The MELANIE project: From a biopsy to automatic protein map interpretation by computer

Appel, Ron D.; Hochstrasser, Denis F.; Funk, Matthieu; Vargas, Javier; Pellegrini, Christian; Müller, Alex F.; Scherrer, Jean-Raoul

doi:10.1002/elps.1150121006

Cited by 153 publications

(63 citation statements)

References 25 publications

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“…It has been continually refined over the years [16,17]. Extensive literature also exists on other programs developed in the early eighties, such as the Tycho system [18], Melanie [19][20][21], GELLAB [22], and the GESA processing system [23], to name just a few (for more on these early systems, see [24,25]). Once a gel has been scanned, advanced algorithms are available for removing background noise, gel artefacts, and horizontal or vertical streaking from the image.…”

Section: A Practical Example: the Pdquest Systemmentioning

confidence: 99%

Numerical approaches for quantitative analysis of two‐dimensional maps: A review of commercial software and home‐made systems

et al. 2005

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The present review attempts to cover a number of methods that have appeared in the last few years for performing quantitative proteome analysis. However, due to the large number of methods described for both electrophoretic and chromatographic approaches, we have limited this review to conventional two-dimensional (2-D) map analysis which couples orthogonally a charge-based step (isoelectric focusing) to a size-based separation step (sodium dodecyl sulfateelectrophoresis). The first and oldest method applied to 2-D map data reduction is based on statistical analysis performed on sets of gels via powerful software packages, such as Melanie, PDQuest, Z3 and Z4000, Phoretix and Progenesis. This method calls for separately running a number of replicas for control and treated samples. The two sets of data are then merged and compared via a number of software packages which we describe. In addition to commerciallyavailable systems, a number of home made approaches for 2-D map comparison have been recently described and are also reviewed. They are based on fuzzyfication of the digitized 2-D gel image coupled to linear discriminant analysis, three-way principal component analysis or a combination of principal component analysis and soft-independent modeling of class analogy. These statistical tools appear to perform well in differential proteomic studies.

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Section: A Practical Example: the Pdquest Systemmentioning

confidence: 99%

Numerical approaches for quantitative analysis of two‐dimensional maps: A review of commercial software and home‐made systems

et al. 2005

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“…A variety of commercial 2-DE analysis software packages are available to perform such tasks in a highly reproducible and automated manner, e.g. ImageMaster (GE Healthcare), PDQuest (BioRad) and Progenesis (Nonlinear Dynamics) (Garrels, 1989;Appel et al, 1991;Rosengren et al, 2003;Medberry et al, 2005).…”

Section: Historical Overview Of 2-dementioning

confidence: 99%

Two-dimensional gel electrophoresis in bacterial proteomics

et al. 2012

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Two-dimensional gel electrophoresis (2-DE) is a gel-based technique widely used for analyzing the protein composition of biological samples. It is capable of resolving complex mixtures containing more than a thousand protein components into individual protein spots through the coupling of two orthogonal biophysical separation techniques: isoelectric focusing (first dimension) and polyacrylamide gel electrophoresis (second dimension). 2-DE is ideally suited for analyzing the entire expressed protein complement of a bacterial cell: its proteome. Its relative simplicity and good reproducibility have led to 2-DE being widely used for exploring proteomics within a wide range of environmental and medically-relevant bacteria. Here we give a broad overview of the basic principles and historical development of gel-based proteomics, and how this powerful approach can be applied for studying bacterial biology and physiology. We highlight specific 2-DE applications that can be used to analyze when, where and how much proteins are expressed. The links between proteomics, genomics and mass spectrometry are discussed. We explore how proteomics involving tandem mass spectrometry can be used to analyze (post-translational) protein modifications or to identify proteins of unknown origin by de novo peptide sequencing. The use of proteome fractionation techniques and non-gel-based proteomic approaches are also discussed. We highlight how the analysis of proteins secreted by bacterial cells (secretomes or exoproteomes) can be used to study infection processes or the immune response. This review is aimed at non-specialists who wish to gain a concise, comprehensive and contemporary overview of the nature and applications of bacterial proteomics.

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“…The first softwares were designed on the basis of those used by astronomers for nocturnal mapping of stars, one such software being named 'Tycho' in honour of the famous astronomer Tycho Brahe (1546-1601) [39]. At the end of the 20th century, other pioneering softwares like Kepler from Large Scale Biology Corporation (Rockville, USA) and MELANIE from the Swiss Institute of Bioinformatics were developed [40]. Over the past decade, an important number of commercial softwares involving more powerful algorithms and statistical tools than the previous generations of such programs were designed to help researchers deal with the sheer quantity of data produced.…”

Section: Brief History On the Creation And Use Of Computer Softwaresmentioning

confidence: 99%

The pitfalls of proteomics experiments without the correct use of bioinformatics tools

Biron¹,

Brun²,

Lefèvre³

et al. 2006

Proteomics

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The elucidation of the entire genomic sequence of various organisms, from viruses to complex metazoans, most recently man, is undoubtedly the greatest triumph of molecular biology since the discovery of the DNA double helix. Over the past two decades, the focus of molecular biology has gradually moved from genomes to proteomes, the intention being to discover the functions of the genes themselves. The postgenomic era stimulated the development of new techniques (e.g. 2-DE and MS) and bioinformatics tools to identify the functions, reactions, interactions and location of the gene products in tissues and/or cells of living organisms. Both 2-DE and MS have been very successfully employed to identify proteins involved in biological phenomena (e.g. immunity, cancer, host-parasite interactions, etc.), although recently, several papers have emphasised the pitfalls of 2-DE experiments, especially in relation to experimental design, poor statistical treatment and the high rate of 'false positive' results with regard to protein identification. In the light of these perceived problems, we review the advantages and misuses of bioinformatics tools -from realisation of 2-DE gels to the identification of candidate protein spots -and suggest some useful avenues to improve the quality of 2-DE experiments. In addition, we present key steps which, in our view, need to be to taken into consideration during such analyses. Lastly, we present novel biological entities named 'interactomes', and the bioinformatics tools developed to analyse the large proteinprotein interaction networks they form, along with several new perspectives of the field.

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The MELANIE project: From a biopsy to automatic protein map interpretation by computer

Cited by 153 publications

References 25 publications

Numerical approaches for quantitative analysis of two‐dimensional maps: A review of commercial software and home‐made systems

Numerical approaches for quantitative analysis of two‐dimensional maps: A review of commercial software and home‐made systems

Two-dimensional gel electrophoresis in bacterial proteomics

The pitfalls of proteomics experiments without the correct use of bioinformatics tools

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