Proteomics [2] is the large-scale study of proteomes. A proteome [3] is a set of proteins produced in an organism, system, or biological context. We may refer to, for instance, the proteome of a species (for example, Homo sapiens) or an organ (for example, the liver). The proteome is not constant; it differs from cell to cell and changes over time. To some degree, the proteome reflects the unde...

Urine, reflecting many changes in the body, is a better source than blood for biomarker discovery. However, even under physiological conditions, the urine proteome often varies. Understanding how various regulating factors affect urine proteome helps link changes to urine proteome with urinary biomarkers of physiological conditions as well as corresponding diseases. To evaluate the possible imp...

With the completion of the genome project, it has been viewed that the proteome is the next major challenge. With heightened expectations comes the need for organizing public effort. The Human Proteome Organization (HUPO) was founded to regroup scientists in the public and private sectors engaged worldwide in various aspects of proteomics. Over the past year, HUPO has strived to develop a missi...

As the first step to discover protein disease biomarkers from saliva, global analyses of the saliva proteome have been carried out since the early 2000s, and more than 3,000 proteins have been identified in human saliva. Recently, ethnic differences in the human plasma proteome have been reported, but such corresponding studies on human saliva in this aspect have not been previously reported. T...

MHC class I (MHC-I) molecules present a blueprint of the intracellular proteome to T cells allowing them control infection or malignant transformation. As response, pathogens and tumor often downmodulate MHC-I mediated antigen presentation escape from immune surveillance. Although fundamental rules are known in detail, players this system not saturated new modules regulation have recently been ...

Proteome profiling techniques rely on the separation of proteins or peptides and their subsequent quantification. The reliability of this technique is still limited because a proteome profiling result does not necessarily represent the true protein composition of the analysed sample, thus seriously hampering proper data interpretation. Many experimentally observed proteome alterations are biolo...

Studies in the MMTV-PyMT (PyMT) breast cancer mouse model have shown a strong influence of the lysosomal cysteine cathepsins B or L on lung metastasis formation. Transgenic expression of human CTSB (tgCTSB) or CTSL (tgCTSL) both led to similar metastatic phenotypes with increased metastatic burden in the PyMT mice. However, recent studies in other tumor models proved marked differences in effec...

Proteome was coined by Marc Wilkins, which he used for the entire complement of protein expressed by a genome, cell, tissue or organism. Proteomics is the study and characterization of complete set of proteins that are present in cell, organ, or organism at a given time [1]. Unlike genomes proteomes have both temporal and spatial variations which escalate the complexity of its study. However, t...

Recent advances in peptide-based (bottom-up) quantitative proteomics and bioinformatics have opened unprecedented opportunities for extensive investigation of cellular proteomes and their dynamics. Here we discuss two approaches currently used to investigate the global dynamics of phosphorylation based on the isolation of phosphorylated proteins or peptides. We evaluate the accuracy of these me...

Although the genome contains all the information necessary for maintenance and perpetuation of life, it is the proteome that repairs, duplicates and expresses the genome and actually performs most cellular functions. Here we reveal strong phenotypes of physiological oxidative proteome damage at the functional and genomic levels. Genome-wide mutations rates and biosynthetic capacity were monitor...