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Items: 1 to 50 of 63

1.

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.

Mol Syst Biol. 2018 Jul 6;14(7):e8242. doi: 10.15252/msb.20188242.

2.

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, Savitski MM, Bork P, Göttig S, Typas A.

Nature. 2018 Jul;559(7713):259-263. doi: 10.1038/s41586-018-0278-9. Epub 2018 Jul 4.

PMID:
29973719
3.

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 May 31;173(6):1495-1507.e18. doi: 10.1016/j.cell.2018.03.053. Epub 2018 Apr 26.

4.

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; MMML Network Project, Bohnenberger H, Rettel M, Lu J, Smits AH, Stein F, Savitski MM, Huber W, Aylon Y, Oren M, Zenz T.

Blood. 2018 Jun 21;131(25):2789-2802. doi: 10.1182/blood-2017-09-806679. Epub 2018 Apr 13.

PMID:
29653964
5.

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 Mar 22;173(1):260-274.e25. doi: 10.1016/j.cell.2018.02.030. Epub 2018 Mar 15.

6.

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.

Nat Commun. 2018 Feb 15;9(1):689. doi: 10.1038/s41467-018-03106-1.

7.

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.

Proc Natl Acad Sci U S A. 2017 Oct 3;114(40):E8498-E8507. doi: 10.1073/pnas.1705972114. Epub 2017 Sep 18.

8.

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

Mateus A, Määttä TA, Savitski MM.

Proteome Sci. 2017 Jun 24;15:13. doi: 10.1186/s12953-017-0122-4. eCollection 2016. Review.

9.

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.

Nat Microbiol. 2017 Apr 10;2:17047. doi: 10.1038/nmicrobiol.2017.47.

PMID:
28394313
10.

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

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.

Nat Chem Biol. 2016 Nov;12(11):908-910. doi: 10.1038/nchembio.2185. Epub 2016 Sep 26.

PMID:
27669419
11.

Chemical Proteomics Reveals Ferrochelatase as a Common Off-target of Kinase Inhibitors.

Klaeger S, Gohlke B, Perrin J, Gupta V, Heinzlmeir S, Helm D, Qiao H, Bergamini G, Handa H, Savitski MM, Bantscheff M, Médard G, Preissner R, Kuster B.

ACS Chem Biol. 2016 May 20;11(5):1245-54. doi: 10.1021/acschembio.5b01063. Epub 2016 Feb 25.

PMID:
26863403
12.

Mutational Analysis of Glycogen Synthase Kinase 3β Protein Kinase Together with Kinome-Wide Binding and Stability Studies Suggests Context-Dependent Recognition of Kinases by the Chaperone Heat Shock Protein 90.

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

Mol Cell Biol. 2016 Jan 11;36(6):1007-18. doi: 10.1128/MCB.01045-15.

13.

Thermal proteome profiling monitors ligand interactions with cellular membrane proteins.

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

Nat Methods. 2015 Dec;12(12):1129-31. doi: 10.1038/nmeth.3652. Epub 2015 Nov 2.

PMID:
26524241
14.

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

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.

Nat Protoc. 2015 Oct;10(10):1567-93. doi: 10.1038/nprot.2015.101. Epub 2015 Sep 17.

PMID:
26379230
15.

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

Savitski MM, Wilhelm M, Hahne H, Kuster B, Bantscheff M.

Mol Cell Proteomics. 2015 Sep;14(9):2394-404. doi: 10.1074/mcp.M114.046995. Epub 2015 May 17.

16.

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

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.

Science. 2014 Oct 3;346(6205):1255784. doi: 10.1126/science.1255784. Epub 2014 Oct 2.

17.

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

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

ACS Chem Biol. 2014 Aug 15;9(8):1736-46. doi: 10.1021/cb500235n. Epub 2014 Jun 6.

PMID:
24877719
18.

Mass-spectrometry-based draft of the human proteome.

Wilhelm M, Schlegl J, Hahne H, Gholami AM, 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.

Nature. 2014 May 29;509(7502):582-7. doi: 10.1038/nature13319.

PMID:
24870543
19.

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

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

Anal Chem. 2014 Apr 1;86(7):3594-601. doi: 10.1021/ac500140s. Epub 2014 Mar 11.

PMID:
24579773
20.

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

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.

ACS Chem Biol. 2014 Feb 21;9(2):495-502. doi: 10.1021/cb400789e. Epub 2013 Dec 10.

PMID:
24533473
21.

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

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

J Proteome Res. 2013 Aug 2;12(8):3586-98. doi: 10.1021/pr400098r. Epub 2013 Jul 2.

PMID:
23768245
22.

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

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

ACS Chem Biol. 2013 Mar 15;8(3):599-607. doi: 10.1021/cb3005879. Epub 2013 Jan 7.

PMID:
23215245
23.

High-resolution enabled TMT 8-plexing.

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

Anal Chem. 2012 Aug 21;84(16):7188-94. doi: 10.1021/ac301553x. Epub 2012 Aug 8.

PMID:
22881393
24.

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

Bantscheff M, Lemeer S, Savitski MM, Kuster B.

Anal Bioanal Chem. 2012 Sep;404(4):939-65. doi: 10.1007/s00216-012-6203-4. Epub 2012 Jul 8. Review.

PMID:
22772140
25.

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

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.

Nat Chem Biol. 2012 Apr 29;8(6):576-82. doi: 10.1038/nchembio.957. Erratum in: Nat Chem Biol. 2012 Aug;8(8):737.

PMID:
22544264
26.

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

Zubarev RA, Good DM, Savitski MM.

J Am Soc Mass Spectrom. 2012 Jun;23(6):1015-8. doi: 10.1007/s13361-012-0374-2. Epub 2012 Apr 17.

PMID:
22528204
27.

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

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

Anal Chem. 2011 Dec 1;83(23):8959-67. doi: 10.1021/ac201760x. Epub 2011 Nov 4.

PMID:
22017476
28.

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

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.

Nature. 2011 Oct 2;478(7370):529-33. doi: 10.1038/nature10509.

29.

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

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

Anal Chem. 2011 Oct 15;83(20):7651-6. doi: 10.1021/ac201843e. Epub 2011 Sep 28.

30.

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

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.

Nat Biotechnol. 2011 Mar;29(3):255-65. doi: 10.1038/nbt.1759. Epub 2011 Jan 23.

PMID:
21258344
31.

Confident phosphorylation site localization using the Mascot Delta Score.

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

Mol Cell Proteomics. 2011 Feb;10(2):M110.003830. doi: 10.1074/mcp.M110.003830. Epub 2010 Nov 6.

32.

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

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

Anal Chem. 2010 Dec 1;82(23):9843-9. doi: 10.1021/ac102083q. Epub 2010 Oct 29.

PMID:
21033674
33.

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

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

J Proteome Res. 2011 Feb 4;10(2):529-40. doi: 10.1021/pr100742r. Epub 2010 Nov 18.

PMID:
20973479
34.

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

Savitski MM, Mathieson T, Becher I, Bantscheff M.

J Proteome Res. 2010 Nov 5;9(11):5511-6. doi: 10.1021/pr1006813. Epub 2010 Sep 21.

PMID:
20836569
35.

Unbiased detection of posttranslational modifications using mass spectrometry.

Savitski MF, Savitski MM.

Methods Mol Biol. 2010;673:203-10. doi: 10.1007/978-1-60761-842-3_12.

PMID:
20835800
36.

Neuropeptidomic analysis of the embryonic Japanese quail diencephalon.

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

BMC Dev Biol. 2010 Mar 18;10:30. doi: 10.1186/1471-213X-10-30.

37.

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

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

J Am Soc Mass Spectrom. 2010 Oct;21(10):1668-79. doi: 10.1016/j.jasms.2010.01.012. Epub 2010 Jan 25.

38.

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

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

Mol Cell Proteomics. 2011 Mar;10(3):M900229MCP200. doi: 10.1074/mcp.M900229-MCP200. Epub 2010 Jan 28.

39.

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

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

J Proteome Res. 2010 Mar 5;9(3):1226-35. doi: 10.1021/pr900723c.

PMID:
19954255
40.

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

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

Anal Chem. 2009 May 15;81(10):3738-45. doi: 10.1021/ac802532j.

PMID:
19382811
41.

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

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

Anal Chem. 2008 Nov 1;80(21):8089-94. doi: 10.1021/ac800944u. Epub 2008 Oct 7.

PMID:
18837516
42.

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

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

J Am Soc Mass Spectrom. 2008 Dec;19(12):1755-63. doi: 10.1016/j.jasms.2008.08.003. Epub 2008 Aug 9.

43.

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

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.

J Proteome Res. 2008 Jul;7(7):2897-910. doi: 10.1021/pr8000546. Epub 2008 Jun 11.

PMID:
18543961
44.

Identification of dominant signaling pathways from proteomics expression data.

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

J Proteomics. 2008 Apr 30;71(1):89-96. doi: 10.1016/j.jprot.2008.01.004. Epub 2008 Jan 17.

PMID:
18541477
45.

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

Zubarev RA, Zubarev AR, Savitski MM.

J Am Soc Mass Spectrom. 2008 Jun;19(6):753-61. doi: 10.1016/j.jasms.2008.03.007. Epub 2008 Mar 28.

46.

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

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

J Proteome Res. 2007 Oct;6(10):4063-7. Epub 2007 Aug 21.

PMID:
17711326
47.

Peptide fragmentation and phospho-site detection.

Savitski MM, Fälth M.

Expert Rev Proteomics. 2007 Aug;4(4):445-6. No abstract available.

PMID:
17705702
48.

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

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

Analyst. 2007 Aug;132(8):768-76. Epub 2007 Jun 13.

PMID:
17646876
49.

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

Savitski MM, Kjeldsen F, Nielsen ML, Zubarev RA.

J Proteome Res. 2007 Jul;6(7):2669-73. Epub 2007 May 16.

PMID:
17503798
50.

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

Savitski MM, Nielsen ML, Zubarev RA.

Anal Chem. 2007 Mar 15;79(6):2296-302. Epub 2007 Feb 3.

PMID:
17274597

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