A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study

Albaum S, Hahne H, Otto A, Haußmann U, Becher D, Poetsch A, Goesmann A, Nattkemper TW (2011)
Proteome Science 9(1): 30.

Zeitschriftenaufsatz | Veröffentlicht | Englisch
 
Download
OA
Autor/in
; ; ; ; ; ; ;
Abstract / Bemerkung
Background: Mass spectrometry-based proteomics has reached a stage where it is possible to comprehensively analyze the whole proteome of a cell in one experiment. Here, the employment of stable isotopes has become a standard technique to yield relative abundance values of proteins. In recent times, more and more experiments are conducted that depict not only a static image of the up- or down-regulated proteins at a distinct time point but instead compare developmental stages of an organism or varying experimental conditions. Results: Although the scientific questions behind these experiments are of course manifold, there are, nevertheless, two questions that commonly arise: 1) which proteins are differentially regulated regarding the selected experimental conditions, and 2) are there groups of proteins that show similar abundance ratios, indicating that they have a similar turnover? We give advice on how these two questions can be answered and comprehensively compare a variety of commonly applied computational methods and their outcomes. Conclusions: This work provides guidance through the jungle of computational methods to analyze mass spectrometry-based isotope-labeled datasets and recommends an effective and easy-to-use evaluation strategy. We demonstrate our approach with three recently published datasets on Bacillus subtilis [1,2] and Corynebacterium glutamicum [3]. Special focus is placed on the application and validation of cluster analysis methods. All applied methods were implemented within the rich internet application QuPE [4]. Results can be found at http://qupe.cebitec.uni-bielefeld.de webcite.
Erscheinungsjahr
2011
Zeitschriftentitel
Proteome Science
Band
9
Ausgabe
1
Seite(n)
30
ISSN
1477-5956
Finanzierungs-Informationen
Article Processing Charge funded by the Deutsche Forschungsgemeinschaft and the Open Access Publication Fund of Bielefeld University.
Page URI
https://pub.uni-bielefeld.de/record/2300063

Zitieren

Albaum S, Hahne H, Otto A, et al. A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study. Proteome Science. 2011;9(1):30.
Albaum, S., Hahne, H., Otto, A., Haußmann, U., Becher, D., Poetsch, A., Goesmann, A., et al. (2011). A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study. Proteome Science, 9(1), 30. doi:10.1186/1477-5956-9-30
Albaum, S., Hahne, H., Otto, A., Haußmann, U., Becher, D., Poetsch, A., Goesmann, A., and Nattkemper, T. W. (2011). A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study. Proteome Science 9, 30.
Albaum, S., et al., 2011. A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study. Proteome Science, 9(1), p 30.
S. Albaum, et al., “A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study”, Proteome Science, vol. 9, 2011, pp. 30.
Albaum, S., Hahne, H., Otto, A., Haußmann, U., Becher, D., Poetsch, A., Goesmann, A., Nattkemper, T.W.: A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study. Proteome Science. 9, 30 (2011).
Albaum, Stefan, Hahne, H., Otto, A., Haußmann, U., Becher, D., Poetsch, A., Goesmann, Alexander, and Nattkemper, Tim Wilhelm. “A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study”. Proteome Science 9.1 (2011): 30.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
This Item is protected by copyright and/or related rights. [...]
Volltext(e)
Access Level
OA Open Access
Zuletzt Hochgeladen
2019-09-06T08:57:36Z
MD5 Prüfsumme
cd6b7c0ccb37c84b9da6b0583ad79907

Export

Markieren/ Markierung löschen
Markierte Publikationen

Open Data PUB

Web of Science

Dieser Datensatz im Web of Science®

Quellen

PMID: 21663690
PubMed | Europe PMC

Suchen in

Google Scholar