Since more than a decade proteomics is the method of choice for the life science sector as genetics could not cure all human diseases. Unfortunately, the world of proteins is far more complex than the genome; and a proper analysis can be extremely expensive and time consuming. In addition, the need of standards, standard operation procedures (SOPs) and common rules is obvious. Therefore, the Hu...

Biological membranes are essential for cell viability. Their functional characteristics strongly depend on their protein content, which consists of transmembrane (integral) and peripherally associated membrane proteins. Both integral and peripheral inner membrane proteins mediate a plethora of biological processes. Whereas transmembrane proteins have characteristic hydrophobic stretches and can...

Proteomics is a branch in biology that aims to comprehensively characterize a proteome. Mass spectrometry based proteomics has proven to be the most powerful approach to achieve this goal. This thesis introduces statistical concepts to optimally design and validate shotgun proteomics experiments and thereby enables to efficiently achieve reliable and extensive proteome coverage. The first part ...

introduction the proteome is the full complement of proteins expressed by a cell or tissue at any given time or environmental condition. proteomics is the study and identification of this set or subset of proteins (abersold & man, 2003 cristea et al., 2004). whereas the genome is composed of all the potential genes that can be expressed as proteins, the proteome is composed of all proteins actu...

In clinical studies of statins (class of drugs lowering plasma cholesterol levels), transient low-molecular-weight proteinuria was observed. The causes of statin-induced proteinuria in the patient background of those studies (cardiovascular and kidney disease) are multifactorial and, therefore, a matter of debate. In light of this, it seemed interesting to investigate the effect of statins on t...

For nearly three decades, the sequence of the human mitochondrial genome (mtDNA) has provided a molecular framework for understanding maternally inherited diseases. However, the vast majority of human mitochondrial disorders are caused by nuclear genome defects, which is not surprising since the mtDNA encodes only 13 proteins. Advances in genomics, mass spectrometry, and computation have only r...

The next step in the understanding of the genome organization, after the determination of complete sequences, involves proteomics. The proteome includes the whole set of protein-protein interactions, and two recent independent studies have shown that its topology displays a number of surprising features shared by other complex networks, both natural and artificial. In order to understand the or...

Proteomics has proved invaluable in generating large-scale quantitative data; however, the development of systems approaches for examining the proteome in vivo has lagged behind. To evaluate protein abundance and localization on a proteome scale, we exploited the yeast GFP-fusion collection in a pipeline combining automated genetics, high-throughput microscopy, and computational feature analysi...

LOCATE is a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of mouse and human proteins. Over the past 2 years, the data in LOCATE have grown substantially. The database now contains high-quality localization data for 20% of the mouse proteome and general localization annotation for nearly 36% of the mouse proteome. The proteom...