


}, keywords = {Adenosine, Adenosine Triphosphate, Amino Acid Sequence, Bacterial Proteins, Computer Simulation, Humans, Models, Biological, Molecular Sequence Data, Mycobacterium tuberculosis, Protein Binding, Proteomics, Tuberculosis}, issn = {1879-1301}, doi = {10.1016/j.chembiol.2012.11.008}, author = {Ansong, Charles and Ortega, Corrie and Payne, Samuel H and Haft, Daniel H and Chauvign{\`e}-Hines, Lacie M and Lewis, Michael P and Ollodart, Anja R and Purvine, Samuel O and Shukla, Anil K and Fortuin, Suereta and Smith, Richard D and Adkins, Joshua N and Grundner, Christoph and Wright, Aaron T} } @article {497, title = {Coupled transcriptome and proteome analysis of human lymphotropic tumor viruses: insights on the detection and discovery of viral genes.}, journal = {BMC Genomics}, year = {2011}, abstract = {

BACKGROUND: Kaposi{\textquoteright}s sarcoma-associated herpesvirus (KSHV) and Epstein-Barr virus (EBV) are related human tumor viruses that cause primary effusion lymphomas (PEL) and Burkitt{\textquoteright}s lymphomas (BL), respectively. Viral genes expressed in naturally-infected cancer cells contribute to disease pathogenesis; knowing which viral genes are expressed is critical in understanding how these viruses cause cancer. To evaluate the expression of viral genes, we used high-resolution separation and mass spectrometry coupled with custom tiling arrays to align the viral proteomes and transcriptomes of three PEL and two BL cell lines under latent and lytic culture conditions.

RESULTS: The majority of viral genes were efficiently detected at the transcript and/or protein level on manipulating the viral life cycle. Overall the correlation of expressed viral proteins and transcripts was highly complementary in both validating and providing orthogonal data with latent/lytic viral gene expression. Our approach also identified novel viral genes in both KSHV and EBV, and extends viral genome annotation. Several previously uncharacterized genes were validated at both transcript and protein levels.

CONCLUSIONS: This systems biology approach coupling proteome and transcriptome measurements provides a comprehensive view of viral gene expression that could not have been attained using each methodology independently. Detection of viral proteins in combination with viral transcripts is a potentially powerful method for establishing virus-disease relationships.

}, keywords = {Genes, Viral, Herpesvirus 4, Human, Herpesvirus 8, Human, Humans, Mass Spectrometry, Proteome, Transcriptome}, doi = {10.1186/1471-2164-12-625}, author = {Dresang, Lindsay R and Teuton, Jeremy R and Feng, Huichen and Jacobs, Jon M and Camp, David G and Purvine, Samuel O and Gritsenko, Marina A and Li, Zhihua and Smith, Richard D and Sugden, Bill and Moore, Patrick S and Chang, Yuan} } @article {357, title = {Improved methods for the enrichment and analysis of glycated peptides.}, journal = {Anal Chem}, year = {2008}, abstract = {

Nonenzymatic glycation of tissue proteins has important implications in the development of complications of diabetes mellitus. Herein we report improved methods for the enrichment and analysis of glycated peptides using boronate affinity chromatography and electron-transfer dissociation mass spectrometry, respectively. The enrichment of glycated peptides was improved by replacing an off-line desalting step with an online wash of column-bound glycated peptides using 50 mM ammonium acetate, followed by elution with 100 mM acetic acid. The analysis of glycated peptides by MS/MS was improved by considering only higher charged (\> or = 3) precursor ions during data-dependent acquisition, which increased the number of glycated peptide identifications. Similarly, the use of supplemental collisional activation after electron transfer (ETcaD) resulted in more glycated peptide identifications when the MS survey scan was acquired with enhanced resolution. Acquiring ETD-MS/MS data at a normal MS survey scan rate, in conjunction with the rejection of both 1+ and 2+ precursor ions, increased the number of identified glycated peptides relative to ETcaD or the enhanced MS survey scan rate. Finally, an evaluation of trypsin, Arg-C, and Lys-C showed that tryptic digestion of glycated proteins was comparable to digestion with Lys-C and that both were better than Arg-C in terms of the number of glycated peptides and corresponding glycated proteins identified by LC-MS/MS.

}, keywords = {Blood Proteins, Boronic Acids, Chromatography, Affinity, Glycosylation, Humans, Peptide Fragments, Proteomics, Spectrometry, Mass, Electrospray Ionization}, doi = {10.1021/ac801704j}, author = {Zhang, Qibin and Schepmoes, Athena A and Brock, Jonathan W C and Wu, Si and Moore, Ronald J and Purvine, Samuel O and Baynes, John W and Smith, Richard D and Metz, Thomas O} } @article {367, title = {Targeted protein degradation by Salmonella under phagosome-mimicking culture conditions investigated using comparative peptidomics.}, journal = {Mol Cell Proteomics}, year = {2007}, abstract = {

The pathogen Salmonella enterica is known to cause both food poisoning and typhoid fever. Because of the emergence of antibiotic-resistant isolates and the threat of bioterrorism (e.g. contamination of the food supply), there is a growing need to study this bacterium. In this investigation, comparative peptidomics was used to study S. enterica serovar Typhimurium cultured in either a rich medium or in an acidic, low magnesium, and minimal nutrient medium designed to roughly mimic the macrophage phagosomal environment (within which Salmonella are known to survive). Native peptides from cleared cell lysates were enriched by using isopropanol extraction and analyzed by using both LC-MS/MS and LC-FTICR-MS. We identified and quantified 5,163 peptides originating from 682 proteins, and the data clearly indicated that compared with Salmonella cultured in the rich medium, cells cultured in the phagosome-mimicking medium had dramatically higher abundances of a wide variety of protein degradation products, especially from ribosomal proteins. Salmonella from the same cultures were also analyzed using traditional, bottom-up proteomic methods, and when the peptidomics and proteomics data were analyzed together, two clusters of proteins targeted for proteolysis were tentatively identified. Possible roles of targeted proteolysis by phagocytosed Salmonella are discussed.

}, keywords = {Bacterial Proteins, Chromatography, Liquid, Culture Media, Humans, Molecular Weight, Peptide Fragments, Phagosomes, Proteomics, Salmonella typhimurium, Tandem Mass Spectrometry}, doi = {10.1074/mcp.M600282-MCP200}, author = {Manes, Nathan P and Gustin, Jean K and Rue, Joanne and Mottaz, Heather M and Purvine, Samuel O and Norbeck, Angela D and Matthew E. Monroe and Zimmer, Jennifer S D and Metz, Thomas O and Adkins, Joshua N and Smith, Richard D and Heffron, Fred} }