Protein turnover quantification in a multi-labeling approach - from data calculation to evaluation
Trötschel C, Albaum S, Wolff D, Schröder S, Goesmann A, Nattkemper TW, Poetsch A (2012)
Molecular & Cellular Proteomics 11(8): 512-526.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Trötschel, C;
Albaum, StefanUniBi
;
Wolff, D;
Schröder, S;
Goesmann, AlexanderUniBi
;
Nattkemper, Tim WilhelmUniBi
;
Poetsch, A.
![](https://pub.uni-bielefeld.de/images/icon_orcid.png)
![](https://pub.uni-bielefeld.de/images/icon_orcid.png)
![](https://pub.uni-bielefeld.de/images/icon_orcid.png)
Einrichtung
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Arbeitsgruppe T. Nattkemper
Center of Excellence - Cognitive Interaction Technology CITEC
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Centrum für Biotechnologie > Arbeitsgruppe T. Nattkemper
Center of Excellence - Cognitive Interaction Technology CITEC
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Abstract / Bemerkung
Liquid chromatography coupled to tandem mass spectrometry in combination with stable-isotope labeling is an established and widely spread method to measure gene expression on the protein level. However, it is often not considered that two opposing processes are responsible for the amount of a protein in a cell - the synthesis as well as the degradation. With this work, we provide an integrative, high-throughput method - from the experimental setup to the bioinformatics analysis - to measure synthesis and degradation rates of an organism's proteome. Applicability of the approach is demonstrated with an investigation of heat shock response, a well-understood regulatory mechanism in bacteria, on the biotechnologically relevant Corynebacterium glutamicum. Utilizing a multi-labeling approach using both heavy stable nitrogen as well as carbon isotopes cells are metabolically labeled in a pulse chase experiment to trace the labels' incorporation in newly synthesized proteins and its loss during protein degradation. Our work aims not only at the calculation of protein turnover rates but also at their statistical evaluation, including variance and hierarchical cluster analysis using the rich internet application QuPE.
Stichworte
Protein Synthesis;
Protein Degradation;
Data evaluation;
Bioinformatics;
Quantification;
Protein Turnover;
Tandem Mass Spectrometry;
Algorithms
Erscheinungsjahr
2012
Zeitschriftentitel
Molecular & Cellular Proteomics
Band
11
Ausgabe
8
Seite(n)
512-526
ISSN
1535-9476
eISSN
1535-9484
Page URI
https://pub.uni-bielefeld.de/record/2498232
Zitieren
Trötschel C, Albaum S, Wolff D, et al. Protein turnover quantification in a multi-labeling approach - from data calculation to evaluation. Molecular & Cellular Proteomics. 2012;11(8):512-526.
Trötschel, C., Albaum, S., Wolff, D., Schröder, S., Goesmann, A., Nattkemper, T. W., & Poetsch, A. (2012). Protein turnover quantification in a multi-labeling approach - from data calculation to evaluation. Molecular & Cellular Proteomics, 11(8), 512-526. doi:10.1074/mcp.M111.014134
Trötschel, C, Albaum, Stefan, Wolff, D, Schröder, S, Goesmann, Alexander, Nattkemper, Tim Wilhelm, and Poetsch, A. 2012. “Protein turnover quantification in a multi-labeling approach - from data calculation to evaluation”. Molecular & Cellular Proteomics 11 (8): 512-526.
Trötschel, C., Albaum, S., Wolff, D., Schröder, S., Goesmann, A., Nattkemper, T. W., and Poetsch, A. (2012). Protein turnover quantification in a multi-labeling approach - from data calculation to evaluation. Molecular & Cellular Proteomics 11, 512-526.
Trötschel, C., et al., 2012. Protein turnover quantification in a multi-labeling approach - from data calculation to evaluation. Molecular & Cellular Proteomics, 11(8), p 512-526.
C. Trötschel, et al., “Protein turnover quantification in a multi-labeling approach - from data calculation to evaluation”, Molecular & Cellular Proteomics, vol. 11, 2012, pp. 512-526.
Trötschel, C., Albaum, S., Wolff, D., Schröder, S., Goesmann, A., Nattkemper, T.W., Poetsch, A.: Protein turnover quantification in a multi-labeling approach - from data calculation to evaluation. Molecular & Cellular Proteomics. 11, 512-526 (2012).
Trötschel, C, Albaum, Stefan, Wolff, D, Schröder, S, Goesmann, Alexander, Nattkemper, Tim Wilhelm, and Poetsch, A. “Protein turnover quantification in a multi-labeling approach - from data calculation to evaluation”. Molecular & Cellular Proteomics 11.8 (2012): 512-526.
Link(s) zu Volltext(en)
Access Level
![Restricted access for author/reviewer only. Restricted](https://pub.uni-bielefeld.de/images/access_restricted.png)
Daten bereitgestellt von European Bioinformatics Institute (EBI)
12 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Metabolic profile of 1,5-diaminopentane producing Corynebacterium glutamicum under scale-down conditions: Blueprint for robustness to bioreactor inhomogeneities.
Limberg MH, Schulte J, Aryani T, Mahr R, Baumgart M, Bott M, Wiechert W, Oldiges M., Biotechnol Bioeng 114(3), 2017
PMID: 27641904
Limberg MH, Schulte J, Aryani T, Mahr R, Baumgart M, Bott M, Wiechert W, Oldiges M., Biotechnol Bioeng 114(3), 2017
PMID: 27641904
Protein turnover analysis in Salmonella Typhimurium during infection by dynamic SILAC, Topograph, and quantitative proteomics.
Wang Z, Han QQ, Zhou MT, Chen X, Guo L., J Basic Microbiol 56(7), 2016
PMID: 26773230
Wang Z, Han QQ, Zhou MT, Chen X, Guo L., J Basic Microbiol 56(7), 2016
PMID: 26773230
The CatSper channel controls chemosensation in sea urchin sperm.
Seifert R, Flick M, Bönigk W, Alvarez L, Trötschel C, Poetsch A, Müller A, Goodwin N, Pelzer P, Kashikar ND, Kremmer E, Jikeli J, Timmermann B, Kuhl H, Fridman D, Windler F, Kaupp UB, Strünker T., EMBO J 34(3), 2015
PMID: 25535245
Seifert R, Flick M, Bönigk W, Alvarez L, Trötschel C, Poetsch A, Müller A, Goodwin N, Pelzer P, Kashikar ND, Kremmer E, Jikeli J, Timmermann B, Kuhl H, Fridman D, Windler F, Kaupp UB, Strünker T., EMBO J 34(3), 2015
PMID: 25535245
Quantitative analysis of protein turnover in plants.
Nelson CJ, Li L, Millar AH., Proteomics 14(4-5), 2014
PMID: 24323582
Nelson CJ, Li L, Millar AH., Proteomics 14(4-5), 2014
PMID: 24323582
Protein turnover forms one of the highest maintenance costs in Lactococcus lactis.
Lahtvee PJ, Seiman A, Arike L, Adamberg K, Vilu R., Microbiology 160(pt 7), 2014
PMID: 24739216
Lahtvee PJ, Seiman A, Arike L, Adamberg K, Vilu R., Microbiology 160(pt 7), 2014
PMID: 24739216
Proteins with high turnover rate in barley leaves estimated by proteome analysis combined with in planta isotope labeling.
Nelson CJ, Alexova R, Jacoby RP, Millar AH., Plant Physiol 166(1), 2014
PMID: 25082890
Nelson CJ, Alexova R, Jacoby RP, Millar AH., Plant Physiol 166(1), 2014
PMID: 25082890
Proteome turnover in bacteria: current status for Corynebacterium glutamicum and related bacteria.
Trötschel C, Albaum SP, Poetsch A., Microb Biotechnol 6(6), 2013
PMID: 23425033
Trötschel C, Albaum SP, Poetsch A., Microb Biotechnol 6(6), 2013
PMID: 23425033
The need for agriculture phenotyping: "moving from genotype to phenotype".
Boggess MV, Lippolis JD, Hurkman WJ, Fagerquist CK, Briggs SP, Gomes AV, Righetti PG, Bala K., J Proteomics 93(), 2013
PMID: 23563084
Boggess MV, Lippolis JD, Hurkman WJ, Fagerquist CK, Briggs SP, Gomes AV, Righetti PG, Bala K., J Proteomics 93(), 2013
PMID: 23563084
Using the ubiquitin-modified proteome to monitor protein homeostasis function.
Carrano AC, Bennett EJ., Mol Cell Proteomics 12(12), 2013
PMID: 23704779
Carrano AC, Bennett EJ., Mol Cell Proteomics 12(12), 2013
PMID: 23704779
A novel pulse-chase SILAC strategy measures changes in protein decay and synthesis rates induced by perturbation of proteostasis with an Hsp90 inhibitor.
Fierro-Monti I, Racle J, Hernandez C, Waridel P, Hatzimanikatis V, Quadroni M., PLoS One 8(11), 2013
PMID: 24312217
Fierro-Monti I, Racle J, Hernandez C, Waridel P, Hatzimanikatis V, Quadroni M., PLoS One 8(11), 2013
PMID: 24312217
Developments in quantitative mass spectrometry for the analysis of proteome dynamics.
Hughes C, Krijgsveld J., Trends Biotechnol 30(12), 2012
PMID: 23107010
Hughes C, Krijgsveld J., Trends Biotechnol 30(12), 2012
PMID: 23107010
Proteome dynamics: revisiting turnover with a global perspective.
Claydon AJ, Beynon R., Mol Cell Proteomics 11(12), 2012
PMID: 23125033
Claydon AJ, Beynon R., Mol Cell Proteomics 11(12), 2012
PMID: 23125033
71 References
Daten bereitgestellt von Europe PubMed Central.
Correlation of mRNA and protein in complex biological samples.
Maier T, Guell M, Serrano L., FEBS Lett. 583(24), 2009
PMID: 19850042
Maier T, Guell M, Serrano L., FEBS Lett. 583(24), 2009
PMID: 19850042
Global signatures of protein and mRNA expression levels.
de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C., Mol Biosyst 5(12), 2009
PMID: 20023718
de Sousa Abreu R, Penalva LO, Marcotte EM, Vogel C., Mol Biosyst 5(12), 2009
PMID: 20023718
Non-coding RNA genes and the modern RNA world.
Eddy SR., Nat. Rev. Genet. 2(12), 2001
PMID: 11733745
Eddy SR., Nat. Rev. Genet. 2(12), 2001
PMID: 11733745
The N-end rule in bacteria.
Tobias JW, Shrader TE, Rocap G, Varshavsky A., Science 254(5036), 1991
PMID: 1962196
Tobias JW, Shrader TE, Rocap G, Varshavsky A., Science 254(5036), 1991
PMID: 1962196
The ClpXP and ClpAP proteases degrade proteins with carboxy-terminal peptide tails added by the SsrA-tagging system.
Gottesman S, Roche E, Zhou Y, Sauer RT., Genes Dev. 12(9), 1998
PMID: 9573050
Gottesman S, Roche E, Zhou Y, Sauer RT., Genes Dev. 12(9), 1998
PMID: 9573050
Degradation of carboxy-terminal-tagged cytoplasmic proteins by the Escherichia coli protease HflB (FtsH).
Herman C, Thevenet D, Bouloc P, Walker GC, D'Ari R., Genes Dev. 12(9), 1998
PMID: 9573051
Herman C, Thevenet D, Bouloc P, Walker GC, D'Ari R., Genes Dev. 12(9), 1998
PMID: 9573051
Turnover of endogenous SsrA-tagged proteins mediated by ATP-dependent proteases in Escherichia coli.
Lies M, Maurizi MR., J. Biol. Chem. 283(34), 2008
PMID: 18550539
Lies M, Maurizi MR., J. Biol. Chem. 283(34), 2008
PMID: 18550539
The rate of interaction of the amino acids of the diet with the tissue proteins.
SPRINSON DB, RITTENBERG D., J. Biol. Chem. 180(2), 1949
PMID: 18147157
SPRINSON DB, RITTENBERG D., J. Biol. Chem. 180(2), 1949
PMID: 18147157
Dual channel imaging of two-dimensional electropherograms in Bacillus subtilis.
Bernhardt J, Buttner K, Scharf C, Hecker M., Electrophoresis 20(11), 1999
PMID: 10493127
Bernhardt J, Buttner K, Scharf C, Hecker M., Electrophoresis 20(11), 1999
PMID: 10493127
Clp-dependent proteolysis down-regulates central metabolic pathways in glucose-starved Bacillus subtilis.
Gerth U, Kock H, Kusters I, Michalik S, Switzer RL, Hecker M., J. Bacteriol. 190(1), 2007
PMID: 17981983
Gerth U, Kock H, Kusters I, Michalik S, Switzer RL, Hecker M., J. Bacteriol. 190(1), 2007
PMID: 17981983
Dynamics of protein turnover, a missing dimension in proteomics.
Pratt JM, Petty J, Riba-Garcia I, Robertson DH, Gaskell SJ, Oliver SG, Beynon RJ., Mol. Cell Proteomics 1(8), 2002
PMID: 12376573
Pratt JM, Petty J, Riba-Garcia I, Robertson DH, Gaskell SJ, Oliver SG, Beynon RJ., Mol. Cell Proteomics 1(8), 2002
PMID: 12376573
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics.
Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M., Mol. Cell Proteomics 1(5), 2002
PMID: 12118079
Ong SE, Blagoev B, Kratchmarova I, Kristensen DB, Steen H, Pandey A, Mann M., Mol. Cell Proteomics 1(5), 2002
PMID: 12118079
Turnover of the human proteome: determination of protein intracellular stability by dynamic SILAC.
Doherty MK, Hammond DE, Clague MJ, Gaskell SJ, Beynon RJ., J. Proteome Res. 8(1), 2009
PMID: 18954100
Doherty MK, Hammond DE, Clague MJ, Gaskell SJ, Beynon RJ., J. Proteome Res. 8(1), 2009
PMID: 18954100
Multitagging proteomic strategy to estimate protein turnover rates in dynamic systems.
Jayapal KP, Sui S, Philp RJ, Kok YJ, Yap MG, Griffin TJ, Hu WS., J. Proteome Res. 9(5), 2010
PMID: 20184388
Jayapal KP, Sui S, Philp RJ, Kok YJ, Yap MG, Griffin TJ, Hu WS., J. Proteome Res. 9(5), 2010
PMID: 20184388
Multiplexed protein quantitation in Saccharomyces cerevisiae using amine-reactive isobaric tagging reagents.
Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ., Mol. Cell Proteomics 3(12), 2004
PMID: 15385600
Ross PL, Huang YN, Marchese JN, Williamson B, Parker K, Hattan S, Khainovski N, Pillai S, Dey S, Daniels S, Purkayastha S, Juhasz P, Martin S, Bartlet-Jones M, He F, Jacobson A, Pappin DJ., Mol. Cell Proteomics 3(12), 2004
PMID: 15385600
Protein cleavage strategies for an improved analysis of the membrane proteome.
Fischer F, Poetsch A., Proteome Sci 4(), 2006
PMID: 16512920
Fischer F, Poetsch A., Proteome Sci 4(), 2006
PMID: 16512920
Accurate quantitation of protein expression and site-specific phosphorylation.
Oda Y, Huang K, Cross FR, Cowburn D, Chait BT., Proc. Natl. Acad. Sci. U.S.A. 96(12), 1999
PMID: 10359756
Oda Y, Huang K, Cross FR, Cowburn D, Chait BT., Proc. Natl. Acad. Sci. U.S.A. 96(12), 1999
PMID: 10359756
Synthesis/degradation ratio mass spectrometry for measuring relative dynamic protein turnover.
Cargile BJ, Bundy JL, Grunden AM, Stephenson JL Jr., Anal. Chem. 76(1), 2004
PMID: 14697036
Cargile BJ, Bundy JL, Grunden AM, Stephenson JL Jr., Anal. Chem. 76(1), 2004
PMID: 14697036
Protein dynamics in iron-starved Mycobacterium tuberculosis revealed by turnover and abundance measurement using hybrid-linear ion trap-Fourier transform mass spectrometry.
Rao PK, Rodriguez GM, Smith I, Li Q., Anal. Chem. 80(18), 2008
PMID: 18690695
Rao PK, Rodriguez GM, Smith I, Li Q., Anal. Chem. 80(18), 2008
PMID: 18690695
Quantitative proteomics by metabolic labeling of model organisms.
Gouw JW, Krijgsveld J, Heck AJ., Mol. Cell Proteomics 9(1), 2009
PMID: 19955089
Gouw JW, Krijgsveld J, Heck AJ., Mol. Cell Proteomics 9(1), 2009
PMID: 19955089
QuantiSpec--Quantitative mass spectrometry data analysis of (15)N-metabolically labeled proteins.
Haegler K, Mueller NS, Maccarrone G, Hunyadi-Gulyas E, Webhofer C, Filiou MD, Zhang Y, Turck CW., J Proteomics 71(6), 2008
PMID: 19028610
Haegler K, Mueller NS, Maccarrone G, Hunyadi-Gulyas E, Webhofer C, Filiou MD, Zhang Y, Turck CW., J Proteomics 71(6), 2008
PMID: 19028610
Proteome scale turnover analysis in live animals using stable isotope metabolic labeling.
Zhang Y, Reckow S, Webhofer C, Boehme M, Gormanns P, Egge-Jacobsen WM, Turck CW., Anal. Chem. 83(5), 2011
PMID: 21314131
Zhang Y, Reckow S, Webhofer C, Boehme M, Gormanns P, Egge-Jacobsen WM, Turck CW., Anal. Chem. 83(5), 2011
PMID: 21314131
A data processing pipeline for Mammalian proteome dynamics studies using stable isotope metabolic labeling
Guan S., Price J., Prusiner S., Ghaemmaghami S., Burlingame A.., 2011
Guan S., Price J., Prusiner S., Ghaemmaghami S., Burlingame A.., 2011
Analysis of proteome dynamics in the mouse brain.
Price JC, Guan S, Burlingame A, Prusiner SB, Ghaemmaghami S., Proc. Natl. Acad. Sci. U.S.A. 107(32), 2010
PMID: 20699386
Price JC, Guan S, Burlingame A, Prusiner SB, Ghaemmaghami S., Proc. Natl. Acad. Sci. U.S.A. 107(32), 2010
PMID: 20699386
Production of L-Threonine by Analog-Resistant Mutants
Kase H., Nakayama K.., 1972
Kase H., Nakayama K.., 1972
Role of the ssu and seu genes of Corynebacterium glutamicum ATCC 13032 in utilization of sulfonates and sulfonate esters as sulfur sources.
Koch DJ, Ruckert C, Rey DA, Mix A, Puhler A, Kalinowski J., Appl. Environ. Microbiol. 71(10), 2005
PMID: 16204527
Koch DJ, Ruckert C, Rey DA, Mix A, Puhler A, Kalinowski J., Appl. Environ. Microbiol. 71(10), 2005
PMID: 16204527
Physiological adaptation of Corynebacterium glutamicum to benzoate as alternative carbon source - a membrane proteome-centric view.
Haussmann U, Qi SW, Wolters D, Rogner M, Liu SJ, Poetsch A., Proteomics 9(14), 2009
PMID: 19639586
Haussmann U, Qi SW, Wolters D, Rogner M, Liu SJ, Poetsch A., Proteomics 9(14), 2009
PMID: 19639586
Universal sample preparation method for proteome analysis.
Wisniewski JR, Zougman A, Nagaraj N, Mann M., Nat. Methods 6(5), 2009
PMID: 19377485
Wisniewski JR, Zougman A, Nagaraj N, Mann M., Nat. Methods 6(5), 2009
PMID: 19377485
The complete Corynebacterium glutamicum ATCC 13032 genome sequence and its impact on the production of L-aspartate-derived amino acids and vitamins.
Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Kramer R, Linke B, McHardy AC, Meyer F, Mockel B, Pfefferle W, Puhler A, Rey DA, Ruckert C, Rupp O, Sahm H, Wendisch VF, Wiegrabe I, Tauch A., J. Biotechnol. 104(1-3), 2003
PMID: 12948626
Kalinowski J, Bathe B, Bartels D, Bischoff N, Bott M, Burkovski A, Dusch N, Eggeling L, Eikmanns BJ, Gaigalat L, Goesmann A, Hartmann M, Huthmacher K, Kramer R, Linke B, McHardy AC, Meyer F, Mockel B, Pfefferle W, Puhler A, Rey DA, Ruckert C, Rupp O, Sahm H, Wendisch VF, Wiegrabe I, Tauch A., J. Biotechnol. 104(1-3), 2003
PMID: 12948626
DTASelect and Contrast: tools for assembling and comparing protein identifications from shotgun proteomics.
Tabb DL, McDonald WH, Yates JR 3rd., J. Proteome Res. 1(1), 2002
PMID: 12643522
Tabb DL, McDonald WH, Yates JR 3rd., J. Proteome Res. 1(1), 2002
PMID: 12643522
Randomized sequence databases for tandem mass spectrometry peptide and protein identification.
Higdon R, Hogan JM, Van Belle G, Kolker E., OMICS 9(4), 2005
PMID: 16402894
Higdon R, Hogan JM, Van Belle G, Kolker E., OMICS 9(4), 2005
PMID: 16402894
Qupe--a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments.
Albaum SP, Neuweger H, Franzel B, Lange S, Mertens D, Trotschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A., Bioinformatics 25(23), 2009
PMID: 19808875
Albaum SP, Neuweger H, Franzel B, Lange S, Mertens D, Trotschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A., Bioinformatics 25(23), 2009
PMID: 19808875
Isotopic Pattern Calculator
Nolting D.., 2008
Nolting D.., 2008
Atomic weights and isotopic compositions
Coursey J., Schwab D., Dragoset R.., 2005
Coursey J., Schwab D., Dragoset R.., 2005
Optimization and testing of mass spectral library search algorithms for compound identification.
Stein SE, Scott DR., J. Am. Soc. Mass Spectrom. 5(9), 1994
PMID: 24222034
Stein SE, Scott DR., J. Am. Soc. Mass Spectrom. 5(9), 1994
PMID: 24222034
A correlation algorithm for the automated quantitative analysis of shotgun proteomics data.
MacCoss MJ, Wu CC, Liu H, Sadygov R, Yates JR 3rd., Anal. Chem. 75(24), 2003
PMID: 14670053
MacCoss MJ, Wu CC, Liu H, Sadygov R, Yates JR 3rd., Anal. Chem. 75(24), 2003
PMID: 14670053
Automated statistical analysis of protein abundance ratios from data generated by stable-isotope dilution and tandem mass spectrometry.
Li XJ, Zhang H, Ranish JA, Aebersold R., Anal. Chem. 75(23), 2003
PMID: 14640741
Li XJ, Zhang H, Ranish JA, Aebersold R., Anal. Chem. 75(23), 2003
PMID: 14640741
Robust estimation of peptide abundance ratios and rigorous scoring of their variability and bias in quantitative shotgun proteomics.
Pan C, Kora G, Tabb DL, Pelletier DA, McDonald WH, Hurst GB, Hettich RL, Samatova NF., Anal. Chem. 78(20), 2006
PMID: 17037910
Pan C, Kora G, Tabb DL, Pelletier DA, McDonald WH, Hurst GB, Hettich RL, Samatova NF., Anal. Chem. 78(20), 2006
PMID: 17037910
Comparison of public peak detection algorithms for MALDI mass spectrometry data analysis.
Yang C, He Z, Yu W., BMC Bioinformatics 10(), 2009
PMID: 19126200
Yang C, He Z, Yu W., BMC Bioinformatics 10(), 2009
PMID: 19126200
Improved peak detection in mass spectrum by incorporating continuous wavelet transform-based pattern matching.
Du P, Kibbe WA, Lin SM., Bioinformatics 22(17), 2006
PMID: 16820428
Du P, Kibbe WA, Lin SM., Bioinformatics 22(17), 2006
PMID: 16820428
How high G+C Gram-positive bacteria and in particular bifidobacteria cope with heat stress: protein players and regulators.
Ventura M, Canchaya C, Zhang Z, Bernini V, Fitzgerald GF, van Sinderen D., FEMS Microbiol. Rev. 30(5), 2006
PMID: 16911042
Ventura M, Canchaya C, Zhang Z, Bernini V, Fitzgerald GF, van Sinderen D., FEMS Microbiol. Rev. 30(5), 2006
PMID: 16911042
A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study.
Albaum SP, Hahne H, Otto A, Haußmann U, Becher D, Poetsch A, Goesmann A, Nattkemper TW., Proteome Sci 9(), 2011
PMID: 21663690
Albaum SP, Hahne H, Otto A, Haußmann U, Becher D, Poetsch A, Goesmann A, Nattkemper TW., Proteome Sci 9(), 2011
PMID: 21663690
A simple sequentially rejective multiple test procedure
Holm S.., 1979
Holm S.., 1979
Distribution-free two-sample tests for scale
Fligner M., Killeen T.., 1976
Fligner M., Killeen T.., 1976
An analysis of variance test for normality (Complete Samples)
Shapiro S., Wilk M.., 1965
Shapiro S., Wilk M.., 1965
Microarray studies reveal a 'differential response' to moderate or severe heat shock of the HrcA- and HspR-dependent systems in Corynebacterium glutamicum.
Barreiro C, Nakunst D, Huser AT, de Paz HD, Kalinowski J, Martin JF., Microbiology (Reading, Engl.) 155(Pt 2), 2009
PMID: 19202085
Barreiro C, Nakunst D, Huser AT, de Paz HD, Kalinowski J, Martin JF., Microbiology (Reading, Engl.) 155(Pt 2), 2009
PMID: 19202085
Validating clustering for gene expression data.
Yeung KY, Haynor DR, Ruzzo WL., Bioinformatics 17(4), 2001
PMID: 11301299
Yeung KY, Haynor DR, Ruzzo WL., Bioinformatics 17(4), 2001
PMID: 11301299
Hierarchical grouping to optimize an objective function
Ward J.., 1963
Ward J.., 1963
A criterion for determining the number of groups in a data set using sum-of-squares clustering
Krzanowski W., Lai Y.., 1988
Krzanowski W., Lai Y.., 1988
Regulation by proteolysis: energy-dependent proteases and their targets.
Gottesman S, Maurizi MR., Microbiol. Rev. 56(4), 1992
PMID: 1480111
Gottesman S, Maurizi MR., Microbiol. Rev. 56(4), 1992
PMID: 1480111
The COG database: a tool for genome-scale analysis of protein functions and evolution.
Tatusov RL, Galperin MY, Natale DA, Koonin EV., Nucleic Acids Res. 28(1), 2000
PMID: 10592175
Tatusov RL, Galperin MY, Natale DA, Koonin EV., Nucleic Acids Res. 28(1), 2000
PMID: 10592175
A quantitative analysis software tool for mass spectrometry-based proteomics.
Park SK, Venable JD, Xu T, Yates JR 3rd., Nat. Methods 5(4), 2008
PMID: 18345006
Park SK, Venable JD, Xu T, Yates JR 3rd., Nat. Methods 5(4), 2008
PMID: 18345006
New algorithm for 15N/14N quantitation with LC-ESI-MS using an LTQ-FT mass spectrometer.
Andreev VP, Li L, Rejtar T, Li Q, Ferry JG, Karger BL., J. Proteome Res. 5(8), 2006
PMID: 16889428
Andreev VP, Li L, Rejtar T, Li Q, Ferry JG, Karger BL., J. Proteome Res. 5(8), 2006
PMID: 16889428
Ultrahigh-speed calculation of isotope distributions.
Rockwood AL, Van Orden SL., Anal. Chem. 68(13), 1996
PMID: 21619291
Rockwood AL, Van Orden SL., Anal. Chem. 68(13), 1996
PMID: 21619291
Quantitative analysis of isotope distributions in proteomic mass spectrometry using least-squares Fourier transform convolution.
Sperling E, Bunner AE, Sykes MT, Williamson JR., Anal. Chem. 80(13), 2008
PMID: 18522437
Sperling E, Bunner AE, Sykes MT, Williamson JR., Anal. Chem. 80(13), 2008
PMID: 18522437
Computation of the isotopic distribution in two dimensions.
Fernandez-de-Cossio J., Anal. Chem. 82(15), 2010
PMID: 20614924
Fernandez-de-Cossio J., Anal. Chem. 82(15), 2010
PMID: 20614924
Efficient calculation of exact mass isotopic distributions.
Snider RK., J. Am. Soc. Mass Spectrom. 18(8), 2007
PMID: 17583532
Snider RK., J. Am. Soc. Mass Spectrom. 18(8), 2007
PMID: 17583532
Smoothing and Differentiation of Data by Simplified Least Squares Procedures
Savitzky A., Golay M.., 1964
Savitzky A., Golay M.., 1964
Regulation of the heat-shock response.
Yura T, Nakahigashi K., Curr. Opin. Microbiol. 2(2), 1999
PMID: 10322172
Yura T, Nakahigashi K., Curr. Opin. Microbiol. 2(2), 1999
PMID: 10322172
Selective identification of newly synthesized proteins in mammalian cells using bioorthogonal noncanonical amino acid tagging (BONCAT).
Dieterich DC, Link AJ, Graumann J, Tirrell DA, Schuman EM., Proc. Natl. Acad. Sci. U.S.A. 103(25), 2006
PMID: 16769897
Dieterich DC, Link AJ, Graumann J, Tirrell DA, Schuman EM., Proc. Natl. Acad. Sci. U.S.A. 103(25), 2006
PMID: 16769897
Identification and quantitation of newly synthesized proteins in Escherichia coli by enrichment of azidohomoalanine-labeled peptides with diagonal chromatography.
Kramer G, Sprenger RR, Back J, Dekker HL, Nessen MA, van Maarseveen JH, de Koning LJ, Hellingwerf KJ, de Jong L, de Koster CG., Mol. Cell Proteomics 8(7), 2009
PMID: 19321432
Kramer G, Sprenger RR, Back J, Dekker HL, Nessen MA, van Maarseveen JH, de Koning LJ, Hellingwerf KJ, de Jong L, de Koster CG., Mol. Cell Proteomics 8(7), 2009
PMID: 19321432
Structure and function of bacterial sigma factors.
Helmann JD, Chamberlin MJ., Annu. Rev. Biochem. 57(), 1988
PMID: 3052291
Helmann JD, Chamberlin MJ., Annu. Rev. Biochem. 57(), 1988
PMID: 3052291
Regulation of Corynebacterium glutamicum heat shock response by the extracytoplasmic-function sigma factor SigH and transcriptional regulators HspR and HrcA.
Ehira S, Teramoto H, Inui M, Yukawa H., J. Bacteriol. 191(9), 2009
PMID: 19270092
Ehira S, Teramoto H, Inui M, Yukawa H., J. Bacteriol. 191(9), 2009
PMID: 19270092
The extracytoplasmic function-type sigma factor SigM of Corynebacterium glutamicum ATCC 13032 is involved in transcription of disulfide stress-related genes.
Nakunst D, Larisch C, Huser AT, Tauch A, Puhler A, Kalinowski J., J. Bacteriol. 189(13), 2007
PMID: 17483229
Nakunst D, Larisch C, Huser AT, Tauch A, Puhler A, Kalinowski J., J. Bacteriol. 189(13), 2007
PMID: 17483229
Genome-wide transcription profiling of Corynebacterium glutamicum after heat shock and during growth on acetate and glucose.
Muffler A, Bettermann S, Haushalter M, Horlein A, Neveling U, Schramm M, Sorgenfrei O., J. Biotechnol. 98(2-3), 2002
PMID: 12141991
Muffler A, Bettermann S, Haushalter M, Horlein A, Neveling U, Schramm M, Sorgenfrei O., J. Biotechnol. 98(2-3), 2002
PMID: 12141991
Heat shock proteome analysis of wild-type Corynebacterium glutamicum ATCC 13032 and a spontaneous mutant lacking GroEL1, a dispensable chaperone.
Barreiro C, Gonzalez-Lavado E, Brand S, Tauch A, Martin JF., J. Bacteriol. 187(3), 2005
PMID: 15659666
Barreiro C, Gonzalez-Lavado E, Brand S, Tauch A, Martin JF., J. Bacteriol. 187(3), 2005
PMID: 15659666
Transcriptional analysis of the groES-groEL1, groEL2, and dnaK genes in Corynebacterium glutamicum: characterization of heat shock-induced promoters.
Barreiro C, Gonzalez-Lavado E, Patek M, Martin JF., J. Bacteriol. 186(14), 2004
PMID: 15231814
Barreiro C, Gonzalez-Lavado E, Patek M, Martin JF., J. Bacteriol. 186(14), 2004
PMID: 15231814
An analysis of the effect of changes in growth temperature on proteolysis in vivo in the psychrophilic bacterium Vibrio sp. strain ANT-300.
Araki T., J. Gen. Microbiol. 138(10), 1992
PMID: 1336030
Araki T., J. Gen. Microbiol. 138(10), 1992
PMID: 1336030
Stable isotope metabolic labeling with a novel N-enriched bacteria diet for improved proteomic analyses of mouse models for psychopathologies.
Frank E, Kessler MS, Filiou MD, Zhang Y, Maccarrone G, Reckow S, Bunck M, Heumann H, Turck CW, Landgraf R, Hambsch B., PLoS ONE 4(11), 2009
PMID: 19915716
Frank E, Kessler MS, Filiou MD, Zhang Y, Maccarrone G, Reckow S, Bunck M, Heumann H, Turck CW, Landgraf R, Hambsch B., PLoS ONE 4(11), 2009
PMID: 19915716
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 22493176
PubMed | Europe PMC
Suchen in