Quantitative proteome analysis in cardiovascular physiology and pathology. I. Data processing

Grussenmeyer, Thomas; Meili-Butz, Silvia; Dieterle, Thomas; Traunecker, Emmanuel; Carrel, Thierry P; Lefkovits, Ivan (2008). Quantitative proteome analysis in cardiovascular physiology and pathology. I. Data processing. Journal of proteome research, 7(12), pp. 5211-20. Washington, D.C.: American Chemical Society 10.1021/pr8005292

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Methodological evaluation of the proteomic analysis of cardiovascular-tissue material has been performed with a special emphasis on establishing examinations that allow reliable quantitative analysis of silver-stained readouts. Reliability, reproducibility, robustness and linearity were addressed and clarified. In addition, several types of normalization procedures were evaluated and new approaches are proposed. It has been found that the silver-stained readout offers a convenient approach for quantitation if a linear range for gel loading is defined. In addition, a broad range of a 10-fold input (loading 20-200 microg per gel) fulfills the linearity criteria, although at the lowest input (20 microg) a portion of protein species will remain undetected. The method is reliable and reproducible within a range of 65-200 microg input. The normalization procedure using the sum of all spot intensities from a silver-stained 2D pattern has been shown to be less reliable than other approaches, namely, normalization through median or through involvement of interquartile range. A special refinement of the normalization through virtual segmentation of pattern, and calculation of normalization factor for each stratum provides highly satisfactory results. The presented results not only provide evidence for the usefulness of silver-stained gels for quantitative evaluation, but they are directly applicable to the research endeavor of monitoring alterations in cardiovascular pathophysiology.

Item Type:

Journal Article (Original Article)

Division/Institute:

04 Faculty of Medicine > Department of Cardiovascular Disorders (DHGE) > Clinic of Cardiovascular Surgery

UniBE Contributor:

Carrel, Thierry

ISSN:

1535-3893

ISBN:

19367704

Publisher:

American Chemical Society

Language:

English

Submitter:

Factscience Import

Date Deposited:

04 Oct 2013 15:05

Last Modified:

04 May 2014 23:20

Publisher DOI:

10.1021/pr8005292

PubMed ID:

19367704

Web of Science ID:

000261478700016

URI:

https://boris.unibe.ch/id/eprint/28294 (FactScience: 119572)

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