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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. Dorfer V, et al. J Proteome Res. 2014 Aug 1;13(8):3679-84. doi: 10.1021/pr500202e. Epub 2014 Jun 26. J Proteome Res. 2014. PMID: 24909410 Free PMC article.
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. Pichler P, et al. Anal Chem. 2010 Aug 1;82(15):6549-58. doi: 10.1021/ac100890k. Anal Chem. 2010. PMID: 20593797 Free PMC article.
Lesson from the stoichiometry determination of the cohesin complex: a short protease mediated elution increases the recovery from cross-linked antibody-conjugated beads.
Holzmann J, Fuchs J, Pichler P, Peters JM, Mechtler K. Holzmann J, et al. J Proteome Res. 2011 Feb 4;10(2):780-9. doi: 10.1021/pr100927x. Epub 2010 Nov 18. J Proteome Res. 2011. PMID: 21043528 Free PMC article.
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. Roitinger E, et al. Mol Cell Proteomics. 2015 Mar;14(3):556-71. doi: 10.1074/mcp.M114.040352. Epub 2015 Jan 5. Mol Cell Proteomics. 2015. PMID: 25561503 Free PMC article.
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. Moczulska KE, et al. J Proteome Res. 2014 Oct 3;13(10):4310-24. doi: 10.1021/pr500456t. Epub 2014 Sep 22. J Proteome Res. 2014. PMID: 25157418
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. Pichler P, et al. J Proteome Res. 2012 Nov 2;11(11):5540-7. doi: 10.1021/pr300163u. Epub 2012 Oct 22. J Proteome Res. 2012. PMID: 23088386 Free PMC article.
Universal and confident phosphorylation site localization using phosphoRS.
Taus T, Köcher T, Pichler P, Paschke C, Schmidt A, Henrich C, Mechtler K. Taus T, et al. J Proteome Res. 2011 Dec 2;10(12):5354-62. doi: 10.1021/pr200611n. Epub 2011 Nov 10. J Proteome Res. 2011. PMID: 22073976
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