature22294.

A Ratiometric Sensor for Imaging Insulin Secretion in Single β Cells.

Schifferer M, Yushchenko DA, Stein F, Bolbat A, Schultz C

Cell chemical biology 2017

doi:10.1016/j.chembiol.2017.03.001.

Identification of a feedback loop involving beta-glucosidase 2 and its product sphingosine sheds light on the molecular mechanisms in Gaucher disease.

Schonauer S, Körschen HG, Penno A, Rennhack A, Breiden B, Sandhoff K, Gutbrod K, Dörmann P, Raju DN, Haberkant P, Gerl MJ, Brügger B, Zigdon H, Vardi A, Futerman AH, Thiele C, Wachten D

The Journal of biological chemistry 2017

doi:10.1074/jbc.m116.762831.

Structure of the mycobacterial ESX-5 type VII secretion system membrane complex by single-particle analysis.

Beckham KS, Ciccarelli L, Bunduc CM, Mertens HD, Ummels R, Lugmayr W, Mayr J, Rettel M, Savitski MM, Svergun DI, Bitter W, Wilmanns M, Marlovits TC, Parret AH, Houben EN

Nature microbiology 2017

doi:10.1038/nmicrobiol.2017.47.

Spatiotemporal Analysis of a Glycolytic Activity Gradient Linked to Mouse Embryo Mesoderm Development

Bulusu V, Prior N, Snaebjornsson MT, Kuehne A, Sonnen KF, Kress J, Stein F, Schultz C, Sauer U, Aulehla A

Developmental cell 2017

doi:10.1016/j.devcel.2017.01.015.

Trifunctional lipid probes for comprehensive studies of single lipid species in living cells.

Höglinger D, Nadler A, Haberkant P, Kirkpatrick J, Schifferer M, Stein F, Hauke S, Porter FD, Schultz C

Proceedings of the National Academy of Sciences of the United States of America 2017

doi:10.1073/pnas.1611096114.

High-Content Imaging Platform for Profiling Intracellular Signaling Network Activity in Living Cells.

Kuchenov D, Laketa V, Stein F, Salopiata F, Klingmüller U, Schultz C

Cell chemical biology 2016

doi:10.1016/j.chembiol.2016.11.008.

In planta determination of the mRNA-binding proteome of Arabidopsis etiolated seedlings.

Reichel M, Liao Y, Rettel M, Ragan C, Evers M, Alleaume AM, Horos R, Hentze MW, Preiss T, Millar AA

The Plant cell 2016

doi:10.1105/tpc.16.00562.

A standardized production pipeline for high profile targets from Mycobacterium tuberculosis.

Milewski MC, Broger T, Kirkpatrick J, Filomena A, Komadina D, Schneiderhan-Marra N, Wilmanns M, Parret AH

Proteomics. Clinical applications 2016

doi:10.1002/prca.201600033.

Comprehensive Identification of RNA-Binding Domains in Human Cells.

Castello A, Fischer B, Frese CK, Horos R, Alleaume AM, Foehr S, Curk T, Krijgsveld J, Hentze MW

MOLECULAR CELL 2016

doi:10.1016/j.molcel.2016.06.029.

Identification of RNA-binding proteins in macrophages by interactome capture.

Liepelt A, Naarmann-de Vries IS, Simons N, Eichelbaum K, Foehr S, Archer SK, Castello A, Usadel B, Krijgsveld J, Preiss T, Marx G, Hentze MW, Ostareck DH, Ostareck-Lederer A

Molecular & cellular proteomics : MCP 2016

doi:10.1074/mcp.M115.056564.

An atomic model of HIV-1 capsid-SP1 reveals structures regulating assembly and maturation.

Schur FK, Obr M, Hagen WJ, Wan W, Jakobi AJ, Kirkpatrick JM, Sachse C, Kräusslich HG, Briggs JA

Science (New York, N.Y.) 2016

doi:10.1126/science.aaf9620.

The Cardiomyocyte RNA-Binding Proteome: Links to Intermediary Metabolism and Heart Disease

Liao Y, Castello A, Fischer B, Leicht S, Föehr S, Frese C, Ragan C, Kurscheid S, Pagler E, Yang H, Krijgsveld J, Hentze MW, Preiss T

Cell Reports 2016

doi:10.1016/j.celrep.2016.06.084.

Global changes of the RNA-bound proteome during the maternal-to-zygotic transition in <i>Drosophila</i>.

Sysoev VO, Fischer B, Frese CK, Gupta I, Krijgsveld J, Hentze MW, Castello A, Ephrussi A

Nature communications 2016

doi:10.1038/ncomms12128.

Identification of maturation-specific proteins by single-cell proteomics of human oocytes.

Virant-Klun I, Leicht S, Hughes C, Krijgsveld J

Molecular & cellular proteomics : MCP 2016

doi:10.1074/mcp.M115.056887.

RhVI1 is a membrane-anchored vacuolar invertase highly expressed in Rosa hybrida L. petals.

Farci D, Collu G, Kirkpatrick J, Esposito F, Piano D

Journal of experimental botany 2016

doi:10.1093/jxb/erw148.

Crystal structure of the CTP1L endolysin reveals how its activity is regulated by a secondary translation product.

Dunne M, Leicht S, Krichel B, Mertens HD, Thompson A, Krijgsveld J, Svergun DI, Gómez-Torres N, Garde S, Uetrecht C, Narbad A, Mayer MJ, Meijers R

The Journal of biological chemistry 2015

doi:10.1074/jbc.M115.671172.

Proteomic analysis reveals branch-specific regulation of the unfolded protein response by nonsense-mediated mRNA decay.

Sieber J, Hauer C, Bhuvanagiri M, Leicht S, Krijgsveld J, Neu-Yilik G, Hentze MW, Kulozik AE

Molecular & cellular proteomics : MCP 2016

doi:10.1074/mcp.M115.054056.

Isolation of Plant Photosystem II Complexes by Fractional Solubilization.

Haniewicz P, Floris D, Farci D, Kirkpatrick J, Loi MC, Büchel C, Bochtler M, Piano D

Frontiers in plant science 2015

doi:10.3389/fpls.2015.01100.

The RNA-binding proteomes from yeast to man harbour conserved enigmRBPs.

Beckmann BM, Horos R, Fischer B, Castello A, Eichelbaum K, Alleaume AM, Schwarzl T, Curk T, Foehr S, Huber W, Krijgsveld J, Hentze MW

Nature communications 2015

doi:10.1038/ncomms10127.

Ataxin-10 is part of a cachexokine cocktail triggering cardiac metabolic dysfunction in cancer cachexia.

Schäfer M, Oeing CU, Rohm M, Baysal-Temel E, Lehmann LH, Bauer R, Volz HC, Boutros M, Sohn D, Sticht C, Gretz N, Eichelbaum K, Werner T, Hirt MN, Eschenhagen T, Müller-Decker K, Strobel O, Hackert T, Krijgsveld J, Katus HA, Berriel Diaz M, Backs J, Herzig S

Molecular Metabolism 2016

doi:10.1016/j.molmet.2015.11.004.

Transcription Factor 7 Limits Regulatory T Cell Generation in the Thymus.

Barra MM, Richards DM, Hansson J, Hofer AC, Delacher M, Hettinger J, Krijgsveld J, Feuerer M

Journal of immunology (Baltimore, Md. : 1950) 2015

doi:10.4049/jimmunol.1500821.

Inflammation-induced emergency megakaryopoiesis driven by hematopoietic stem cell-like megakaryocyte progenitors.

Haas S, Hansson J, Klimmeck D, Loeffler D, Velten L, Uckelmann H, Wurzer S, Prendergast ÁM, Schnell A, Hexel K, Santarella-Mellwig R, Blaszkiewicz S, Kuck A, Geiger H, Milsom MD, Steinmetz LM, Schroeder T, Trumpp A, Krijgsveld J, Essers MA

Cell stem cell 2015

doi:10.1016/j.stem.2015.07.007.

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum.

Bock T, Chen WH, Ori A, Malik N, Silva-Martin N, Huerta-Cepas J, Powell ST, Kastritis PL, Smyshlyaev G, Vonkova I, Kirkpatrick J, Doerks T, Nesme L, Baßler J, Kos M, Hurt E, Carlomagno T, Gavin AC, Barabas O, Müller CW, van Noort V, Beck M, Bork P

Nucleic acids research 2014

doi:10.1093/nar/gku1147.

5-azacytidine inhibits nonsense-mediated decay in a MYC-dependent fashion.

Bhuvanagiri M, Lewis J, Putzker K, Becker JP, Leicht S, Krijgsveld J, Batra R, Turnwald B, Jovanovic B, Hauer C, Sieber J, Hentze MW, Kulozik AE

EMBO molecular medicine 2014

doi:10.15252/emmm.201404461.

Quantitative proteomics reveals the dynamics of protein changes during Drosophila oocyte maturation and the oocyte-to-embryo transition.

Kronja I, Whitfield ZJ, Yuan B, Dzeyk K, Kirkpatrick J, Krijgsveld J, Orr-Weaver TL

Proceedings of the National Academy of Sciences of the United States of America 2014

doi:10.1073/pnas.1418657111.

Unnatural Amino Acid Mutagenesis Reveals Dimerization As a Negative Regulatory Mechanism of VHR's Phosphatase Activity

Pavic K, Rios P, Dzeyk K, Koehler C, Lemke EA, Köhn M

ACS chemical biology 2014

doi:10.1021/cb500240n.

New features of the cell wall of the radio-resistant bacterium Deinococcus radiodurans

Farci D, Bowler MW, Kirkpatrick J, McSweeney S, Tramontano E, Piano D

Biochimica et biophysica acta 2014

doi:10.1016/j.bbamem.2014.02.014.

Widespread Changes in the Posttranscriptional Landscape at the Drosophila Oocyte-to-Embryo Transition

Kronja I, Yuan B, Eichhorn SW, Dzeyk K, Krijgsveld J, Bartel DP, Orr-Weaver TL

Cell reports 2014

doi:10.1016/j.celrep.2014.05.002.

Src kinase modulates the apoptotic p53 pathway by altering HIPK2 localization

Polonio-Vallon T, Kirkpatrick J, Krijgsveld J, Hofmann TG

Cell cycle (Georgetown, Tex.) 2013

doi:10.4161/cc.26857.

Proteomes of animal oocytes: what can we learn for human oocytes in the in vitro fertilization programme?

Virant-Klun I, Krijgsveld J

BioMed Research International 2014

doi:10.1155/2014/856907.

Comprehensive histone phosphorylation analysis and identification of Pf14-3-3 protein as a histone H3 phosphorylation reader in malaria parasites

Dastidar EG, Dzeyk K, Krijgsveld J, Malmquist NA, Doerig C, Scherf A, Lopez-Rubio JJ

PloS one 2013

doi:10.1371/journal.pone.0053179.

Anticancer compound ABT-263 accelerates apoptosis in virus-infected cells and imbalances cytokine production and lowers survival rates of infected mice

Kakkola L, Denisova OV, Tynell J, Viiliäinen J, Ysenbaert T, Matos RC, Nagaraj A, Ohman T, Kuivanen S, Paavilainen H, Feng L, Yadav B, Julkunen I, Vapalahti O, Hukkanen V, Stenman J, Aittokallio T, Verschuren EW, Ojala PM, Nyman T, Saelens X, Dzeyk K, Kainov DE

Cell death & disease 2013

doi:10.1038/cddis.2013.267.

Developments in quantitative mass spectrometry for the analysis of proteome dynamics

Hughes C, Krijgsveld J

Trends in biotechnology 2012

doi:10.1016/j.tibtech.2012.09.007.

Immune response to seasonal influenza A virus infection: a proteomic approach

Teran LM, Rüggeberg S, Santiago J, Fuentes-Arenas F, Hernández JL, Montes-Vizuet AR, Xinping L, Franz T

Archives of medical research 2012

doi:10.1016/j.arcmed.2012.08.008.

Arginine deficiency leads to impaired cofilin dephosphorylation in activated human T lymphocytes

Feldmeyer N, Wabnitz G, Leicht S, Luckner-Minden C, Schiller M, Franz T, Conradi R, Kropf P, Müller I, Ho AD, Samstag Y, Munder M

International immunology 2012

doi:10.1093/intimm/dxs004.

MSQuant: a platform for stable isotope-based quantitative proteomics

Gouw JW, Krijgsveld J

Methods in molecular biology (Clifton, N.J.) 2012

doi:10.1007/978-1-61779-885-6_31.

The ecoresponsive genome of Daphnia pulex

Colbourne JK, Pfrender ME, Gilbert D, Thomas WK, Tucker A, Oakley TH, Tokishita S, Aerts A, Arnold GJ, Basu MK, Bauer DJ, Cáceres CE, Carmel L, Casola C, Choi JH, Detter JC, Dong Q, Dusheyko S, Eads BD, Fröhlich T, Geiler-Samerotte KA, Gerlach D, Hatcher P, Jogdeo S, Krijgsveld J, Kriventseva EV, Kültz D, Laforsch C, Lindquist E, Lopez J, Manak JR, Muller J, Pangilinan J, Patwardhan RP, Pitluck S, Pritham EJ, Rechtsteiner A, Rho M, Rogozin IB, Sakarya O, Salamov A, Schaack S, Shapiro H, Shiga Y, Skalitzky C, Smith Z, Souvorov A, Sung W, Tang Z, Tsuchiya D, Tu H, Vos H, Wang M, Wolf YI, Yamagata H, Yamada T, Ye Y, Shaw JR, Andrews J, Crease TJ, Tang H, Lucas SM, Robertson HM, Bork P, Koonin EV, Zdobnov EM, Grigoriev IV, Lynch M, Boore JL

Science (New York, N.Y.) 2011

doi:10.1126/science.1197761.

Metabolic labeling of model organisms using heavy nitrogen (15N)

Gouw JW, Tops BB, Krijgsveld J

Methods in molecular biology (Clifton, N.J.) 2011

doi:10.1007/978-1-61779-148-2_2.

Madin-Darby canine kidney cells are increased in aerobic glycolysis when cultured on flat and stiff collagen-coated surfaces rather than in physiological 3-D cultures

Pampaloni F, Stelzer EH, Leicht S, Marcello M

Proteomics 2010

doi:10.1002/pmic.201000236.

Microtubule motility on reconstituted meiotic chromatin

Bieling P, Kronja I, Surrey T

Current biology : CB 2010

doi:10.1016/j.cub.2010.02.067.

Molecular variability of FLT3/ITD mutants and their impact on the differentiation program of 32D cells: implications for the biological properties of AML blasts

Pekova S, Ivanek R, Dvorak M, Rueggeberg S, Leicht S, Li X, Franz T, Kozak T, Vrba J, Koza V, Karas M, Schwarz J, Cetkovsky P, Prucha M

Leukemia research 2009

doi:10.1016/j.leukres.2009.01.004.

XMAP215-EB1 interaction is required for proper spindle assembly and chromosome segregation in Xenopus egg extract

Kronja I, Kruljac-Letunic A, Caudron-Herger M, Bieling P, Karsenti E

Molecular biology of the cell 2009

doi:10.1091/mbc.e08-10-1051.

Loss of the Mili-interacting Tudor domain-containing protein-1 activates transposons and alters the Mili-associated small RNA profile

Reuter M, Chuma S, Tanaka T, Franz T, Stark A, Pillai RS

Nature structural & molecular biology 2009

doi:10.1038/nsmb.1615.

CaM kinase II initiates meiotic spindle depolymerization independently of APC/C activation

Reber S, Over S, Kronja I, Gruss OJ

The Journal of cell biology 2008

doi:10.1083/jcb.200807006.

Muscle RING-finger protein-1 (MuRF1) as a connector of muscle energy metabolism and protein synthesis

Koyama S, Hata S, Witt CC, Ono Y, Lerche S, Ojima K, Chiba T, Doi N, Kitamura F, Tanaka K, Abe K, Witt SH, Rybin V, Gasch A, Franz T, Labeit S, Sorimachi H

Journal of molecular biology 2008

doi:10.1016/j.jmb.2007.11.049.

Discrete states of a protein interaction network govern interphase and mitotic microtubule dynamics

Niethammer P, Kronja I, Kandels-Lewis S, Rybina S, Bastiaens P, Karsenti E

PLoS biology 2007

doi:10.1371/journal.pbio.0050029.

Silicone/graphite coating for on-target desalting and improved peptide mapping performance of matrix-assisted laser desorption/ionization-mass spectrometry targets in proteomic experiments

Li X, Wilm M, Franz T

Proteomics 2005

doi:10.1002/pmic.200401023.

Threshold values for detergents in protein and peptide samples for mass spectrometry

Funk J, Li X, Franz T

Rapid communications in mass spectrometry : RCM 2005

doi:10.1002/rcm.2142.

Characterization of an Escherichia coli elaC deletion mutant

Schilling O, Rüggeberg S, Vogel A, Rittner N, Weichert S, Schmidt S, Doig S, Franz T, Benes V, Andrews SC, Baum M, Meyer-Klaucke W

Biochemical and biophysical research communications 2004

doi:10.1016/j.bbrc.2004.05.227.

Structural basis of dynamic glycine receptor clustering by gephyrin

Sola M, Bavro VN, Timmins J, Franz T, Ricard-Blum S, Schoehn G, Ruigrok RW, Paarmann I, Saiyed T, O'Sullivan GA, Schmitt B, Betz H, Weissenhorn W

The EMBO journal 2004

doi:10.1038/sj.emboj.7600256.

Isolation and characterisation of the rabies virus N degrees-P complex produced in insect cells

Mavrakis M, Iseni F, Mazza C, Schoehn G, Ebel C, Gentzel M, Franz T, Ruigrok RW

Virology 2003

doi:10.1006/viro.2002.1748.

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