EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany

Biography

  • PhD 2007, Uppsala University.
    Group leader Cellzome, Heidelberg.
    Team leader and Head of Proteomics Core Facility at EMBL since 2016.
    Joint Appointment with the Structural and Computational Biology Unit.

Publications

Total: 58 publication(s)

2017

Do H, Makthal N, VanderWal AR, Rettel M, Savitski MM, Peschek N, Papenfort K, Olsen RJ, Musser JM, Kumaraswami M. (2017)

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

Proc Natl Acad Sci U S A doi: 10.1073/pnas.1705972114
Europe PMC | doi

Wilhelm M, Hahne H, Savitski M, Marx H, Lemeer S, Bantscheff M, Kuster B. (2017)

Wilhelm et al. reply.

Nature 547(7664) doi: 10.1038/nature22294
Europe PMC | doi

Mateus A, Määttä TA, Savitski MM. (2017)

Thermal proteome profiling: unbiased assessment of protein state through heat-induced stability changes.

Proteome Sci 15 doi: 10.1186/s12953-017-0122-4
Europe PMC | doi

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. (2017)

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

Nat Microbiol 2:17047. doi: 10.1038/nmicrobiol.2017.47
Europe PMC | doi


2016

Becher I, Werner T, Doce C, Zaal EA, Tögel I, Khan CA, Rueger A, Muelbaier M, Salzer E, Berkers CR, Fitzpatrick PF, Bantscheff M, Savitski MM. (2016)

Thermal profiling reveals phenylalanine hydroxylase as an off-target of panobinostat.

Nat. Chem. Biol. 12(11):908-910. doi: 10.1038/nchembio.2185
Europe PMC | doi

Jin J, Tian R, Pasculescu A, Dai AY, Williton K, Taylor L, Savitski MM, Bantscheff M, Woodgett JR, Colwill K, Pawson T. (2016)

Mutational analysis of GSK3β protein kinase together with kinome-wide binding and stability studies suggest context-dependent recognition of kinases by the chaperone HSP90.

Mol Cell Biol doi: 10.1128/MCB.01045-15
Europe PMC | doi


2015

Reinhard FB, Eberhard D, Werner T, Franken H, Childs D, Doce C, Savitski MF, Huber W, Bantscheff M, Savitski MM, Drewes G. (2015)

Thermal proteome profiling monitors ligand interactions with cellular membrane proteins.

Nat. Methods 12(12):1129-1131. doi: 10.1038/nmeth.3652
Europe PMC | doi

Franken H, Mathieson T, Childs D, Sweetman GM, Werner T, Tögel I, Doce C, Gade S, Bantscheff M, Drewes G, Reinhard FB, Huber W, Savitski MM. (2015)

Thermal proteome profiling for unbiased identification of direct and indirect drug targets using multiplexed quantitative mass spectrometry.

Nat Protoc 10(10):1567-1593. doi: 10.1038/nprot.2015.101
Europe PMC | doi

Savitski MM, Wilhelm M, Hahne H, Kuster B, Bantscheff M. (2015)

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets.

Mol. Cell Proteomics 14(9):2394-2404. doi: 10.1074/mcp.m114.046995
Europe PMC | doi


2014

Savitski MM, Reinhard FB, Franken H, Werner T, Savitski MF, Eberhard D, Martinez Molina D, Jafari R, Dovega RB, Klaeger S, Kuster B, Nordlund P, Bantscheff M, Drewes G. (2014)

Tracking cancer drugs in living cells by thermal profiling of the proteome.

Science 346(6205):55. doi: 10.1126/science.1255784
Europe PMC | doi

Becher I, Dittmann A, Savitski MM, Hopf C, Drewes G, Bantscheff M. (2014)

Chemoproteomics reveals time-dependent binding of histone deacetylase inhibitors to endogenous repressor complexes.

ACS Chem. Biol. 9(8):1736-1746. doi: 10.1021/cb500235n
Europe PMC | doi

Wilhelm M, Schlegl J, Hahne H, Moghaddas Gholami A, Lieberenz M, Savitski MM, Ziegler E, Butzmann L, Gessulat S, Marx H, Mathieson T, Lemeer S, Schnatbaum K, Reimer U, Wenschuh H, Mollenhauer M, Slotta-Huspenina J, Boese JH, Bantscheff M, Gerstmair A, Faerber F, Kuster B. (2014)

Mass-spectrometry-based draft of the human proteome.

Nature 509(7502):582-587. doi: 10.1038/nature13319
Europe PMC | doi

Werner T, Sweetman G, Savitski MF, Mathieson T, Bantscheff M, Savitski MM. (2014)

Ion coalescence of neutron encoded TMT 10-plex reporter ions.

Anal Chem 86(7):3594-3601. doi: 10.1021/ac500140s
Europe PMC | doi

Dittmann A, Werner T, Chung CW, Savitski MM, Fälth Savitski M, Grandi P, Hopf C, Lindon M, Neubauer G, Prinjha RK, Bantscheff M, Drewes G. (2014)

The commonly used PI3-kinase probe LY294002 is an inhibitor of BET bromodomains.

ACS Chem. Biol. 9(2):495-502. doi: 10.1021/cb400789e
Europe PMC | doi


2013

Savitski MM, Mathieson T, Zinn N, Sweetman G, Doce C, Becher I, Pachl F, Kuster B, Bantscheff M. (2013)

Measuring and managing ratio compression for accurate iTRAQ/TMT quantification.

J. Proteome Res. 12(8):3586-3598. doi: 10.1021/pr400098r
Europe PMC | doi

Becher I, Savitski MM, Savitski MF, Hopf C, Bantscheff M, Drewes G. (2013)

Affinity profiling of the cellular kinome for the nucleotide cofactors ATP, ADP, and GTP.

ACS Chem. Biol. 8(3):599-607. doi: 10.1021/cb3005879
Europe PMC | doi


2012

Bantscheff M, Lemeer S, Savitski MM, Kuster B. (2012)

Quantitative mass spectrometry in proteomics: critical review update from 2007 to the present.

Anal Bioanal Chem 404(4):939-965. doi: 10.1007/s00216-012-6203-4
Europe PMC | doi

Werner T, Becher I, Sweetman G, Doce C, Savitski MM, Bantscheff M. (2012)

High-resolution enabled TMT 8-plexing.

Anal. Chem. 84(16):7188-7194. doi: 10.1021/ac301553x
Europe PMC | doi

Bergamini G, Bell K, Shimamura S, Werner T, Cansfield A, Müller K, Perrin J, Rau C, Ellard K, Hopf C, Doce C, Leggate D, Mangano R, Mathieson T, O'Mahony A, Plavec I, Rharbaoui F, Reinhard F, Savitski MM, Ramsden N, Hirsch E, Drewes G, Rausch O, Bantscheff M, Neubauer G. (2012)

A selective inhibitor reveals PI3Kγ dependence of T(H)17 cell differentiation.

Nat. Chem. Biol. 8(6):576-582. doi: 10.1038/nchembio.957
Europe PMC | doi

Zubarev RA, Good DM, Savitski MM. (2012)

Radical a-ions in electron capture dissociation: on the origin of species.

J. Am. Soc. Mass Spectrom. 23(6):1015-1018. doi: 10.1007/s13361-012-0374-2
Europe PMC | doi


2011

Savitski MM, Sweetman G, Askenazi M, Marto JA, Lang M, Zinn N, Bantscheff M. (2011)

Delayed fragmentation and optimized isolation width settings for improvement of protein identification and accuracy of isobaric mass tag quantification on Orbitrap-type mass spectrometers.

Anal. Chem. 83(23):8959-8967. doi: 10.1021/ac201760x
Europe PMC | doi

Dawson MA, Prinjha RK, Dittmann A, Giotopoulos G, Bantscheff M, Chan WI, Robson SC, Chung CW, Hopf C, Savitski MM, Huthmacher C, Gudgin E, Lugo D, Beinke S, Chapman TD, Roberts EJ, Soden PE, Auger KR, Mirguet O, Doehner K, Delwel R, Burnett AK, Jeffrey P, Drewes G, Lee K, Huntly BJ, Kouzarides T. (2011)

Inhibition of BET recruitment to chromatin as an effective treatment for MLL-fusion leukaemia.

Nature 478(7370):529-533. doi: 10.1038/nature10509
Europe PMC | doi

Ledvina AR, Savitski MM, Zubarev AR, Good DM, Coon JJ, Zubarev RA. (2011)

Increased throughput of proteomics analysis by multiplexing high-resolution tandem mass spectra.

Anal. Chem. 83(20):7651-7656. doi: 10.1021/ac201843e
Europe PMC | doi

Bantscheff M, Hopf C, Savitski MM, Dittmann A, Grandi P, Michon AM, Schlegl J, Abraham Y, Becher I, Bergamini G, Boesche M, Delling M, Dümpelfeld B, Eberhard D, Huthmacher C, Mathieson T, Poeckel D, Reader V, Strunk K, Sweetman G, Kruse U, Neubauer G, Ramsden NG, Drewes G. (2011)

Chemoproteomics profiling of HDAC inhibitors reveals selective targeting of HDAC complexes.

Nat. Biotechnol. 29(3):255-265. doi: 10.1038/nbt.1759
Europe PMC | doi

Scholz B, Sköld K, Kultima K, Fernandez C, Waldemarson S, Savitski MM, Söderquist M, Borén M, Stella R, Andrén P, Zubarev R, James P. (2011)

Impact of temperature dependent sampling procedures in proteomics and peptidomics--a characterization of the liver and pancreas post mortem degradome.

Mol. Cell Proteomics 10(3) doi: 10.1074/mcp.m900229-mcp200
Europe PMC | doi

Marín-Vicente C, Guerrero-Valero M, Nielsen ML, Savitski MM, Gómez-Fernández JC, Zubarev RA, Corbalán-García S. (2011)

ATP enhances neuronal differentiation of PC12 cells by activating PKCα interactions with cytoskeletal proteins.

J. Proteome Res. 10(2):529-540. doi: 10.1021/pr100742r
Europe PMC | doi

Savitski MM, Lemeer S, Boesche M, Lang M, Mathieson T, Bantscheff M, Kuster B. (2011)

Confident phosphorylation site localization using the Mascot Delta Score.

Mol. Cell Proteomics 10(2) doi: 10.1074/mcp.m110.003830
Europe PMC | doi


2010

Savitski MM, Scholten A, Sweetman G, Mathieson T, Bantscheff M. (2010)

Evaluation of data analysis strategies for improved mass spectrometry-based phosphoproteomics.

Anal. Chem. 82(23):9843-9849. doi: 10.1021/ac102083q
Europe PMC | doi

Savitski MM, Mathieson T, Becher I, Bantscheff M. (2010)

H-score, a mass accuracy driven rescoring approach for improved peptide identification in modification rich samples.

J. Proteome Res. 9(11):5511-5516. doi: 10.1021/pr1006813
Europe PMC | doi

Savitski MM, Fischer F, Mathieson T, Sweetman G, Lang M, Bantscheff M. (2010)

Targeted data acquisition for improved reproducibility and robustness of proteomic mass spectrometry assays.

J. Am. Soc. Mass Spectrom. 21(10):1668-1679. doi: 10.1016/j.jasms.2010.01.012
Europe PMC | doi

Hermansson M, Artemenko K, Ossipova E, Eriksson H, Lengqvist J, Makrygiannakis D, Catrina AI, Nicholas AP, Klareskog L, Savitski M, Zubarev RA, Jakobsson PJ. (2010)

MS analysis of rheumatoid arthritic synovial tissue identifies specific citrullination sites on fibrinogen.

Proteomics Clin Appl 4(5):511-518. doi: 10.1002/prca.200900088
Europe PMC | doi

Alm H, Scholz B, Kultima K, Nilsson A, Andrén PE, Savitski MM, Bergman A, Stigson M, Fex-Svenningsen A, Dencker L. (2010)

In vitro neurotoxicity of PBDE-99: immediate and concentration-dependent effects on protein expression in cerebral cortex cells.

J. Proteome Res. 9(3):1226-1235. doi: 10.1021/pr900723c
Europe PMC | doi

Savitski MF, Savitski MM. (2010)

Unbiased detection of posttranslational modifications using mass spectrometry.

Methods Mol. Biol. 673:203-210. doi: 10.1007/978-1-60761-842-3_12
Europe PMC | doi

Scholz B, Alm H, Mattsson A, Nilsson A, Kultima K, Savitski MM, Fälth M, Sköld K, Brunström B, Andren PE, Dencker L. (2010)

Neuropeptidomic analysis of the embryonic Japanese quail diencephalon.

BMC Dev. Biol. 10 doi: 10.1186/1471-213x-10-30
Europe PMC | doi


2009

Artemenko KA, Zubarev AR, Samgina TY, Lebedev AT, Savitski MM, Zubarev RA. (2009)

Two dimensional mass mapping as a general method of data representation in comprehensive analysis of complex molecular mixtures.

Anal. Chem. 81(10):3738-3745. doi: 10.1021/ac802532j
Europe PMC | doi


2008

Savitski MM, Fälth M, Fung YM, Adams CM, Zubarev RA. (2008)

Bifurcating fragmentation behavior of gas-phase tryptic peptide dications in collisional activation.

J. Am. Soc. Mass Spectrom. 19(12):1755-1763. doi: 10.1016/j.jasms.2008.08.003
Europe PMC | doi

Fälth M, Savitski MM, Nielsen ML, Kjeldsen F, Andren PE, Zubarev RA. (2008)

Analytical utility of small neutral losses from reduced species in electron capture dissociation studied using SwedECD database.

Anal. Chem. 80(21):8089-8094. doi: 10.1021/ac800944u
Europe PMC | doi

Bergström Lind S, Molin M, Savitski MM, Emilsson L, Aström J, Hedberg L, Adams C, Nielsen ML, Engström A, Elfineh L, Andersson E, Zubarev RA, Pettersson U. (2008)

Immunoaffinity enrichments followed by mass spectrometric detection for studying global protein tyrosine phosphorylation.

J. Proteome Res. 7(7):2897-2910. doi: 10.1021/pr8000546
Europe PMC | doi

Zubarev RA, Zubarev AR, Savitski MM. (2008)

Electron capture/transfer versus collisionally activated/induced dissociations: solo or duet?

J. Am. Soc. Mass Spectrom. 19(6):753-761. doi: 10.1016/j.jasms.2008.03.007
Europe PMC | doi

Zubarev RA, Nielsen ML, Fung EM, Savitski MM, Kel-Margoulis O, Wingender E, Kel A. (2008)

Identification of dominant signaling pathways from proteomics expression data.

J Proteomics 71(1):89-96. doi: 10.1016/j.jprot.2008.01.004
Europe PMC | doi


2007

Fälth M, Savitski MM, Nielsen ML, Kjeldsen F, Andren PE, Zubarev RA. (2007)

SwedCAD, a database of annotated high-mass accuracy MS/MS spectra of tryptic peptides.

J. Proteome Res. 6(10):4063-4067. doi: 10.1021/pr070345h
Europe PMC | doi

Kjeldsen F, Savitski MM, Nielsen ML, Shi L, Zubarev RA. (2007)

On studying protein phosphorylation patterns using bottom-up LC-MS/MS: the case of human alpha-casein.

Analyst 132(8):768-776. doi: 10.1039/b701902e
Europe PMC | doi

Savitski MM, Kjeldsen F, Nielsen ML, Zubarev RA. (2007)

Relative specificities of water and ammonia losses from backbone fragments in collision-activated dissociation.

J. Proteome Res. 6(7):2669-2673. doi: 10.1021/pr070121z
Europe PMC | doi

Savitski MM, Nielsen ML, Zubarev RA. (2007)

Side-chain losses in electron capture dissociation to improve peptide identification.

Anal. Chem. 79(6):2296-2302. doi: 10.1021/ac0619332
Europe PMC | doi

Savitski MM, Kjeldsen F, Nielsen ML, Garbuzynskiy SO, Galzitskaya OV, Surin AK, Zubarev RA. (2007)

Backbone carbonyl group basicities are related to gas-phase fragmentation of peptides and protein folding.

Angew. Chem. Int. Ed. Engl. 46(9):1481-1484. doi: 10.1002/anie.200603881
Europe PMC | doi

Frank AM, Savitski MM, Nielsen ML, Zubarev RA, Pevzner PA. (2007)

De novo peptide sequencing and identification with precision mass spectrometry.

J. Proteome Res. 6(1):114-123. doi: 10.1021/pr060271u
Europe PMC | doi

Savitski MM, Kjeldsen F, Nielsen ML, Zubarev RA. (2007)

Hydrogen rearrangement to and from radical z fragments in electron capture dissociation of peptides.

J. Am. Soc. Mass Spectrom. 18(1):113-120. doi: 10.1016/j.jasms.2006.09.008
Europe PMC | doi


2006

Nielsen ML, Savitski MM, Zubarev RA. (2006)

Extent of modifications in human proteome samples and their effect on dynamic range of analysis in shotgun proteomics.

Mol. Cell Proteomics 5(12):2384-2391. doi: 10.1074/mcp.m600248-mcp200
Europe PMC | doi

Gorshkov AV, Tarasova IA, Evreinov VV, Savitski MM, Nielsen ML, Zubarev RA, Gorshkov MV. (2006)

Liquid chromatography at critical conditions: comprehensive approach to sequence-dependent retention time prediction.

Anal. Chem. 78(22):7770-7777. doi: 10.1021/ac060913x
Europe PMC | doi

Savitski MM, Kjeldsen F, Nielsen ML, Zubarev RA. (2006)

Complementary sequence preferences of electron-capture dissociation and vibrational excitation in fragmentation of polypeptide polycations.

Angew. Chem. Int. Ed. Engl. 45(32):5301-5303. doi: 10.1002/anie.200601240
Europe PMC | doi

Kjeldsen F, Savitski MM, Adams CM, Zubarev RA. (2006)

Determination of the location of positive charges in gas-phase polypeptide polycations by tandem mass spectrometry

Int J Mass Spectrom 252:204-212. doi: 10.1016/j.ijms.2005.10.009
doi

Savitski MM, Nielsen ML, Zubarev RA. (2006)

ModifiComb, a new proteomic tool for mapping substoichiometric post-translational modifications, finding novel types of modifications, and fingerprinting complex protein mixtures.

Mol. Cell Proteomics 5(5):935-948. doi: 10.1074/mcp.t500034-mcp200
Europe PMC | doi

Köcher T, Savitski MM, Nielsen ML, Zubarev RA. (2006)

PhosTShunter: a fast and reliable tool to detect phosphorylated peptides in liquid chromatography Fourier transform tandem mass spectrometry data sets.

J. Proteome Res. 5(3):659-668. doi: 10.1021/pr0503836
Europe PMC | doi


2005

Savitski MM, Nielsen ML, Zubarev RA. (2005)

New data base-independent, sequence tag-based scoring of peptide MS/MS data validates Mowse scores, recovers below threshold data, singles out modified peptides, and assesses the quality of MS/MS techniques.

Mol. Cell Proteomics 4(8):1180-1188. doi: 10.1074/mcp.t500009-mcp200
Europe PMC | doi

Nielsen ML, Savitski MM, Zubarev RA. (2005)

Improving protein identification using complementary fragmentation techniques in fourier transform mass spectrometry.

Mol. Cell Proteomics 4(6):835-845. doi: 10.1074/mcp.t400022-mcp200
Europe PMC | doi

Savitski MM, Nielsen ML, Kjeldsen F, Zubarev RA. (2005)

Proteomics-grade de novo sequencing approach.

J. Proteome Res. 4(6):2348-2354. doi: 10.1021/pr050288x
Europe PMC | doi


2004

Nielsen ML, Savitski MM, Kjeldsen F, Zubarev RA. (2004)

Physicochemical properties determining the detection probability of tryptic peptides in Fourier transform mass spectrometry. A correlation study.

Anal. Chem. 76(19):5872-5877. doi: 10.1021/ac049571q
Europe PMC | doi

Savitski MM, Ivonin IA, Nielsen ML, Zubarev RA, Tsybin YO, Håkansson P. (2004)

Shifted-basis technique improves accuracy of peak position determination in Fourier transform mass spectrometry.

J. Am. Soc. Mass Spectrom. 15(4):457-461. doi: 10.1016/j.jasms.2003.12.003
Europe PMC | doi