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A draft map of Human Proteome

A draft map of Human Proteome

Over the past decade, the sequencing of human genome initiated a new era revolutionizing the biomedical research. But a map of human proteome with direct measurements of proteins and peptides does not exist yet. Interestingly, two individual groups of scientists  have recently published the draft map of the  human Proteome in  the May, 2014 issue of the same journal, “Nature”. One of the group includes researchers from John Hopkins University, USA and Institute of Bioinformatics in Bangalore, India led by Dr. Akhilesh Pandey and another group of researchers are from Technische Universitaet Muenchen (TUM), Germany, led by Dr.  Bernhard Küster.

Both teams utilized Mass spectrometry data for generating the map which is revolutionary for proteomics studies as next generation sequencing for genomics and transcriptomics. Studying protein is technically challenging than studying genes. Just a list of existing protein is not very helpful unless the accompanying information about the spatial and temporal production of the protein is known. The evidence for protein-coding potential is still largely driven by gene prediction algorithms or complementary DNAs and does not routinely include direct detection/ measurement of proteins/peptides. So in their studies, a large number of MS/MS spectra was found which does not match any annotated protein. These unmatched spectra helped discover over 808 annotations of new proteins. They uncovered new complexities of the human genome, identifying novel proteins and isoforms and tissue specific markers from regions of the genome previously thought to be non-coding.

Dr. Pandey’s team identified proteins encoded by 17,294 genes, which is about 84% of all the genes in the human genome predicted to encode proteins and Dr. Kuster’s team cataloged over 18000 proteins. Furthermore, Dr. Pandey’s team analyzed a variety of healthy human tissues, including seven types of fetal tissues and six types of hematopoetic cells and generated new MS data. The Küster group compiled already available raw mass spec data from databases and colleagues’ contributions. To fill in the data gaps, the Küster lab generated its own mass spec data, analyzing 60 human tissues, 13 body fluids, and 147 cancer cell lines. By using these datasets now researchers can improve the annotations of the genome as well as the algorithms for predicting transcription and translation. Integrating the information from both genomic and proteomic landscapes is likely to accelerate basic and translational research since it will help understand the gene-protein pathway networks more precisely.

The team led by Dr. Pandey has published their map in this large human Proteome catalogue (http://www.humanproteomemap.org) and the team led by Dr. Küster deposited the map in the ProteomicsDB site (http://www.proteomicsdb.org).

{Summarized  kindly by Ms Sabrina Elias at http://www.pbtlabdu.net/ currently at UNLinclon, under a fellowship sponsored by DU, UT Austin and Monsanto’s Beachell-Borlaug International Scholar Program]]

International Scholars Program.]

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