A 2D gel reference map of the basic human heart proteome
ABSTRACT We have undertaken the identification of basic proteins (pH 6-11) of the human heart using 2-DE. Tissue from the left ventricle of human heart was lysed and proteins were separated in the first dimension on pH 6-11 IPG strips using paper-bridge loading followed by separation on 12% SDS polyacrylamide gels in the second dimension. Proteins were then identified by mass spectrometry and analysed using Proline, a proteomic data analysis platform that was developed in-house. The proteome map contains 176 identified spots with 151 unique proteins and has been made available as part of the UCD-2DPAGE database at http://proteomics-portal.ucd.ie:8082. The associated mass spectrometry data have been submitted to PRIDE (Accession number ♯10098). This reference map, and the other heart reference maps available through the UCD-2DPAGE database, will aid further proteomic studies of heart diseases such as dilated cardiomyopathy and ischaemic heart disease.
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- "Recently, the Human Proteome Organization (HUPO) launched the Human Proteome Project (HPP), which generated a map of all the proteins in human tissue, both in normal and disease states . The protein map of several human tissues was characterized, including brain , heart  , kidney , pancreas  , liver  , and plasma   . Over 1000 human testicular proteins have been identified using 2DE combined with MS or 1D SDS-PAGE combined with LC   . "
ABSTRACT: The testes are where spermatogenesis, the sperm-generating process that is unique to men, occurs. Importantly, human spermatogenesis and tumorigenesis share key similarities. Until now, only a few proteins in the human testis have been identified due to limitations of available technology. In this paper, using an advanced proteomics platform, we have identified 7346 unique proteins within the human testis with a high degree of confidence. Immunohistochemistry data from the Human Protein Atlas database show over 90% (1833/2020) of identified proteins can be detected in the human testis using specific antibodies. To make the data widely available to the scientific community, an online Human Testis Proteome Database (HTPD, http://reprod.njmu.edu.cn/htpd/) was built. Many of the identified human testicular proteins are associated with human infertility, especially human testicular predominantly expressed proteins. We characterized six novel cancer/testis genes (TMPRSS12, TPPP2, PRSS55, DMRT1, PIWIL1, HEMGN), which map to cancer-associated genetic variants positions, in both the cancer and testis tissues using genome-wide analyses. Our results provide a molecular connection between spermatogenesis and tumorigenesis and broaden the range of cancer antigen choice available for immunotherapy.Proteomics 02/2013; 13(7). DOI:10.1002/pmic.201200489 · 3.97 Impact Factor
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ABSTRACT: Most protein PageRank studies do not use signal flow direction information in protein interactions because this information was not readily available in large protein databases until recently. Therefore, four questions have yet to be answered: A) What is the general difference between signal emitting and receiving in a protein interactome? B) Which proteins are among the top ranked in directional ranking? C) Are high ranked proteins more evolutionarily conserved than low ranked ones? D) Do proteins with similar ranking tend to have similar subcellular locations? In this study, we address these questions using the forward, reverse, and non-directional PageRank approaches to rank an information-directional network of human proteins and study their evolutionary conservation. The forward ranking gives credit to information receivers, reverse ranking to information emitters, and non-directional ranking mainly to the number of interactions. The protein lists generated by the forward and non-directional rankings are highly correlated, but those by the reverse and non-directional rankings are not. The results suggest that the signal emitting/receiving system is characterized by key-emittings and relatively even receivings in the human protein interactome. Signaling pathway proteins are frequent in top ranked ones. Eight proteins are both informational top emitters and top receivers. Top ranked proteins, except a few species-related novel-function ones, are evolutionarily well conserved. Protein-subunit ranking position reflects subunit function. These results demonstrate the usefulness of different PageRank approaches in characterizing protein networks and provide insights to protein interaction in the cell.PLoS ONE 09/2012; 7(9):e44872. DOI:10.1371/journal.pone.0044872 · 3.23 Impact Factor
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ABSTRACT: Within the past years, we have witnessed a great improvement in mass spectrometry (MS) and proteomics approaches in terms of instrumentation, protein fractionation, and bioinformatics. With the current technology, protein identification alone is no longer sufficient. Both scientists and clinicians want not only to identify proteins but also to identify the protein's posttranslational modifications (PTMs), protein isoforms, protein truncation, protein-protein interaction (PPI), and protein quantitation. Here, we describe the principle of MS and proteomics and strategies to identify proteins, protein's PTMs, protein isoforms, protein truncation, PPIs, and protein quantitation. We also discuss the strengths and weaknesses within this field. Finally, in our concluding remarks we assess the role of mass spectrometry and proteomics in scientific and clinical settings in the near future. This chapter provides an introduction and overview for subsequent chapters that will discuss specific MS proteomic methodologies and their application to specific medical conditions. Other chapters will also touch upon areas that expand beyond proteomics, such as lipidomics and metabolomics.Advances in Experimental Medicine and Biology 01/2014; 806:1-32. DOI:10.1007/978-3-319-06068-2_1 · 2.01 Impact Factor