Publications

ESCO1 and CTCF enable formation of long chromatin loops by protecting cohesin(STAG1) from WAPL.
Wutz G, Ladurner R, St Hilaire BG, Stocsits RR, Nagasaka K, Pignard B, Sanborn A, Tang W, Várnai C, Ivanov MP, Schoenfelder S, van der Lelij P, Huang X, Dürnberger G, Roitinger E, Mechtler K, Davidson IF, Fraser P, Lieberman-Aiden E, Peters JM.
Elife. 2020 Feb 17;9. pii: e52091. doi: 10.7554/eLife.52091. PubMed PMID: 32065581; PubMed Central PMCID: PMC7054000. (abstract)

A synthetic peptide library for benchmarking crosslinking-mass spectrometry search engines for proteins and protein complexes.
Beveridge R, Stadlmann J, Penninger JM, Mechtler K.
Nat Commun. 2020 Feb 6;11(1):742. doi: 10.1038/s41467-020-14608-2. PubMed PMID: 32029734; PubMed Central PMCID: PMC7005041. (abstract)

Autophagy mediates temporary reprogramming and dedifferentiation in plant somatic cells.
Rodriguez E, Chevalier J, Olsen J, Ansbøl J, Kapousidou V, Zuo Z, Svenning S, Loefke C, Koemeda S, Drozdowskyj PS, Jez J, Durnberger G, Kuenzl F, Schutzbier M, Mechtler K, Ebstrup EN, Lolle S, Dagdas Y, Petersen M.
EMBO J. 2020 Feb 17;39(4):e103315. doi: 10.15252/embj.2019103315. Epub 2020 Jan 13. PubMed PMID: 31930531; PubMed Central PMCID: PMC7024839. (abstract)

A novel approach to immunoapheresis of C3a/C3 and proteomic identification of associates.
Winnicki W, Pichler P, Mechtler K, Imre R, Steinmacher I, Sengölge G, Knafl D,Beilhack G, Wagner L.
PeerJ. 2019 Dec 16;7:e8218. doi: 10.7717/peerj.8218. eCollection 2019. PubMed PMID: 31871840; PubMed Central PMCID: PMC6921979. (abstract)

AMPK leads to phosphorylation of the transcription factor Nrf2, tuning transactivation of selected target genes.
Matzinger M, Fischhuber K, Pölöske D, Mechtler K, Heiss EH.
Redox Biol. 2020 Jan;29:101393. doi: 10.1016/j.redox.2019.101393. Epub 2019 Nov 27. PubMed PMID: 31805502; PubMed Central PMCID: PMC6909106. (abstract)

Improved Sensitivity in Low-Input Proteomics Using Micropillar Array-Based Chromatography.
Stadlmann J, Hudecz O, Krššáková G, Ctortecka C, Van Raemdonck G, Op De Beeck J, Desmet G, Penninger JM, Jacobs P, Mechtler K.
Anal Chem. 2019 Nov 19;91(22):14203-14207. doi: 10.1021/acs.analchem.9b02899. Epub 2019 Oct 31. PubMed PMID: 31612716; PubMed Central PMCID: PMC6873107. (abstract)

The H3 histone chaperone NASP(SIM3) escorts CenH3 in Arabidopsis.
Le Goff S, Keçeli BN, Jeřábková H, Heckmann S, Rutten T, Cotterell S, Schubert V, Roitinger E, Mechtler K, Franklin FCH, Tatout C, Houben A, Geelen D, Probst AV, Lermontova I.
Plant J. 2020 Jan;101(1):71-86. doi: 10.1111/tpj.14518. Epub 2019 Oct 14. PubMed PMID: 31463991. (abstract)

Structural analysis of urinary light chains and proteomic analysis of hyaline tubular casts in light chain associated kidney disorders.
Reiter T, Knafl D, Agis H, Mechtler K, Wagner L, Winnicki W.
PeerJ. 2019 Oct 2;7:e7819. doi: 10.7717/peerj.7819. eCollection 2019. PubMed PMID: 31592189; PubMed Central PMCID: PMC6778432. (abstract)

The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation.
Batki J, Schnabl J, Wang J, Handler D, Andreev VI, Stieger CE, Novatchkova M, Lampersberger L, Kauneckaite K, Xie W, Mechtler K, Patel DJ, Brennecke J.
Nat Struct Mol Biol. 2019 Aug;26(8):720-731. doi: 10.1038/s41594-019-0270-6. Epub 2019 Aug 5. PubMed PMID: 31384064; PubMed Central PMCID: PMC6828549. (abstract)

N-terminal β-strand underpins biochemical specialization of an ATG8 isoform.
Zess EK, Jensen C, Cruz-Mireles N, De la Concepcion JC, Sklenar J, Stephani M, Imre R, Roitinger E, Hughes R, Belhaj K, Mechtler K, Menke FLH, Bozkurt T, Banfield MJ, Kamoun S, Maqbool A, Dagdas YF.
PLoS Biol. 2019 Jul 22;17(7):e3000373. doi: 10.1371/journal.pbio.3000373. eCollection 2019 Jul. PubMed PMID: 31329577; PubMed Central PMCID: PMC6675122. (abstract)

Absolute quantification of cohesin, CTCF and their regulators in human cells.
Holzmann J, Politi AZ, Nagasaka K, Hantsche-Grininger M, Walther N, Koch B, Fuchs J, Dürnberger G, Tang W, Ladurner R, Stocsits RR, Busslinger GA, Novák B, Mechtler K, Davidson IF, Ellenberg J, Peters JM.
Elife. 2019 Jun 17;8. pii: e46269. doi: 10.7554/eLife.46269. PubMed PMID: 31204999; PubMed Central PMCID: PMC6606026. (abstract)

MTHFD1 interaction with BRD4 links folate metabolism to transcriptional regulation.
Sdelci S, Rendeiro AF, Rathert P, You W, Lin JG, Ringler A, Hofstätter G, Moll HP, Gürtl B, Farlik M, Schick S, Klepsch F, Oldach M, Buphamalai P, Schischlik F, Májek P, Parapatics K, Schmidl C, Schuster M, Penz T, Buckley DL, Hudecz O, Imre R, Wang SY, Maric HM, Kralovics R, Bennett KL, Müller AC, Mechtler K, Menche J, Bradner JE, Winter GE, Klavins K, Casanova E, Bock C, Zuber J, Kubicek S.
Nat Genet. 2019 Jun;51(6):990-998. doi: 10.1038/s41588-019-0413-z. Epub 2019 May 27. PubMed PMID: 31133746; PubMed Central PMCID: PMC6952269. (abstract)

First Community-Wide, Comparative Cross-Linking Mass Spectrometry Study.
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, Kukačka Z, Liu F, MacCoss MJ, Mechtler K, Mesika R, Moritz RL, Nagaraj N, Nesati V, Neves-Ferreira AGC, Ninnis R, Novák P, O'Reilly FJ, Pelzing M, Petrotchenko E, Piersimoni L, Plasencia M, Pukala T, Rand KD, Rappsilber J, Reichmann D, Sailer C, Sarnowski CP, Scheltema RA, Schmidt C, Schriemer DC, Shi Y, Skehel JM, Slavin M, Sobott F, Solis-Mezarino V, Stephanowitz H, Stengel F, Stieger CE, Trabjerg E, Trnka M, Vilaseca M, Viner R, Xiang Y, Yilmaz S, Zelter A, Ziemianowicz D, Leitner A, Sinz A.
Anal Chem. 2019 Jun 4;91(11):6953-6961. doi: 10.1021/acs.analchem.9b00658. Epub 2019 May 22. PubMed PMID: 31045356; PubMed Central PMCID: PMC6625963. (abstract)

Structure of McsB, a protein kinase for regulated arginine phosphorylation.
Suskiewicz MJ, Hajdusits B, Beveridge R, Heuck A, Vu LD, Kurzbauer R, Hauer K, Thoeny V, Rumpel K, Mechtler K, Meinhart A, Clausen T.
Nat Chem Biol. 2019 May;15(5):510-518. doi: 10.1038/s41589-019-0265-y. Epub 2019 Apr 8. PubMed PMID: 30962626; PubMed Central PMCID: PMC6522372. (abstract)

Spectral Clustering Improves Label-Free Quantification of Low-Abundant Proteins.
Griss J, Stanek F, Hudecz O, Dürnberger G, Perez-Riverol Y, Vizcaíno JA, Mechtler K.
J Proteome Res. 2019 Apr 5;18(4):1477-1485. doi: 10.1021/acs.jproteome.8b00377. Epub 2019 Mar 22. PubMed PMID: 30859831; PubMed Central PMCID: PMC6456873. (abstract)

Optimized Fragmentation Improves the Identification of Peptides Cross-Linked by MS-Cleavable Reagents.
Stieger CE, Doppler P, Mechtler K.
J Proteome Res. 2019 Mar 1;18(3):1363-1370. doi: 10.1021/acs.jproteome.8b00947. Epub 2019 Feb 18. PubMed PMID: 30693776. (abstract)

apQuant: Accurate Label-Free Quantification by Quality Filtering.
Doblmann J, Dusberger F, Imre R, Hudecz O, Stanek F, Mechtler K, Dürnberger G.
J Proteome Res. 2019 Jan 4;18(1):535-541. doi: 10.1021/acs.jproteome.8b00113. Epub 2018 Nov 2. PubMed PMID: 30351950. (abstract)

Structural prediction of protein models using distance restraints derived from cross-linking mass spectrometry data.
Orbán-Németh Z, Beveridge R, Hollenstein DM, Rampler E, Stranzl T, Hudecz O, Doblmann J, Schlögelhofer P, Mechtler K.
Nat Protoc. 2018 Mar;13(3):478-494. doi: 10.1038/nprot.2017.146. Epub 2018 Feb 8. Erratum in: Nat Protoc. 2018 Jul;13(7):1724. PubMed PMID: 29419816; PubMed Central PMCID: PMC5999019. (abstract)

The replicative helicase MCM recruits cohesin acetyltransferase ESCO2 to mediate centromeric sister chromatid cohesion.
Ivanov MP, Ladurner R, Poser I, Beveridge R, Rampler E, Hudecz O, Novatchkova M, Hériché JK, Wutz G, van der Lelij P, Kreidl E, Hutchins JR, Axelsson-Ekker H, Ellenberg J, Hyman AA, Mechtler K, Peters JM.
EMBO J. 2018 Aug 1;37(15). pii: e97150. doi: 10.15252/embj.201797150. Epub 2018 Jun 21. PubMed PMID: 29930102; PubMed Central PMCID: PMC6068434. (abstract)

Mutations that prevent methylation of cohesin render sensitivity to DNA damage in S.
Sanyal S, Molnarova L, Richterova J, Huraiova B, Benko Z, Polakova S, Cipakova I, Sevcovicova A, Gaplovska-Kysela K, Mechtler K, Cipak L, Gregan J.
pombe. J Cell Sci. 2018 Jul 6;131(13). pii: jcs214924. doi: 10.1242/jcs.214924. PubMed PMID: 29898918; PubMed Central PMCID: PMC6051343. (abstract)

CharmeRT: Boosting Peptide Identifications by Chimeric Spectra Identification and Retention Time Prediction.
Dorfer V, Maltsev S, Winkler S, Mechtler K.
J Proteome Res. 2018 Aug 3;17(8):2581-2589. doi: 10.1021/acs.jproteome.7b00836. Epub 2018 Jun 28. PubMed PMID: 29863353; PubMed Central PMCID: PMC6079931. (abstract)

Analysis of PNGase F-Resistant N-Glycopeptides Using SugarQb for Proteome Discoverer 2.
Stadlmann J, Hoi DM, Taubenschmid J, Mechtler K, Penninger JM.
1 Reveals Cryptic Substrate Specificities. Proteomics. 2018 Jul;18(13):e1700436. doi: 10.1002/pmic.201700436. Epub 2018 Jun 10. PubMed PMID: 29775240; PubMed Central PMCID: PMC6055662. (abstract)

UFD-2 is an adaptor-assisted E3 ligase targeting unfolded proteins.
Hellerschmied D, Roessler M, Lehner A, Gazda L, Stejskal K, Imre R, Mechtler K, Dammermann A, Clausen T.
Nat Commun. 2018 Feb 2;9(1):484. doi: 10.1038/s41467-018-02924-7. PubMed PMID: 29396393; PubMed Central PMCID: PMC5797217. (abstract)

Mutations in Vps15 perturb neuronal migration in mice and are associated with neurodevelopmental disease in humans.
Gstrein T, Edwards A, Přistoupilová A, Leca I, Breuss M, Pilat-Carotta S, Hansen AH, Tripathy R, Traunbauer AK, Hochstoeger T, Rosoklija G, Repic M, Landler L, Stránecký V, Dürnberger G, Keane TM, Zuber J, Adams DJ, Flint J, Honzik T, Gut M, Beltran S, Mechtler K, Sherr E, Kmoch S, Gut I, Keays DA.
Nat Neurosci. 2018 Feb;21(2):207-217. doi: 10.1038/s41593-017-0053-5. Epub 2018 Jan 8. Erratum in: Nat Neurosci. 2018 Aug;21(8):1139. PubMed PMID: 29311744; PubMed Central PMCID: PMC5897053. (abstract)

Affinity proteomics reveals extensive phosphorylation of the Brassica chromosome axis protein ASY1 and a network of associated proteins at prophase I of meiosis.
Osman K, Yang J, Roitinger E, Lambing C, Heckmann S, Howell E, Cuacos M, Imre R, Dürnberger G, Mechtler K, Armstrong S, Franklin FCH.
Plant J. 2018 Jan;93(1):17-33. doi: 10.1111/tpj.13752. Epub 2017 Dec 2. PubMed PMID: 29078019; PubMed Central PMCID: PMC5767750. (abstract)

An extracellular network of Arabidopsis leucine-rich repeat receptor kinases.
Smakowska-Luzan E, Mott GA, Parys K, Stegmann M, Howton TC, Layeghifard M, Neuhold J, Lehner A, Kong J, Grünwald K, Weinberger N, Satbhai SB, Mayer D, Busch W, Madalinski M, Stolt-Bergner P, Provart NJ, Mukhtar MS, Zipfel C, Desveaux D, Guttman DS, Belkhadir Y.
Nature. 2018 Jan 18;553(7688):342-346. doi: 10.1038/nature25184. Epub 2018 Jan 10. Erratum in: Nature. 2018 Sep;561(7722):E8. PubMed PMID: 29320478; PubMed Central PMCID: PMC6485605. (abstract)

PhoStar: Identifying Tandem Mass Spectra of Phosphorylated Peptides before Database Search.
Dorl S, Winkler S, Mechtler K, Dorfer V.
J Proteome Res. 2018 Jan 5;17(1):290-295. doi: 10.1021/acs.jproteome.7b00563. Epub 2017 Nov 2. PubMed PMID: 29057658. (abstract)

TORC1 signaling exerts spatial control over microtubule dynamics by promoting nuclear export of Stu2.
van der Vaart B, Fischböck J, Mieck C, Pichler P, Mechtler K, Medema RH, Westermann S.
J Cell Biol. 2017 Nov 6;216(11):3471-3484. doi: 10.1083/jcb.201606080. Epub 2017 Sep 29. PubMed PMID: 28972103; PubMed Central PMCID: PMC5674874. (abstract)

Comparative glycoproteomics of new players in ricin toxicity.
Stadlmann J, Taubenschmid J, Wenzel D, Gattinger A, Dürnberger G, Dusberger F, Elling U, Mach L, Mechtler K, Penninger JM.
Nature. 2017 Sep 28;549(7673):538-542. doi: 10.1038/nature24015. Epub 2017 Sep 20. PubMed PMID: 28959962; PubMed Central PMCID: PMC6003595. (abstract)

A novel non-canonical PIP-box mediates PARG interaction with PCNA.
Kaufmann T, Grishkovskaya I, Polyansky AA, Kostrhon S, Kukolj E, Olek KM, Herbert S, Beltzung E, Mechtler K, Peterbauer T, Gotzmann J, Zhang L, Hartl M, Zagrovic B, Elsayad K, Djinovic-Carugo K, Slade D.
Nucleic Acids Res. 2017 Sep 19;45(16):9741-9759. doi: 10.1093/nar/gkx604. PubMed PMID: 28934471; PubMed Central PMCID: PMC5766153. (abstract)

A vital sugar code for ricin toxicity.
Taubenschmid J, Stadlmann J, Jost M, Klokk TI, Rillahan CD, Leibbrandt A, Mechtler K, Paulson JC, Jude J, Zuber J, Sandvig K, Elling U, Marquardt T, Thiel C, Koerner C, Penninger JM.
Cell Res. 2017 Nov;27(11):1351-1364. doi: 10.1038/cr.2017.116. Epub 2017 Sep 19. PubMed PMID: 28925387; PubMed Central PMCID: PMC5674155. (abstract)

Urinary neprilysin in the critically ill patient.
Pajenda S, Mechtler K, Wagner L.
BMC Nephrol. 2017 May 25;18(1):172. doi: 10.1186/s12882-017-0587-5. PubMed PMID: 28545475; PubMed Central PMCID: PMC5445475. (abstract)

Proceedings of the EuBIC Winter School 2017.
Willems S, Bouyssié D, David M, Locard-Paulet M, Mechtler K, Schwämmle V, Uszkoreit J, Vaudel M, Dorfer V.
J Proteomics. 2017 May 24;161:78-80. doi: 0.1016/j.jprot.2017.04.001. Epub 2017 Apr 4. PubMed PMID: 28385664. (abstract)

Phosphoproteomics with Activated Ion Electron Transfer Dissociation.
Riley NM, Hebert AS, Dürnberger G, Stanek F, Mechtler K, Westphall MS, Coon JJ.
Anal Chem. 2017 Jun 20;89(12):6367-6376. doi: 10.1021/acs.analchem.7b00212. Epub 2017 Apr 17. PubMed PMID: 28383256; PubMed Central PMCID: PMC5555596. (abstract)

SIRT2 regulates nuclear envelope reassembly through ANKLE2 deacetylation.
Kaufmann T, Kukolj E, Brachner A, Beltzung E, Bruno M, Kostrhon S, Opravil S, Hudecz O, Mechtler K, Warren G, Slade D.
J Cell Sci. 2016 Dec 15;129(24):4607-4621. (abstract)

Arginine phosphorylation marks proteins for degradation by a Clp protease.
Trentini DB, Suskiewicz MJ, Heuck A, Kurzbauer R, Deszcz L, Mechtler K, Clausen T.
Nature. 2016 Nov 3;539(7627):48-53. doi: 10.1038/nature20122. (abstract)

Linear ubiquitination by LUBEL has a role in Drosophila heat stress response.
Asaoka T, Almagro J, Ehrhardt C, Tsai I, Schleiffer A, Deszcz L, Junttila S, Ringrose L, Mechtler K, Kavirayani A, Gyenesei A, Hofmann K, Duchek P, Rittinger K, Ikeda F.
EMBO Rep. 2016 Nov;17(11):1624-1640. (abstract)

Molecular basis for cytoplasmic RNA surveillance by uridylation-triggered decay in Drosophila.
Reimão-Pinto MM, Manzenreither RA, Burkard TR, Sledz P, Jinek M, Mechtler K, Ameres SL.
EMBO J. 2016 Nov 15;35(22):2417-2434. (abstract)

MuSK Kinase Activity is Modulated By A Serine Phosphorylation Site in The Kinase Loop.
Camurdanoglu BZ, Hrovat C, Dürnberger G, Madalinski M, Mechtler K, Herbst R.
Sci Rep. 2016 Sep 26;6:33583. doi: 10.1038/srep33583. Erratum in: Sci Rep. 2016 Dec 01;6:38271. PubMed PMID: 27666825; PubMed Central PMCID: PMC5035991. (abstract)

CCAN Assembly Configures Composite Binding Interfaces to Promote Cross-Linking of Ndc80 Complexes at the Kinetochore.
Pekgöz Altunkaya G, Malvezzi F, Demianova Z, Zimniak T, Litos G, Weissmann F, Mechtler K, Herzog F, Westermann S.
Curr Biol. 2016 Sep 12;26(17):2370-8. doi: 10.1016/j.cub.2016.07.005. (abstract)

A Combination of CRISPR/Cas9 and Standardized RNAi as a Versatile Platform for the Characterization of Gene Function.
Wissel S, Kieser A, Yasugi T, Duchek P, Roitinger E, Gokcezade J, Steinmann V, Gaul U, Mechtler K, Förstemann K, Knoblich JA, Neumüller RA.
G3 (Bethesda). 2016 Aug 9;6(8):2467-78. doi: 10.1534/g3.116.028571. (abstract)

Mechanism of APC/CCDC20 activation by mitotic phosphorylation.
Qiao R, Weissmann F, Yamaguchi M, Brown NG, VanderLinden R, Imre R, Jarvis MA, Brunner MR, Davidson IF, Litos G, Haselbach D, Mechtler K, Stark H, Schulman BA, Peters JM.
Proc Natl Acad Sci U S A. 2016 May 10;113(19):E2570-8. doi: 10.1073/pnas.1604929113 (abstract)

Polysialylation controls dendritic cell trafficking by regulating chemokine recognition.
Kiermaier E, Moussion C, Veldkamp CT, Gerardy-Schahn R, de Vries I, Williams LG, Chaffee GR, Phillips AJ, Freiberger F, Imre R, Taleski D, Payne RJ, Braun A, Förster R, Mechtler K, Mühlenhoff M, Volkman BF, Sixt M.
Science. 2016 Jan 8;351(6269):186-90. doi: 10.1126/science.aad0512. (abstract)

Comprehensive Cross-Linking Mass Spectrometry Reveals Parallel Orientation and Flexible Conformations of Plant HOP2-MND1.
Rampler E, Stranzl T, Orban-Nemeth Z, Hollenstein DM, Hudecz O, Schloegelhofer P, Mechtler K.
J Proteome Res. 2015 Dec 4;14(12):5048-62. doi: 10.1021/acs.jproteome.5b00903. (abstract)

Arabidopsis PCH2 Mediates Meiotic Chromosome Remodeling and Maturation of Crossovers.
Lambing C, Osman K, Nuntasoontorn K, West A, Higgins JD, Copenhaver GP, Yang J, Armstrong SJ, Mechtler K, Roitinger E, Franklin FC.
PLoS Genet. 2015 Jul 16;11(7):e1005372. doi: 10.1371/journal.pgen.1005372. eCollection 2015 Jul. (abstract)

Casein Kinase 1 and Phosphorylation of Cohesin Subunit Rec11 (SA3) Promote Meiotic Recombination through Linear Element Formation.
Phadnis N, Cipak L, Polakova S, Hyppa RW, Cipakova I, Anrather D, Karvaiova L, Mechtler K, Smith GR, Gregan J.
PLoS Genet. 2015 May 20;11(5):e1005225. doi: 10.1371/journal.pgen.1005225. eCollection 2015 May. (abstract)

Anion-exchange chromatography of phosphopeptides: weak anion exchange versus strong anion exchange and anion-exchange chromatography versus electrostatic repulsion-hydrophilic interaction chromatography.
Alpert AJ, Hudecz O, Mechtler K.
Anal Chem. 2015 May 5;87(9):4704-11. doi: 10.1021/ac504420c. Epub 2015 Apr 17. (abstract)

Rio1 promotes rDNA stability and downregulates RNA polymerase I to ensure rDNA segregation.
Iacovella MG, Golfieri C, Massari LF, Busnelli S, Pagliuca C, Dal Maschio M, Infantino V, Visintin R, Mechtler K, Ferreira-Cerca S, De Wulf P.
Nat Commun. 2015 Apr 8;6:6643. doi: 10.1038/ncomms7643. (abstract)

Quantitative phosphoproteomics of the ataxia telangiectasia-mutated (ATM) and ataxia telangiectasia-mutated and rad3-related (ATR) dependent DNA damage response in Arabidopsis thaliana.
Roitinger E, Hofer M, Köcher T, Pichler P, Novatchkova M, Yang J, Schlögelhofer P, Mechtler K.
Mol Cell Proteomics. 2015 Mar;14(3):556-71. doi: 10.1074/mcp.M114.040352. Epub 2015 Jan 5. (abstract)

MS Amanda, a universal identification algorithm optimized for high accuracy tandem mass spectra.
Dorfer, V., Pichler, P., Stranzl, T., Stadlmann, J., Taus, T., Winkler, S., Mechtler, K. (2014).
J Proteome Res. 13(8):3679-84 (abstract)

Global analysis of muscle-specific kinase signaling by quantitative phosphoproteomics.
Dürnberger, G., Camurdanoglu, BZ., Tomschik, M., Schutzbier, M., Roitinger, E., Hudecz, O., Mechtler, K., Herbst, R. (2014).
Mol Cell Proteomics. 13(8):1993-2003 (abstract)

Regulation of gene expression through a transcriptional repressor that senses acyl-chain length in membrane phospholipids.
Hofbauer, HF., Schopf, FH., Schleifer, H., Knittelfelder, OL., Pieber, B., Rechberger, GN., Wolinski, H., Gaspar, ML., Kappe, CO., Stadlmann, J., Mechtler, K., Zenz, A., Lohner, K., Tehlivets, O., Henry, SA., Kohlwein, SD. (2014).
Dev Cell. 29(6):729-39 (abstract)

A cooperative mechanism drives budding yeast kinetochore assembly downstream of CENP-A.
Hornung, P., Troc, P., Malvezzi, F., Maier, M., Demianova, Z., Zimniak, T., Litos, G., Lampert, F., Schleiffer, A., Brunner, M., Mechtler, K., Herzog, F., Marlovits, TC., Westermann, S. (2014).
J Cell Biol. 206(4):509-24 (abstract)

Development and performance evaluation of an ultralow flow nanoliquid chromatography-tandem mass spectrometry set-up.
Köcher, T., Pichler, P., De Pra, M., Rieux, L., Swart, R., Mechtler, K. (2014).
Proteomics. 14(17-18):1999-2007 (abstract)

The AAA-ATPase molecular chaperone Cdc48/p97 disassembles sumoylated centromeres, decondenses heterochromatin, and activates ribosomal RNA genes.
Mérai, Z., Chumak, N., García-Aguilar, M., Hsieh, TF., Nishimura, T., Schoft, VK., Bindics, J., Slusarz, L., Arnoux, S., Opravil, S., Mechtler, K., Zilberman, D., Fischer, RL., Tamaru, H. (2014).
Proc Natl Acad Sci U S A. 111(45):16166-71 (abstract)

Deep and precise quantification of the mouse synaptosomal proteome reveals substantial remodeling during postnatal maturation.
Moczulska, KE., Pichler, P., Schutzbier, M., Schleiffer, A., Rumpel, S., Mechtler, K. (2014).
J Proteome Res. 13(10):4310-24 (abstract)

3DSpectra: A 3-dimensional quantification algorithm for LC-MS labeled profile data.
Nasso, S., Hartler, J., Trajanoski, Z., Di Camillo, B., Mechtler, K., Toffolo, GM. (2014).
J Proteomics. 112C:156-165 (abstract)

H3S28 phosphorylation is a hallmark of the transcriptional response to cellular stress.
Sawicka, A., Hartl, D., Goiser, M., Pusch, O., Stocsits, RR., Tamir, IM., Mechtler, K., Seiser, C. (2014).  Genome Res. 24(11):1808-20 (abstract)

Quantitative phosphoproteomics reveals the role of protein arginine phosphorylation in the bacterial stress response.
Schmidt, A., Trentini, DB., Spiess, S., Fuhrmann, J., Ammerer, G., Mechtler, K., Clausen, T. (2014).
Mol Cell Proteomics. 13(2):537-50 (abstract)

Chasing phosphoarginine proteins: development of a selective enrichment method using a phosphatase trap.
Trentini, DB., Fuhrmann, J., Mechtler, K., Clausen, T. (2014).
Mol Cell Proteomics. (abstract)

A DEK Domain-Containing Protein Modulates Chromatin Structure and Function in Arabidopsis.
Waidmann, S., Kusenda, B., Mayerhofer, J., Mechtler, K., Jonak, C. (2014).
Plant Cell. (abstract)

qcML: an exchange format for quality control metrics from mass spectrometry experiments. Mol Cell Proteomics.
Walzer, M., Pernas, LE., Nasso, S., Bittremieux, W., Nahnsen, S., Kelchtermans, P., Pichler, P., van den Toorn, HW., Staes, A., Vandenbussche, J., Mazanek, M., Taus, T., Scheltema, RA., Kelstrup, CD., Gatto, L., van Breukelen, B., Aiche, S., Valkenborg, D., Laukens, K., Lilley, KS., Olsen, JV., Heck, AJ., Mechtler, K., Aebersold, R., Gevaert, K., Vizcaíno, JA., Hermjakob, H., Kohlbacher, O., Martens, L. (2014). 
Mol Cell Proteomics. 2014 Aug;13(8):1905-13 (abstract)

Jagunal homolog 1 is a critical regulator of neutrophil function in fungal host defense.
Wirnsberger, G., Zwolanek, F., Stadlmann, J., Tortola, L., Liu, SW., Perlot, T., Järvinen, P., Dürnberger, G., Kozieradzki, I., Sarao, R., De Martino, A., Boztug, K., Mechtler, K., Kuchler, K., Klein, C., Elling, U., Penninger, JM. (2014).
Nat Genet. 46(9):1028-33 (abstract) 

Unambiguous phosphosite localization using electron-transfer/higher-energy collision dissociation (EThcD).
Frese, CK., Zhou, H., Taus, T., Altelaar, AF., Mechtler, K., Heck, AJ., Mohammed, S. (2013).
J Proteome Res. 12(3):1520-5 (abstract)

Interlaboratory studies and initiatives developing standards for proteomics.
Ivanov, AR., Colangelo, CM., Dufresne, CP., Friedman, DB., Lilley, KS., Mechtler, K., Phinney, BS., Rose, KL., Rudnick, PA., Searle, BC., Shaffer, SA., Weintraub, ST. (2013).
Proteomics. 13(6):904-9 (abstract)

A structural basis for kinetochore recruitment of the Ndc80 complex via two distinct centromere receptors.
Malvezzi, F., Litos, G., Schleiffer, A., Heuck, A., Mechtler, K., Clausen, T., Westermann, S. (2013).
EMBO J. (abstract)

Analysis of meiotic protein complexes from Arabidopsis and brassica using affinity-based proteomics.
Osman, K., Roitinger, E., Yang, J., Armstrong, S., Mechtler, K., Franklin, FC. (2013).
Methods Mol Biol. 990:215-26 (abstract)

Yeast protein phosphatase 2A-Cdc55 regulates the transcriptional response to hyperosmolarity stress by regulating Msn2 and Msn4 chromatin recruitment.
Reiter, W., Klopf, E., De Wever, V., Anrather, D., Petryshyn, A., Roetzer, A., Niederacher, G., Roitinger, E., Dohnal, I., Görner, W., Mechtler, K., Brocard, C., Schüller, C., Ammerer, G. (2013).
Mol Cell Biol. 33(5):1057-72 (abstract)

Studying the fragmentation behavior of peptides with arginine phosphorylation and its influence on phospho-site localization.
Schmidt, A., Ammerer, G., Mechtler, K. (2013).
Proteomics. 13(6):945-54 (abstract)

SIMPATIQCO: A Server-Based Software Suite Which Facilitates Monitoring the Time Course of LC-MS Performance Metrics on Orbitrap Instruments.
Pichler, P., Mazanek, M., Dusberger, F., Weilnböck, L., Huber, CG., Stingl, C., Luider, TM., Straube, WL., Köcher, T., Mechtler, K.
J Proteome Res. 11(11):5540-7 (abstract)

CENP-T proteins are conserved centromere receptors of the Ndc80 complex.
Schleiffer, A., Maier, M., Litos, G., Lampert, F., Hornung, P., Mechtler, K., Westermann, S.
Nat Cell Biol. 14(6):604-13 (abstract)

APC15 mediates CDC20 autoubiquitylation by APC/C(MCC) and disassembly of the mitotic checkpoint complex.
Uzunova, K., Dye, BT., Schutz, H., Ladurner, R., Petzold, G., Toyoda, Y., Jarvis, MA., Brown, NG., Poser, I., Novatchkova, M., Mechtler, K., Hyman, AA., Stark, H., Schulman, BA., Peters, JM.
Nat Struct Mol Biol. 19(11):1116-23 (abstract)

Spatiotemporal regulation of Ipl1/Aurora activity by direct Cdk1 phosphorylation.
Zimniak, T., Fitz, V., Zhou, H., Lampert, F., Opravil, S., Mechtler, K., Stolt-Bergner, P., Westermann, S.
Curr Biol. 22(9):787-93 (abstract)

Drosophila CPEB Orb2A Mediates Memory Independent of Its RNA-Binding Domain.
Krüttner, S., Stepien, B., Noordermeer, JN., Mommaas, MA., Mechtler, K., Dickson, BJ., Keleman, K.
Neuron. 76(2):383-95 (abstract)

Analysis of protein mixtures from whole-cell extracts by single-run nanoLC-MS/MS using ultralong gradients.
Köcher, T., Pichler, P., Swart, R., Mechtler, K. (2012).
Nat Protoc. 7(5):882-90 (abstract)

Inter-Homolog Crossing-Over and Synapsis in Arabidopsis Meiosis Are Dependent on the Chromosome Axis Protein AtASY3.
Ferdous M, Higgins JD, Osman K, Lambing C, Roitinger E, Mechtler K, Armstrong SJ, Perry R, Pradillo M, Cuñado N, Franklin FC.
PLoS Genet. 2012 Feb;8(2):e1002507. Epub 2012 Feb 2. (abstract)

Universal and Confident Phosphorylation Site Localization Using phosphoRS.
Taus T, Köcher T, Pichler P, Paschke C, Schmidt A, Henrich C, Mechtler K.
J Proteome Res. 2011 Dec 2;10(12):5354-62. (abstract)

Systematic phosphorylation analysis of human mitotic protein complexes.

Proteomic analysis of endosomes from genetically modified p14/MP1 mouse embryonic fibroblasts.
Stasyk T, Holzmann J, Stumberger S, Ebner HL, Hess MW, Bonn GK, Mechtler K, Huber LA.
Proteomics. 2010 Nov;10(22):4117-27. doi: 10.1002/pmic.201000258. Epub 2010 Nov 2. PMID: 21080497 (abstract

Lesson from the stoichiometry determination of the cohesin complex; a short protease mediated elution increases the recovery from crosslinked antibody-conjugated beads.
Holzmann J, Fuchs J, Pichler P, Peters JM, Mechtler K.
J Proteome Res. 2010 Nov 3. PMID: 21043528 (abstract)

Laser microsurgery provides evidence for merotelic kinetochore attachments in fission yeast cells lacking Pcs1 or Clr4.
Rumpf C, Cipak L, Schleiffer A, Pidoux A, Mechtler K, Tolic'-Nørrelykke IM, Gregan J.
Cell Cycle. 2010 Oct 1;9(19):3997-4004. Epub 2010 Oct 3. PMID: 20935472 (abstract)

An in vivo RNAi assay identifies major genetic and cellular requirements for primary piRNA biogenesis in Drosophila.
Olivieri D, Sykora MM, Sachidanandam R, Mechtler K, Brennecke J.
EMBO J. 2010 Oct 6;29(19):3301-17. Epub 2010 Sep 3.PMID: 20818334 (abstract)

Live-cell imaging RNAi screen identifies PP2A-B55alpha and importin-beta1 as key mitotic exit regulators in human cells.
Schmitz MH, Held M, Janssens V, Hutchins JR, Hudecz O, Ivanova E, Goris J, Trinkle-Mulcahy L, Lamond AI, Poser I, Hyman AA, Mechtler K, Peters JM, Gerlich DW. Nat Cell Biol. 2010 Sep;12(9):886-93. Epub 2010 Aug 15.PMID: 20711181 (abstract)

Peptide labeling with isobaric tags yields higher identification rates using iTRAQ 4-plex compared to TMT 6-plex and iTRAQ 8-plex on LTQ Orbitrap.
Pichler P, Köcher T, Holzmann J, Mazanek M, Taus T, Ammerer G, Mechtler K.
Anal Chem. 2010 Aug 1;82(15):6549-58.PMID: 20593797 (abstract)

Casein kinase 1 is required for efficient removal of Rec8 during meiosis I.
Rumpf C, Cipak L, Dudas A, Benko Z, Pozgajova M, Riedel CG, Ammerer G, Mechtler K, Gregan J. Cell Cycle. 2010 Jul 21;9(13). PMID: 2058146 abstract)

Raman microspectroscopy reveals long-term extracellular activity of Chlamydiae.
Haider S, Wagner M, Schmid MC, Sixt BS, Christian JG, Häcker G, Pichler P, Mechtler K, Müller A, Baranyi C, Toenshoff ER, Montanaro J, Horn M.
Mol Microbiol. 2010 Aug;77(3):687-700. Epub 2010 Jun 1.PMID: 20545842 (abstract

Peptide orientation affects selectivity in ion-exchange chromatography.
Alpert AJ, Petritis K, Kangas L, Smith RD, Mechtler K, Mitulovi? G, Mohammed S, Heck AJ.
Anal Chem. 2010 Jun 15;82(12):5253-9.PMID: 20481592 (abstract)

Topology and organization of the Salmonella typhimurium type III secretion needle complex components.
Schraidt O, Lefebre MD, Brunner MJ, Schmied WH, Schmidt A, Radics J, Mechtler K, Galán JE, Marlovits TC.
PLoS Pathog. 2010 Apr 1;6(4):e1000824.PMID: 20368966 (abstract)

Systematic analysis of human protein complexes identifies chromosome segregation proteins.
Hutchins JR, Toyoda Y, Hegemann B, Poser I, Hériché JK, Sykora MM, Augsburg M, Hudecz O, Buschhorn BA, Bulkescher J, Conrad C, Comartin D, Schleiffer A, Sarov M, Pozniakovsky A, Slabicki MM, Schloissnig S, Steinmacher I, Leuschner M, Ssykor A, Lawo S, Pelletier L, Stark H, Nasmyth K, Ellenberg J, Durbin R, Buchholz F, Mechtler K, Hyman AA, Peters JM.
Science. 2010 Apr 30;328(5978):593-9. Epub 2010 Apr 1.PMID: 20360068 (abstract)

Rec8 phosphorylation by casein kinase 1 and Cdc7-Dbf4 kinase regulates cohesin cleavage by separase during meiosis.
Katis VL, Lipp JJ, Imre R, Bogdanova A, Okaz E, Habermann B, Mechtler K, Nasmyth K, Zachariae W.
Dev Cell. 2010 Mar 16;18(3):397-409.PMID: 20230747 (abstract)

QIKS--Quantitative identification of kinase substrates.
Morandell S, Grosstessner-Hain K, Roitinger E, Hudecz O, Lindhorst T, Teis D, Wrulich OA, Mazanek M, Taus T, Ueberall F, Mechtler K, Huber LA.
Proteomics. 2010 May;10(10):2015-25.PMID: 20217869 (abstract)

Probing the phosphoproteome of HeLa cells using nanocast metal oxide microspheres for phosphopeptide enrichment.
Leitner A, Sturm M, Hudecz O, Mazanek M, Smått JH, Lindén M, Lindner W, Mechtler K.
Anal Chem. 2010 Apr 1;82(7):2726-33.PMID: 20201521 (abstract)

Reducing the haystack to find the needle: improved protein identification after fast elimination of non-interpretable peptide MS/MS spectra and noise reduction.

A Dam1-based artificial kinetochore is sufficient to promote chromosome segregation in budding yeast.
Kiermaier, E., Woehrer, S., Peng, Y., Mechtler, K., and Westermann, S. (2009).
Nat Cell Biol 11, 1109-1115. (abstract)

High precision quantitative proteomics using iTRAQ on an LTQ Orbitrap: a new mass spectrometric method combining the benefits of all.
Kocher, T., Pichler, P., Schutzbier, M., Stingl, C., Kaul, A., Teucher, N., Hasenfuss, G., Penninger, J.M., and Mechtler, K. (2009).
J Proteome Res 8, 4743-4752. (abstract)

Stoichiometry determination of the MP1-p14 complex using a novel and cost-efficient method to produce an equimolar mixture of standard peptides.
Holzmann, J., Pichler, P., Madalinski, M., Kurzbauer, R., and Mechtler, K. (2009).
Anal Chem 81, 10254-10261. (abstract)

Phosphoregulation of the budding yeast EB1 homologue Bim1p by Aurora/Ipl1p.
Zimniak, T., Stengl, K., Mechtler, K., and Westermann, S. (2009).
J Cell Biol 186, 379-391. (abstract)

An improved strategy for tandem affinity purification-tagging of Schizosaccharomyces pombe genes.
Cipak, L., Spirek, M., Novatchkova, M., Chen, Z., Rumpf, C., Lugmayr, W., Mechtler, K., Ammerer, G., Csaszar, E., and Gregan, J. (2009).
Proteomics 9, 4825-4828. (abstract)

Charting the molecular network of the drug target Bcr-Abl.
Brehme, M., Hantschel, O., Colinge, J., Kaupe, I., Planyavsky, M., Köcher, T., Mechtler, K., Bennett, KL., Superti-Furga, G. (2009).
Proc Natl Acad Sci U S A. 106(18):7414-9 (abstract)

McsB is a protein arginine kinase that phosphorylates and inhibits the heat-shock regulator CtsR.
Fuhrmann, J., Schmidt, A., Spiess, S., Lehner, A., Turgay, K., Mechtler, K., Charpentier, E., Clausen, T. (2009).
Science. 324(5932):1323-7 (abstract)

Structure of the anaphase-promoting complex/cyclosome interacting with a mitotic checkpoint complex.
Herzog, F., Primorac, I., Dube, P., Lenart, P., Sander, B., Mechtler, K., Stark, H., Peters, JM. (2009).
Science. 323(5920):1477-81abstract)

Optimizing the performance of tin dioxide microspheres for phosphopeptide enrichment.
Leitner, A., Sturm, M., Smått, JH., Järn, M., Lindén, M., Mechtler, K., Lindner, W. (2009).
Anal Chim Acta. 638(1):51-7 (abstract)

An innovative method to study target protein-drug interactions by mass spectrometry.
Müller, MQ., de Koning, LJ., Schmidt, A., Ihling, C., Syha, Y., Rau, O., Mechtler, K., Schubert-Zsilavecz, M., Sinz, A. (2009).
J Med Chem. 52(9):2875-9 (abstract)

Building sister chromatid cohesion: smc3 acetylation counteracts an antiestablishment activity.
Rowland, BD., Roig, MB., Nishino, T., Kurze, A., Uluocak, P., Mishra, A., Beckouët, F., Underwood, P., Metson, J., Imre, R., Mechtler, K., Katis, VL., Nasmyth, K. (2009).
Mol Cell. 33(6):763-74 (abstract)