TY  - JOUR
AB  - 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.
DA  - 2011
DO  - 10.1186/1477-5956-9-30
LA  - eng
IS  - 1
PY  - 2011
SN  - 1477-5956
T2  - Proteome Science
TI  - A guide through the computational analysis of isotope-labeled mass spectrometry-based quantitative proteomics data: an application study
UR  - https://nbn-resolving.org/urn:nbn:de:0070-pub-23000631
Y2  - 2024-11-21T21:03:10
ER  -