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Zeng, Zhi,Hincapie, Marina,Pitteri, Sharon J.,Hanash, Samir,Schalkwijk, Joost,Hogan, Jason M.,Wang, Hong,Hancock, William S. American Chemical Society 2011 ANALYTICAL CHEMISTRY - Vol.83 No.12
<P>The discovery of breast cancer associated plasma/serum biomarkers is important for early diagnosis, disease mechanism elucidation, and determination of treatment strategy for the disease. In this study of serum samples, a multidimensional fractionation platform combined with mass spectrometric analysis were used to achieve the identification of medium to lower abundance proteins, as well as to simultaneously detect glycan and abundance changes. Immuno-affinity depletion and multi-lectin chromatography (M-LAC) were integrated into an automated HPLC platform to remove high abundance protein and fractionate glycoproteins. The collected glycoproteomes were then subjected to isoelectric focusing (IEF) separation by a digital ProteomeChip (dPC), followed by in-gel digestion and LC–MS analysis using an Orbitrap mass spectrometer. As a result, the total number of identified proteins increased significantly when the IEF fractionation step was included as part of the platform. Relevant proteins with biological and disease significance were observed and the dynamic range of the serum proteome measurement was extended. In addition, potential glycan changes were indicated by comparing proteins in control and cancer samples in terms of their affinity to the multi-lectin column (M-LAC) and the p<I>I</I> profiles in IEF separation. In conclusion, a proteomics platform including high abundance protein depletion, lectin affinity fractionation, IEF separation, and LC–MS analysis has been applied to discover breast cancer-associated proteins. The following candidates, thrombospondin-1 and 5, alpha-1B-glycoprotein, serum amyloid P-component, and tenascin-X, were selected as promising examples of the use of this platform. They show potential abundance and glycan changes and will be further investigated in future studies.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/ancham/2011/ancham.2011.83.issue-12/ac2002802/production/images/medium/ac-2011-002802_0006.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ac2002802'>ACS Electronic Supporting Info</A></P>
The Chromosome-Centric Human Proteome Project for cataloging proteins encoded in the genome
Paik, Young-Ki,Jeong, Seul-Ki,Omenn, Gilbert S,Uhlen, Mathias,Hanash, Samir,Cho, Sang Yun,Lee, Hyoung-Joo,Na, Keun,Choi, Eun-Young,Yan, Fangfei,Zhang, Fan,Zhang, Yue,Snyder, Michael,Cheng, Yong,Chen, Nature Publishing Group, a division of Macmillan P 2012 Nature biotechnology Vol.30 No.3
Liu, Suli,Im, Hogune,Bairoch, Amos,Cristofanilli, Massimo,Chen, Rui,Deutsch, Eric W.,Dalton, Stephen,Fenyo, David,Fanayan, Susan,Gates, Chris,Gaudet, Pascale,Hincapie, Marina,Hanash, Samir,Kim, Hoguen American Chemical Society 2013 JOURNAL OF PROTEOME RESEARCH Vol.12 No.1
<P>We report progress assembling the parts list for chromosome 17 and illustrate the various processes that we have developed to integrate available data from diverse genomic and proteomic knowledge bases. As primary resources, we have used GPMDB, neXtProt, PeptideAtlas, Human Protein Atlas (HPA), and GeneCards. All sites share the common resource of Ensembl for the genome modeling information. We have defined the chromosome 17 parts list with the following information: 1169 protein-coding genes, the numbers of proteins confidently identified by various experimental approaches as documented in GPMDB, neXtProt, PeptideAtlas, and HPA, examples of typical data sets obtained by RNASeq and proteomic studies of epithelial derived tumor cell lines (disease proteome) and a normal proteome (peripheral mononuclear cells), reported evidence of post-translational modifications, and examples of alternative splice variants (ASVs). We have constructed a list of the 59 “missing” proteins as well as 201 proteins that have inconclusive mass spectrometric (MS) identifications. In this report we have defined a process to establish a baseline for the incorporation of new evidence on protein identification and characterization as well as related information from transcriptome analyses. This initial list of “missing” proteins that will guide the selection of appropriate samples for discovery studies as well as antibody reagents. Also we have illustrated the significant diversity of protein variants (including post-translational modifications, PTMs) using regions on chromosome 17 that contain important oncogenes. We emphasize the need for mandated deposition of proteomics data in public databases, the further development of improved PTM, ASV, and single nucleotide variant (SNV) databases, and the construction of Web sites that can integrate and regularly update such information. In addition, we describe the distribution of both clustered and scattered sets of protein families on the chromosome. Since chromosome 17 is rich in cancer-associated genes, we have focused the clustering of cancer-associated genes in such genomic regions and have used the ERBB2 amplicon as an example of the value of a proteogenomic approach in which one integrates transcriptomic with proteomic information and captures evidence of coexpression through coordinated regulation.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/jprobs/2013/jprobs.2013.12.issue-1/pr300985j/production/images/medium/pr-2012-00985j_0009.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/pr300985j'>ACS Electronic Supporting Info</A></P>
주형건(Hyung Goun Joo),이대영(Dae Young Lee),장다콴(Da Quan Zhang),이강용(Kang Yong Lee),아잠 카미스(Essam Khamis Ibrahim Al-Hanash) 대한기계학회 2009 大韓機械學會論文集A Vol.33 No.4
The protection for copper tarnish was developed by surface treatment method and volatile corrosion inhibiting (VCI) technology. The performance of surface treatment and VCI material is also examined in simulated test environment. Benzotriazole (BTAH) solution that contained molybdate showed best performance than others. Usage of VCI materials with surface treatment was more effective. The protection film foamed on the surface of copper was investigated by auger electron spectroscopy (AES) and X-ray photoelectron spectroscopy (XPS). Molybdate does not participate in the formation of the protective film but promotes the passivation effect. This facilitates the stabilization of the cuprous oxide film, and strengthens the adsorption of BTAH.
Kim, Yong-Sam,Son, Ok Lye,Lee, Ju Yeon,Kim, Sun Hee,Oh, Sejeong,Lee, Yoon Suk,Kim, Cheorl-Ho,Yoo, Jong Shin,Lee, Jeong-Hwa,Miyoshi, Eiji,Taniguchi, Naoyuki,Hanash, Samir M.,Yoo, Hyang Sook,Ko, Jeong H WILEY-VCH Verlag 2008 Proteomics Vol.8 No.16
<P>N-acetylglucosaminyltransferase V (GnT-V) has been reported to be upregulated in malignant cancer cells, and its targets have been sought after with regard to biomarker identification. The low capacity and high false positive rates of 2-DE gel-based lectin blots using phytohemagglutinin-L<SUB>4</SUB> (L-PHA) prompted us to develop a novel protocol for identifying GnT-V targets, in which serum proteins were subjected to immunodepletion, alkylation, and lectin precipitation using L-PHA coupled to avidin–agarose bead complexes, and tryptic digestion. Proteins captured by L-PHA conjugates were analyzed by a nano-LC-FT-ICR/LTQ MS. Here, we report 26 candidate biomarkers for colorectal cancer (CRC) that show 100% specificity and sensitivities of greater than 50%. Not only can these candidate proteins be used as analytes for validation, but the novel protocol described herein can be applied to biomarker discovery in nonCRCs. </P>