• [26] Smaller projects have also used protein structure prediction to help map the proteome of individual organisms, for example provides coverage of multiple protein
    isoforms for over 20,000 genes in the human genome.

  • Numerous methods are available to study proteins, sets of proteins, or the whole proteome.

  • Size and contents The genomes of viruses and prokaryotes encode a relatively well-defined proteome as each protein can be predicted with high confidence, based on its open
    reading frame (in viruses ranging from ~3 to ~1000, in bacteria ranging from about 500 proteins to about 10,000).

  • A cellular proteome is the collection of proteins found in a particular cell type under a particular set of environmental conditions such as exposure to hormone stimulation.

  • Wilkins used the term to describe the entire complement of proteins expressed by a genome, cell, tissue or organism.

  • [9] Comparative proteomic analyses of 11 cell lines demonstrated the similarity between the metabolic processes of each cell line; 11,731 proteins were completely identified
    from this study.

  • It can also be useful to consider an organism’s complete proteome, which can be conceptualized as the complete set of proteins from all of the various cellular proteomes.

  • The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time.

  • By using antibodies specific to the protein of interest, it is possible to probe for the presence of specific proteins from a mixture of proteins.

  • Much like the human genome project, these projects seek to find and collect evidence for all predicted protein coding genes in the human genome.

  • [6] Importance in cancer The proteome can be used in order to comparatively analyze different cancer cell lines.

  • The term proteome has also been used to refer to the collection of proteins in certain sub-cellular systems, such as organelles.

  • The Human Proteome Map currently (October 2020) claims 17,294 proteins and ProteomicsDB 15,479, using different criteria.

  • [7] The differences in protein expression can help identify novel cancer signaling mechanisms.

  • This study profiled 30 histologically normal human samples resulting in the identification of proteins coded by 17,294 genes.

  • The term dark proteome coined by Perdigão and colleagues, defines regions of proteins that have no detectable sequence homology to other proteins of known three-dimensional
    structure and therefore cannot be modeled by homology.

  • It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions.

  • Proteomic studies have been used in order to identify the likelihood of metastasis in bladder cancer cell lines KK47 and YTS1 and were found to have 36 unregulated and 74
    down regulated proteins.

  • [15] However, most protein prediction algorithms use certain cut-offs, such as 50 or 100 amino acids, so small proteins are often missed by such predictions.

  • It allows for very sensitive separation of different kinds of proteins based on their affinity for a matrix.

  • [27] Protein databases The Human Protein Atlas contains information about the human proteins in cells, tissues, and organs.

  • Because the range in protein contents in plasma is very large, it is difficult to detect proteins that tend to be scarce when compared to abundant proteins.

  • [25] Protein structure prediction[edit] Protein structure prediction can be used to provide three-dimensional protein structure predictions of whole proteomes.


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