Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments
Albaum S, Neuweger H, Fraenzel B, Lange S, Mertens D, Troetschel C, Wolters D, Kalinowski J, Nattkemper TW, Goesmann A (2009)
Bioinformatics 25(23): 3128-3134.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
Es wurden keine Dateien hochgeladen. Nur Publikationsnachweis!
Autor*in
Albaum, StefanUniBi ;
Neuweger, HeikoUniBi;
Fraenzel, Benjamin;
Lange, Sita;
Mertens, Dominik;
Troetschel, Christian;
Wolters, Dirk;
Kalinowski, JörnUniBi;
Nattkemper, Tim WilhelmUniBi ;
Goesmann, AlexanderUniBi
Einrichtung
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Technische Fakultät > AG Biodata Mining
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Center of Excellence - Cognitive Interaction Technology CITEC
Centrum für Biotechnologie > Arbeitsgruppe J. Kalinowski
Centrum für Biotechnologie > Arbeitsgruppe T. Nattkemper
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Institut für Bioinformatik
Technische Fakultät > AG Genominformatik
Technische Fakultät > AG Biodata Mining
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Center of Excellence - Cognitive Interaction Technology CITEC
Centrum für Biotechnologie > Arbeitsgruppe J. Kalinowski
Centrum für Biotechnologie > Arbeitsgruppe T. Nattkemper
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Institut für Bioinformatik
Technische Fakultät > AG Genominformatik
Abstract / Bemerkung
Motivation: The goal of present-omics sciences is to understand biological systems as a whole in terms of interactions of the individual cellular components. One of the main building blocks in this field of study is proteomics where tandem mass spectrometry (LC-MS/MS) in combination with isotopic labelling techniques provides a common way to obtain a direct insight into regulation at the protein level. Methods to identify and quantify the peptides contained in a sample are well established, and their output usually results in lists of identified proteins and calculated relative abundance values. The next step is to move ahead from these abstract lists and apply statistical inference methods to compare measurements, to identify genes that are significantly up-or down-regulated, or to detect clusters of proteins with similar expression profiles. Results: We introduce the Rich Internet Application (RIA) Qupe providing comprehensive data management and analysis functions for LC-MS/MS experiments. Starting with the import of mass spectra data the system guides the experimenter through the process of protein identification by database search, the calculation of protein abundance ratios, and in particular, the statistical evaluation of the quantification results including multivariate analysis methods such as analysis of variance or hierarchical cluster analysis. While a data model to store these results has been developed, a well-defined programming interface facilitates the integration of novel approaches. A compute cluster is utilized to distribute computationally intensive calculations, and a web service allows to interchange information with other -omics software applications. To demonstrate that Qupe represents a step forward in quantitative proteomics analysis an application study on Corynebacterium glutamicum has been carried out.
Erscheinungsjahr
2009
Zeitschriftentitel
Bioinformatics
Band
25
Ausgabe
23
Seite(n)
3128-3134
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/1589531
Zitieren
Albaum S, Neuweger H, Fraenzel B, et al. Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. Bioinformatics. 2009;25(23):3128-3134.
Albaum, S., Neuweger, H., Fraenzel, B., Lange, S., Mertens, D., Troetschel, C., Wolters, D., et al. (2009). Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. Bioinformatics, 25(23), 3128-3134. https://doi.org/10.1093/bioinformatics/btp568
Albaum, Stefan, Neuweger, Heiko, Fraenzel, Benjamin, Lange, Sita, Mertens, Dominik, Troetschel, Christian, Wolters, Dirk, Kalinowski, Jörn, Nattkemper, Tim Wilhelm, and Goesmann, Alexander. 2009. “Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments”. Bioinformatics 25 (23): 3128-3134.
Albaum, S., Neuweger, H., Fraenzel, B., Lange, S., Mertens, D., Troetschel, C., Wolters, D., Kalinowski, J., Nattkemper, T. W., and Goesmann, A. (2009). Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. Bioinformatics 25, 3128-3134.
Albaum, S., et al., 2009. Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. Bioinformatics, 25(23), p 3128-3134.
S. Albaum, et al., “Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments”, Bioinformatics, vol. 25, 2009, pp. 3128-3134.
Albaum, S., Neuweger, H., Fraenzel, B., Lange, S., Mertens, D., Troetschel, C., Wolters, D., Kalinowski, J., Nattkemper, T.W., Goesmann, A.: Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments. Bioinformatics. 25, 3128-3134 (2009).
Albaum, Stefan, Neuweger, Heiko, Fraenzel, Benjamin, Lange, Sita, Mertens, Dominik, Troetschel, Christian, Wolters, Dirk, Kalinowski, Jörn, Nattkemper, Tim Wilhelm, and Goesmann, Alexander. “Qupe-a Rich Internet Application to take a step forward in the analysis of mass spectrometry-based quantitative proteomics experiments”. Bioinformatics 25.23 (2009): 3128-3134.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
17 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Codon Usage Heterogeneity in the Multipartite Prokaryote Genome: Selection-Based Coding Bias Associated with Gene Location, Expression Level, and Ancestry.
López JL, Lozano MJ, Lagares A, Fabre ML, Draghi WO, Del Papa MF, Pistorio M, Becker A, Wibberg D, Schlüter A, Pühler A, Blom J, Goesmann A, Lagares A., MBio 10(3), 2019
PMID: 31138741
López JL, Lozano MJ, Lagares A, Fabre ML, Draghi WO, Del Papa MF, Pistorio M, Becker A, Wibberg D, Schlüter A, Pühler A, Blom J, Goesmann A, Lagares A., MBio 10(3), 2019
PMID: 31138741
An sRNA and Cold Shock Protein Homolog-Based Feedforward Loop Post-transcriptionally Controls Cell Cycle Master Regulator CtrA.
Robledo M, Schlüter JP, Loehr LO, Linne U, Albaum SP, Jiménez-Zurdo JI, Becker A., Front Microbiol 9(), 2018
PMID: 29740411
Robledo M, Schlüter JP, Loehr LO, Linne U, Albaum SP, Jiménez-Zurdo JI, Becker A., Front Microbiol 9(), 2018
PMID: 29740411
Regulation of Polyhydroxybutyrate Accumulation in Sinorhizobium meliloti by the Trans-Encoded Small RNA MmgR.
Lagares A, Borella GC, Linne U, Becker A, Valverde C., J Bacteriol 199(8), 2017
PMID: 28167519
Lagares A, Borella GC, Linne U, Becker A, Valverde C., J Bacteriol 199(8), 2017
PMID: 28167519
Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris.
Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ., Microbiology 163(8), 2017
PMID: 28795660
Schatschneider S, Schneider J, Blom J, Létisse F, Niehaus K, Goesmann A, Vorhölter FJ., Microbiology 163(8), 2017
PMID: 28795660
Approaches for targeted proteomics and its potential applications in neuroscience.
Sethi S, Chourasia D, Parhar IS., J Biosci 40(3), 2015
PMID: 26333406
Sethi S, Chourasia D, Parhar IS., J Biosci 40(3), 2015
PMID: 26333406
The cytosolic and extracellular proteomes of Actinoplanes sp. SE50/110 led to the identification of gene products involved in acarbose metabolism.
Wendler S, Hürtgen D, Kalinowski J, Klein A, Niehaus K, Schulte F, Schwientek P, Wehlmann H, Wehmeier UF, Pühler A., J Biotechnol 167(2), 2013
PMID: 22944206
Wendler S, Hürtgen D, Kalinowski J, Klein A, Niehaus K, Schulte F, Schwientek P, Wehlmann H, Wehmeier UF, Pühler A., J Biotechnol 167(2), 2013
PMID: 22944206
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
Dynamic protein phosphorylation during the growth of Xanthomonas campestris pv. campestris B100 revealed by a gel-based proteomics approach.
Musa YR, Bäsell K, Schatschneider S, Vorhölter FJ, Becher D, Niehaus K., J Biotechnol 167(2), 2013
PMID: 23792782
Musa YR, Bäsell K, Schatschneider S, Vorhölter FJ, Becher D, Niehaus K., J Biotechnol 167(2), 2013
PMID: 23792782
Global proteome survey of protocatechuate- and glucose-grown Corynebacterium glutamicum reveals multiple physiological differences.
Haussmann U, Poetsch A., J Proteomics 75(9), 2012
PMID: 22450470
Haussmann U, Poetsch A., J Proteomics 75(9), 2012
PMID: 22450470
Protein turnover quantification in a multilabeling approach: from data calculation to evaluation.
Trötschel C, Albaum SP, Wolff D, Schröder S, Goesmann A, Nattkemper TW, Poetsch A., Mol Cell Proteomics 11(8), 2012
PMID: 22493176
Trötschel C, Albaum SP, Wolff D, Schröder S, Goesmann A, Nattkemper TW, Poetsch A., Mol Cell Proteomics 11(8), 2012
PMID: 22493176
A critical appraisal of techniques, software packages, and standards for quantitative proteomic analysis.
Gonzalez-Galarza FF, Lawless C, Hubbard SJ, Fan J, Bessant C, Hermjakob H, Jones AR., OMICS 16(9), 2012
PMID: 22804616
Gonzalez-Galarza FF, Lawless C, Hubbard SJ, Fan J, Bessant C, Hermjakob H, Jones AR., OMICS 16(9), 2012
PMID: 22804616
In vitro functional analyses of arrhythmogenic right ventricular cardiomyopathy-associated desmoglein-2-missense variations.
Gaertner A, Klauke B, Stork I, Niehaus K, Niemann G, Gummert J, Milting H., PLoS One 7(10), 2012
PMID: 23071725
Gaertner A, Klauke B, Stork I, Niehaus K, Niemann G, Gummert J, Milting H., PLoS One 7(10), 2012
PMID: 23071725
Pathogenomics of Xanthomonas: understanding bacterium-plant interactions.
Ryan RP, Vorhölter FJ, Potnis N, Jones JB, Van Sluys MA, Bogdanove AJ, Dow JM., Nat Rev Microbiol 9(5), 2011
PMID: 21478901
Ryan RP, Vorhölter FJ, Potnis N, Jones JB, Van Sluys MA, Bogdanove AJ, Dow JM., Nat Rev Microbiol 9(5), 2011
PMID: 21478901
GProX, a user-friendly platform for bioinformatics analysis and visualization of quantitative proteomics data.
Rigbolt KT, Vanselow JT, Blagoev B., Mol Cell Proteomics 10(8), 2011
PMID: 21602510
Rigbolt KT, Vanselow JT, Blagoev B., Mol Cell Proteomics 10(8), 2011
PMID: 21602510
ProteoConnections: a bioinformatics platform to facilitate proteome and phosphoproteome analyses.
Courcelles M, Lemieux S, Voisin L, Meloche S, Thibault P., Proteomics 11(13), 2011
PMID: 21630457
Courcelles M, Lemieux S, Voisin L, Meloche S, Thibault P., Proteomics 11(13), 2011
PMID: 21630457
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
Role of novel dimeric Photosystem II (PSII)-Psb27 protein complex in PSII repair.
Grasse N, Mamedov F, Becker K, Styring S, Rögner M, Nowaczyk MM., J Biol Chem 286(34), 2011
PMID: 21737447
Grasse N, Mamedov F, Becker K, Styring S, Rögner M, Nowaczyk MM., J Biol Chem 286(34), 2011
PMID: 21737447
63 References
Daten bereitgestellt von Europe PubMed Central.
Allaire, Macromedia flash MX - a next-generation rich client. Technical report Macromedia white paper. (), 2002
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G., Nat. Genet. 25(1), 2000
PMID: 10802651
A Dendrite method for cluster analysis
Calinski, Commun. Stat. 3(), 1974
Calinski, Commun. Stat. 3(), 1974
The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.
Cote RG, Jones P, Apweiler R, Hermjakob H., BMC Bioinformatics 7(), 2006
PMID: 16507094
Cote RG, Jones P, Apweiler R, Hermjakob H., BMC Bioinformatics 7(), 2006
PMID: 16507094
MaxQuant enables high peptide identification rates, individualized p.p.b.-range mass accuracies and proteome-wide protein quantification.
Cox J, Mann M., Nat. Biotechnol. 26(12), 2008
PMID: 19029910
Cox J, Mann M., Nat. Biotechnol. 26(12), 2008
PMID: 19029910
TANDEM: matching proteins with tandem mass spectra.
Craig R, Beavis RC., Bioinformatics 20(9), 2004
PMID: 14976030
Craig R, Beavis RC., Bioinformatics 20(9), 2004
PMID: 14976030
A cluster separation measure.
Davies DL, Bouldin DW., IEEE Trans Pattern Anal Mach Intell 1(2), 1979
PMID: 21868852
Davies DL, Bouldin DW., IEEE Trans Pattern Anal Mach Intell 1(2), 1979
PMID: 21868852
EMMA 2--a MAGE-compliant system for the collaborative analysis and integration of microarray data.
Dondrup M, Albaum SP, Griebel T, Henckel K, Junemann S, Kahlke T, Kleindt CK, Kuster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Puhler A, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19200358
Dondrup M, Albaum SP, Griebel T, Henckel K, Junemann S, Kahlke T, Kleindt CK, Kuster H, Linke B, Mertens D, Mittard-Runte V, Neuweger H, Runte KJ, Tauch A, Tille F, Puhler A, Goesmann A., BMC Bioinformatics 10(), 2009
PMID: 19200358
Target-decoy search strategy for increased confidence in large-scale protein identifications by mass spectrometry.
Elias JE, Gygi SP., Nat. Methods 4(3), 2007
PMID: 17327847
Elias JE, Gygi SP., Nat. Methods 4(3), 2007
PMID: 17327847
PROTEIOS: an open source proteomics initiative.
Garden P, Alm R, Hakkinen J., Bioinformatics 21(9), 2005
PMID: 15691852
Garden P, Alm R, Hakkinen J., Bioinformatics 21(9), 2005
PMID: 15691852
Open mass spectrometry search algorithm.
Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH., J. Proteome Res. 3(5), 2004
PMID: 15473683
Geer LY, Markey SP, Kowalak JA, Wagner L, Xu M, Maynard DM, Yang X, Shi W, Bryant SH., J. Proteome Res. 3(5), 2004
PMID: 15473683
Building a BRIDGE for the integration of heterogeneous data from functional genomics into a platform for systems biology.
Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651858
Goesmann A, Linke B, Rupp O, Krause L, Bartels D, Dondrup M, McHardy AC, Wilke A, Puhler A, Meyer F., J. Biotechnol. 106(2-3), 2003
PMID: 14651858
Gudgin, SOAP version 1.2. (), 2008
Quantitative analysis of complex protein mixtures using isotope-coded affinity tags.
Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R., Nat. Biotechnol. 17(10), 1999
PMID: 10504701
Gygi SP, Rist B, Gerber SA, Turecek F, Gelb MH, Aebersold R., Nat. Biotechnol. 17(10), 1999
PMID: 10504701
The proteios software environment: an extensible multiuser platform for management and analysis of proteomics data.
Hakkinen J, Vincic G, Mansson O, Warell K, Levander F., J. Proteome Res. 8(6), 2009
PMID: 19354269
Hakkinen J, Vincic G, Mansson O, Warell K, Levander F., J. Proteome Res. 8(6), 2009
PMID: 19354269
MASPECTRAS: a platform for management and analysis of proteomics LC-MS/MS data.
Hartler J, Thallinger GG, Stocker G, Sturn A, Burkard TR, Korner E, Rader R, Schmidt A, Mechtler K, Trajanoski Z., BMC Bioinformatics 8(), 2007
PMID: 17567892
Hartler J, Thallinger GG, Stocker G, Sturn A, Burkard TR, Korner E, Rader R, Schmidt A, Mechtler K, Trajanoski Z., BMC Bioinformatics 8(), 2007
PMID: 17567892
Mass spectrometric identification of proteins in complex post-genomic projects. Soluble proteins of the metabolically versatile, denitrifying 'Aromatoleum' sp. strain EbN1.
Hufnagel P, Rabus R., J. Mol. Microbiol. Biotechnol. 11(1-2), 2006
PMID: 16825790
Hufnagel P, Rabus R., J. Mol. Microbiol. Biotechnol. 11(1-2), 2006
PMID: 16825790
Interface21, Spring framework. (), 2008
Johnson, 2003
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
KEGG: kyoto encyclopedia of genes and genomes.
Kanehisa M, Goto S., Nucleic Acids Res. 28(1), 2000
PMID: 10592173
Kanehisa M, Goto S., Nucleic Acids Res. 28(1), 2000
PMID: 10592173
Empirical statistical model to estimate the accuracy of peptide identifications made by MS/MS and database search.
Keller A, Nesvizhskii AI, Kolker E, Aebersold R., Anal. Chem. 74(20), 2002
PMID: 12403597
Keller A, Nesvizhskii AI, Kolker E, Aebersold R., Anal. Chem. 74(20), 2002
PMID: 12403597
TOPP--the OpenMS proteomics pipeline.
Kohlbacher O, Reinert K, Gropl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M., Bioinformatics 23(2), 2007
PMID: 17237091
Kohlbacher O, Reinert K, Gropl C, Lange E, Pfeifer N, Schulz-Trieglaff O, Sturm M., Bioinformatics 23(2), 2007
PMID: 17237091
Bioinformatics analysis of mass spectrometry-based proteomics data sets.
Kumar C, Mann M., FEBS Lett. 583(11), 2009
PMID: 19306877
Kumar C, Mann M., FEBS Lett. 583(11), 2009
PMID: 19306877
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
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
PRIDE: the proteomics identifications database.
Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R., Proteomics 5(13), 2005
PMID: 16041671
Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R., Proteomics 5(13), 2005
PMID: 16041671
Mass, mzML 1.0.0 specification. (), 2008
Performace evaluation of some clustering algorithms and validity indices
Maulik, IEEE Trans. Pattern Anal. Mach. Intell. 24(), 2002
Maulik, IEEE Trans. Pattern Anal. Mach. Intell. 24(), 2002
GenDB--an open source genome annotation system for prokaryote genomes.
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
Meyer F, Goesmann A, McHardy AC, Bartels D, Bekel T, Clausen J, Kalinowski J, Linke B, Rupp O, Giegerich R, Puhler A., Nucleic Acids Res. 31(8), 2003
PMID: 12682369
An assessment of software solutions for the analysis of mass spectrometry based quantitative proteomics data.
Mueller LN, Brusniak MY, Mani DR, Aebersold R., J. Proteome Res. 7(1), 2008
PMID: 18173218
Mueller LN, Brusniak MY, Mani DR, Aebersold R., J. Proteome Res. 7(1), 2008
PMID: 18173218
A statistical model for identifying proteins by tandem mass spectrometry.
Nesvizhskii AI, Keller A, Kolker E, Aebersold R., Anal. Chem. 75(17), 2003
PMID: 14632076
Nesvizhskii AI, Keller A, Kolker E, Aebersold R., Anal. Chem. 75(17), 2003
PMID: 14632076
Analysis and validation of proteomic data generated by tandem mass spectrometry.
Nesvizhskii AI, Vitek O, Aebersold R., Nat. Methods 4(10), 2007
PMID: 17901868
Nesvizhskii AI, Vitek O, Aebersold R., Nat. Methods 4(10), 2007
PMID: 17901868
MeltDB: a software platform for the analysis and integration of metabolomics experiment data.
Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A., Bioinformatics 24(23), 2008
PMID: 18765459
Neuweger H, Albaum SP, Dondrup M, Persicke M, Watt T, Niehaus K, Stoye J, Goesmann A., Bioinformatics 24(23), 2008
PMID: 18765459
Visualizing post genomics data-sets on customized pathway maps by ProMeTra-aeration-dependent gene expression and metabolism of Corynebacterium glutamicum as an example.
Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Huser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A., BMC Syst Biol 3(), 2009
PMID: 19698148
Neuweger H, Persicke M, Albaum SP, Bekel T, Dondrup M, Huser AT, Winnebald J, Schneider J, Kalinowski J, Goesmann A., BMC Syst Biol 3(), 2009
PMID: 19698148
NextApp, Echo web framework. (), 2008
Object, OMG model driven architecture. (), 2008
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
The proteomics standards initiative.
Orchard S, Hermjakob H, Apweiler R., Proteomics 3(7), 2003
PMID: 12872238
Orchard S, Hermjakob H, Apweiler R., Proteomics 3(7), 2003
PMID: 12872238
Common interchange standards for proteomics data: Public availability of tools and schema.
Orchard S, Hermjakob H, Julian RK Jr, Runte K, Sherman D, Wojcik J, Zhu W, Apweiler R., Proteomics 4(2), 2004
PMID: 14760721
Orchard S, Hermjakob H, Julian RK Jr, Runte K, Sherman D, Wojcik J, Zhu W, Apweiler R., Proteomics 4(2), 2004
PMID: 14760721
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
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
A common open representation of mass spectrometry data and its application to proteomics research.
Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R., Nat. Biotechnol. 22(11), 2004
PMID: 15529173
Pedrioli PG, Eng JK, Hubley R, Vogelzang M, Deutsch EW, Raught B, Pratt B, Nilsson E, Angeletti RH, Apweiler R, Cheung K, Costello CE, Hermjakob H, Huang S, Julian RK, Kapp E, McComb ME, Oliver SG, Omenn G, Paton NW, Simpson R, Smith R, Taylor CF, Zhu W, Aebersold R., Nat. Biotechnol. 22(11), 2004
PMID: 15529173
Evaluation of multidimensional chromatography coupled with tandem mass spectrometry (LC/LC-MS/MS) for large-scale protein analysis: the yeast proteome.
Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP., J. Proteome Res. 2(1), 2003
PMID: 12643542
Peng J, Elias JE, Thoreen CC, Licklider LJ, Gygi SP., J. Proteome Res. 2(1), 2003
PMID: 12643542
Probability-based protein identification by searching sequence databases using mass spectrometry data.
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS., Electrophoresis 20(18), 1999
PMID: 10612281
Perkins DN, Pappin DJ, Creasy DM, Cottrell JS., Electrophoresis 20(18), 1999
PMID: 10612281
DAnTE: a statistical tool for quantitative analysis of -omics data.
Polpitiya AD, Qian WJ, Jaitly N, Petyuk VA, Adkins JN, Camp DG 2nd, Anderson GA, Smith RD., Bioinformatics 24(13), 2008
PMID: 18453552
Polpitiya AD, Qian WJ, Jaitly N, Petyuk VA, Adkins JN, Camp DG 2nd, Anderson GA, Smith RD., Bioinformatics 24(13), 2008
PMID: 18453552
Proteomics, analysisXML. (), 2008
The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data.
Ramos H, Shannon P, Aebersold R., Bioinformatics 24(18), 2008
PMID: 18635572
Ramos H, Shannon P, Aebersold R., Bioinformatics 24(18), 2008
PMID: 18635572
Computational Proteomics Analysis System (CPAS): an extensible, open-source analytic system for evaluating and publishing proteomic data and high throughput biological experiments.
Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whiteaker J, Whitaker J, States D, Hanash S, Paulovich A, McIntosh MW., J. Proteome Res. 5(1), 2006
PMID: 16396501
Rauch A, Bellew M, Eng J, Fitzgibbon M, Holzman T, Hussey P, Igra M, Maclean B, Lin CW, Detter A, Fang R, Faca V, Gafken P, Zhang H, Whiteaker J, Whitaker J, States D, Hanash S, Paulovich A, McIntosh MW., J. Proteome Res. 5(1), 2006
PMID: 16396501
Red, Hibernate. (), 2008
An easy-to-use Decoy Database Builder software tool, implementing different decoy strategies for false discovery rate calculation in automated MS/MS protein identifications.
Reidegeld KA, Eisenacher M, Kohl M, Chamrad D, Korting G, Bluggel M, Meyer HE, Stephan C., Proteomics 8(6), 2008
PMID: 18338823
Reidegeld KA, Eisenacher M, Kohl M, Chamrad D, Korting G, Bluggel M, Meyer HE, Stephan C., Proteomics 8(6), 2008
PMID: 18338823
R: A Language and Environment for Statistical Computing
R, 2008
R, 2008
OpenMS - an open-source software framework for mass spectrometry.
Sturm M, Bertsch A, Gropl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O., BMC Bioinformatics 9(), 2008
PMID: 18366760
Sturm M, Bertsch A, Gropl C, Hildebrandt A, Hussong R, Lange E, Pfeifer N, Schulz-Trieglaff O, Zerck A, Reinert K, Kohlbacher O., BMC Bioinformatics 9(), 2008
PMID: 18366760
Sun, Sun grid engine. (), 2009
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
The COG database: an updated version includes eukaryotes.
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510
Tatusov RL, Fedorova ND, Jackson JD, Jacobs AR, Kiryutin B, Koonin EV, Krylov DM, Mazumder R, Mekhedov SL, Nikolskaya AN, Rao BS, Smirnov S, Sverdlov AV, Vasudevan S, Wolf YI, Yin JJ, Natale DA., BMC Bioinformatics 4(), 2003
PMID: 12969510
The minimum information about a proteomics experiment (MIAPE).
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H., Nat. Biotechnol. 25(8), 2007
PMID: 17687369
Taylor CF, Paton NW, Lilley KS, Binz PA, Julian RK Jr, Jones AR, Zhu W, Apweiler R, Aebersold R, Deutsch EW, Dunn MJ, Heck AJ, Leitner A, Macht M, Mann M, Martens L, Neubert TA, Patterson SD, Ping P, Seymour SL, Souda P, Tsugita A, Vandekerckhove J, Vondriska TM, Whitelegge JP, Wilkins MR, Xenarios I, Yates JR 3rd, Hermjakob H., Nat. Biotechnol. 25(8), 2007
PMID: 17687369
Urbanek, rJava: Low-level R to Java interface. (), 2009
The universal protein resource (UniProt).
UniProt Consortium., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18045787
UniProt Consortium., Nucleic Acids Res. 36(Database issue), 2007
PMID: 18045787
An automated multidimensional protein identification technology for shotgun proteomics.
Wolters DA, Washburn MP, Yates JR 3rd., Anal. Chem. 73(23), 2001
PMID: 11774908
Wolters DA, Washburn MP, Yates JR 3rd., Anal. Chem. 73(23), 2001
PMID: 11774908
Method to correlate tandem mass spectra of modified peptides to amino acid sequences in the protein database.
Yates JR 3rd, Eng JK, McCormack AL, Schieltz D., Anal. Chem. 67(8), 1995
PMID: 7741214
Yates JR 3rd, Eng JK, McCormack AL, Schieltz D., Anal. Chem. 67(8), 1995
PMID: 7741214
ProbID: a probabilistic algorithm to identify peptides through sequence database searching using tandem mass spectral data.
Zhang N, Aebersold R, Schwikowski B., Proteomics 2(10), 2002
PMID: 12422357
Zhang N, Aebersold R, Schwikowski B., Proteomics 2(10), 2002
PMID: 12422357
Amino acid residue specific stable isotope labeling for quantitative proteomics.
Zhu H, Pan S, Gu S, Bradbury EM, Chen X., Rapid Commun. Mass Spectrom. 16(22), 2002
PMID: 12415544
Zhu H, Pan S, Gu S, Bradbury EM, Chen X., Rapid Commun. Mass Spectrom. 16(22), 2002
PMID: 12415544
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 19808875
PubMed | Europe PMC
Suchen in