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Search Results: 1 - 10 of 176919 matches for " Matthew E Monroe "
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Estimating probabilities of peptide database identifications to LC-FTICR-MS observations
Kevin K Anderson, Matthew E Monroe, Don S Daly
Proteome Science , 2006, DOI: 10.1186/1477-5956-4-1
Abstract: After a tryptically digested protein mixture is analyzed by LC-FTICR-MS, the observed masses and normalized elution times of the detected features are statistically matched to the theoretical masses and elution times of known peptides listed in a large database. The probability of matching is estimated for each peptide in the reference database using statistical classification methods assuming bivariate Gaussian probability distributions on the uncertainties in the masses and the normalized elution times.A database of 69,220 features from 32 LC-FTICR-MS analyses of a tryptically digested bovine serum albumin (BSA) sample was matched to a database populated with 97% false positive peptides. The percentage of high confidence identifications was found to be consistent with other database search procedures. BSA database peptides were identified with high confidence on average in 14.1 of the 32 analyses. False positives were identified on average in just 2.7 analyses.Using a priori probabilities that contrast peptides from expected and unexpected proteins was shown to perform better in identifying target peptides than using equally likely a priori probabilities. This is because a large percentage of the target peptides were similar to unexpected peptides which were included to be false positives. The use of triplicate analyses with a "2 out of 3" reporting rule was shown to have excellent rejection of false positives.The high-throughput determination of the identities and abundances of peptides and proteins in a biological sample is important to systems biology research. Although many different proteomics methodologies are in use today, Pacific Northwest National Laboratory (PNNL) has implemented a high-throughput process based on multiple mass spectrometry technologies, including liquid chromatography coupled to Fourier transform ion cyclotron resonance mass spectrometry (LC-FTICR-MS) [1-4]. This high-throughput process is diagramed in Figure 1.The PNNL proteomic analys
Comparative Bacterial Proteomics: Analysis of the Core Genome Concept
Stephen J. Callister, Lee Ann McCue, Joshua E. Turse, Matthew E. Monroe, Kenneth J. Auberry, Richard D. Smith, Joshua N. Adkins, Mary S. Lipton
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0001542
Abstract: While comparative bacterial genomic studies commonly predict a set of genes indicative of common ancestry, experimental validation of the existence of this core genome requires extensive measurement and is typically not undertaken. Enabled by an extensive proteome database developed over six years, we have experimentally verified the expression of proteins predicted from genomic ortholog comparisons among 17 environmental and pathogenic bacteria. More exclusive relationships were observed among the expressed protein content of phenotypically related bacteria, which is indicative of the specific lifestyles associated with these organisms. Although genomic studies can establish relative orthologous relationships among a set of bacteria and propose a set of ancestral genes, our proteomics study establishes expressed lifestyle differences among conserved genes and proposes a set of expressed ancestral traits.
Phosphoproteomics Profiling of Human Skin Fibroblast Cells Reveals Pathways and Proteins Affected by Low Doses of Ionizing Radiation
Feng Yang,Katrina M. Waters,John H. Miller,Marina A. Gritsenko,Rui Zhao,Xiuxia Du,Eric A. Livesay,Samuel O. Purvine,Matthew E. Monroe,Yingchun Wang,David G. Camp II,Richard D. Smith,David L. Stenoien
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0014152
Abstract: High doses of ionizing radiation result in biological damage; however, the precise relationships between long-term health effects, including cancer, and low-dose exposures remain poorly understood and are currently extrapolated using high-dose exposure data. Identifying the signaling pathways and individual proteins affected at the post-translational level by radiation should shed valuable insight into the molecular mechanisms that regulate dose-dependent responses to radiation.
Dynamic proteomic profiling of a unicellular cyanobacterium Cyanothece ATCC51142 across light-dark diurnal cycles
Uma K Aryal, Jana St?ckel, Ravi K Krovvidi, Marina A Gritsenko, Matthew E Monroe, Ronald J Moore, David W Koppenaal, Richard D Smith, Himadri B Pakrasi, Jon M Jacobs
BMC Systems Biology , 2011, DOI: 10.1186/1752-0509-5-194
Abstract: To expand upon the current knowledge of protein expression patterns in Cyanothece ATCC51142, we performed quantitative proteomic analysis using partial ("unsaturated") metabolic labeling and high mass accuracy LC-MS analysis. This dynamic proteomic profiling identified 721 actively synthesized proteins with significant temporal changes in expression throughout the light-dark cycles, of which 425 proteins matched with previously characterized cycling transcripts. The remaining 296 proteins contained a cluster of proteins uniquely involved in DNA replication and repair, protein degradation, tRNA synthesis and modification, transport and binding, and regulatory functions. Functional classification of labeled proteins suggested that proteins involved in respiration and glycogen metabolism showed increased expression in the dark cycle together with nitrogenase, suggesting that N2-fixation is mediated by higher respiration and glycogen metabolism. Results indicated that Cyanothece ATCC51142 might utilize alternative pathways for carbon (C) and nitrogen (N) acquisition, particularly, aspartic acid and glutamate as substrates of C and N, respectively. Utilization of phosphoketolase (PHK) pathway for the conversion of xylulose-5P to pyruvate and acetyl-P likely constitutes an alternative strategy to compensate higher ATP and NADPH demand.This study provides a deeper systems level insight into how Cyanothece ATCC51142 modulates cellular functions to accommodate photosynthesis and N2-fixation within the single cell.Oxygenic photosynthetic cyanobacteria are widely recognized for their important role in the global carbon cycle [1], and have generated significant interest as a potential solution for carbon-neutral energy production and carbon (C) sequestration [2]. Some unicellular cyanobacteria such as Cyanothece and Crocosphaera are also capable of biological N2-fixation (diazotrophic) [3], and play a significant role in marine nitrogen (N) cycle [4]. One of the most important
Experimental annotation of post-translational features and translated coding regions in the pathogen Salmonella Typhimurium
Charles Ansong, Nikola Toli?, Samuel O Purvine, Steffen Porwollik, Marcus Jones, Hyunjin Yoon, Samuel H Payne, Jessica L Martin, Meagan C Burnet, Matthew E Monroe, Pratap Venepally, Richard D Smith, Scott N Peterson, Fred Heffron, Michael McClelland, Joshua N Adkins
BMC Genomics , 2011, DOI: 10.1186/1471-2164-12-433
Abstract: We experimentally annotated the bacterial pathogen Salmonella Typhimurium 14028, using "shotgun" proteomics to accurately uncover the translational landscape and post-translational features. The data provide protein-level experimental validation for approximately half of the predicted protein-coding genes in Salmonella and suggest revisions to several genes that appear to have incorrectly assigned translational start sites, including a potential novel alternate start codon. Additionally, we uncovered 12 non-annotated genes missed by gene prediction programs, as well as evidence suggesting a role for one of these novel ORFs in Salmonella pathogenesis. We also characterized post-translational features in the Salmonella genome, including chemical modifications and proteolytic cleavages. We find that bacteria have a much larger and more complex repertoire of chemical modifications than previously thought including several novel modifications. Our in vivo proteolysis data identified more than 130 signal peptide and N-terminal methionine cleavage events critical for protein function.This work highlights several ways in which application of proteomics data can improve the quality of genome annotations to facilitate novel biological insights and provides a comprehensive proteome map of Salmonella as a resource for systems analysis.Many aspects of modern biological research are dependent on accurate identification of the protein-coding genes in each genome, as well as the nature of the mature functional protein products, a process commonly referred to as genome annotation. With the exponential increase in the number of sequenced prokaryotic genomes afforded by advances in genome sequencing technologies over the last decade, present day prokaryotic genome annotation is essentially an automated high-throughput process that relies heavily on de novo gene prediction programs [1-3].While de novo gene prediction programs have significantly improved for prokaryotic genomes consider
High and Low Doses of Ionizing Radiation Induce Different Secretome Profiles in a Human Skin Model
Qibin Zhang, Melissa Matzke, Athena A. Schepmoes, Ronald J. Moore, Bobbie-Jo Webb-Robertson, Zeping Hu, Matthew E. Monroe, Wei-Jun Qian, Richard D. Smith, William F. Morgan
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0092332
Abstract: It is postulated that secreted soluble factors are important contributors of bystander effect and adaptive responses observed in low dose ionizing radiation. Using multidimensional liquid chromatography-mass spectrometry based proteomics, we quantified the changes of skin tissue secretome – the proteins secreted from a full thickness, reconstituted 3-dimensional skin tissue model 48 hr after exposure to 3, 10 and 200 cGy of X-rays. Overall, 135 proteins showed statistical significant difference between the sham (0 cGy) and any of the irradiated groups (3, 10 or 200 cGy) on the basis of Dunnett adjusted t-test; among these, 97 proteins showed a trend of downregulation and 9 proteins showed a trend of upregulation with increasing radiation dose. In addition, there were 21 and 8 proteins observed to have irregular trends with the 10 cGy irradiated group either having the highest or the lowest level among all three radiated doses. Moreover, two proteins, carboxypeptidase E and ubiquitin carboxyl-terminal hydrolase isozyme L1 were sensitive to ionizing radiation, but relatively independent of radiation dose. Conversely, proteasome activator complex subunit 2 protein appeared to be sensitive to the dose of radiation, as rapid upregulation of this protein was observed when radiation doses were increased from 3, to 10 or 200 cGy. These results suggest that different mechanisms of action exist at the secretome level for low and high doses of ionizing radiation.
Top-Down Characterization of the Post-Translationally Modified Intact Periplasmic Proteome from the Bacterium Novosphingobium aromaticivorans
Si Wu,Roslyn N. Brown,Samuel H. Payne,Da Meng,Rui Zhao,Nikola Toli?,Li Cao,Anil Shukla,Matthew E. Monroe,Ronald J. Moore,Mary S. Lipton,Ljiljana Pa?a-Toli?
International Journal of Proteomics , 2013, DOI: 10.1155/2013/279590
Abstract: The periplasm of Gram-negative bacteria is a dynamic and physiologically important subcellular compartment where the constant exposure to potential environmental insults amplifies the need for proper protein folding and modifications. Top-down proteomics analysis of the periplasmic fraction at the intact protein level provides unrestricted characterization and annotation of the periplasmic proteome, including the post-translational modifications (PTMs) on these proteins. Here, we used single-dimension ultra-high pressure liquid chromatography coupled with the Fourier transform mass spectrometry (FTMS) to investigate the intact periplasmic proteome of Novosphingobium aromaticivorans. Our top-down analysis provided the confident identification of 55 proteins in the periplasm and characterized their PTMs including signal peptide removal, N-terminal methionine excision, acetylation, glutathionylation, pyroglutamate, and disulfide bond formation. This study provides the first experimental evidence for the expression and periplasmic localization of many hypothetical and uncharacterized proteins and the first unrestrictive, large-scale data on PTMs in the bacterial periplasm. 1. Introduction The periplasm of Gram-negative bacteria is a hydrated gel located between the cytoplasmic and outer membranes and is comprised of peptidoglycan (cell wall), proteins, carbohydrates, and small solutes [1–3]. The periplasm is a dynamic subcellular compartment important for trafficking of molecules into and out of cells, maintaining cellular osmotic balance, envelope structure, responding to environmental cues and stresses, electron transport, xenobiotic metabolism, and protein folding and modification [4]. The periplasm provides a good model system to study protein biogenesis, composition, sorting, and modification at the molecular level. Indeed, it is analogous in many ways to the endoplasmic reticulum of eukaryotic cells in terms of transport, folding, and quality control [3]. Localization to the periplasm and beyond often involves an N-terminal secretion signal that targets the protein for translocation across the cytoplasmic membrane via the general secretory pathway [5]. These secretion signals (also known as signal peptides) are cleaved by signal peptidases located in the cytoplasmic membrane [6]. Thus, it is expected that signal peptide cleavage is a common modification in the periplasmic proteome. Compared to the cytoplasm, the periplasm is more vulnerable to changes in pH, temperature, and osmolarity in the external environment [4, 7, 8]. For structural stability in
Integrative Analysis of the Mitochondrial Proteome in Yeast
Holger Prokisch,Curt Scharfe,David G. Camp II,Wenzhong Xiao,Lior David,Christophe Andreoli,Matthew E. Monroe,Ronald J. Moore,Marina A. Gritsenko,Christian Kozany,Kim K. Hixson,Heather M. Mottaz,Hans Zischka,Marius Ueffing,Zelek S. Herman,Ronald W. Davis,Thomas Meitinger,Peter J. Oefner,Richard D. Smith,Lars M. Steinmetz
PLOS Biology , 2012, DOI: 10.1371/journal.pbio.0020160
Abstract: In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans.
Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae
Alexandra C. Schrimpe-Rutledge, Marcus B. Jones, Sadhana Chauhan, Samuel O. Purvine, James A. Sanford, Matthew E. Monroe, Heather M. Brewer, Samuel H. Payne, Charles Ansong, Bryan C. Frank, Richard D. Smith, Scott N. Peterson, Vladimir L. Motin, Joshua N. Adkins
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0033903
Abstract: Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. The annotation process is now performed almost exclusively in an automated fashion to balance the large number of sequences generated. One possible way of reducing errors inherent to automated computational annotations is to apply data from omics measurements (i.e. transcriptional and proteomic) to the un-annotated genome with a proteogenomic-based approach. Here, the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species. Transcriptomic and proteomic data derived from highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis Pestoides F, and Y. pseudotuberculosis PB1/+) was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 incorrect (i.e., observed frameshifts, extended start sites, and translated pseudogenes) protein-coding sequences within the three current genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent pathogen, thus the discovery of many translated pseudogenes, including the insertion-ablated argD, underscores a need for functional analyses to investigate hypotheses related to divergence. Refinements included the discovery of a seemingly essential ribosomal protein, several virulence-associated factors, a transcriptional regulator, and many hypothetical proteins that were missed during annotation.
Integrative Analysis of the Mitochondrial Proteome in Yeast
Holger Prokisch equal contributor,Curt Scharfe equal contributor,David G Camp II equal contributor,Wenzhong Xiao equal contributor,Lior David,Christophe Andreoli,Matthew E Monroe,Ronald J Moore,Marina A Gritsenko,Christian Kozany,Kim K Hixson,Heather M Mottaz,Hans Zischka,Marius Ueffing,Zelek S Herman,Ronald W Davis,Thomas Meitinger,Peter J Oefner,Richard D Smith,Lars M Steinmetz
PLOS Biology , 2004, DOI: 10.1371/journal.pbio.0020160
Abstract: In this study yeast mitochondria were used as a model system to apply, evaluate, and integrate different genomic approaches to define the proteins of an organelle. Liquid chromatography mass spectrometry applied to purified mitochondria identified 546 proteins. By expression analysis and comparison to other proteome studies, we demonstrate that the proteomic approach identifies primarily highly abundant proteins. By expanding our evaluation to other types of genomic approaches, including systematic deletion phenotype screening, expression profiling, subcellular localization studies, protein interaction analyses, and computational predictions, we show that an integration of approaches moves beyond the limitations of any single approach. We report the success of each approach by benchmarking it against a reference set of known mitochondrial proteins, and predict approximately 700 proteins associated with the mitochondrial organelle from the integration of 22 datasets. We show that a combination of complementary approaches like deletion phenotype screening and mass spectrometry can identify over 75% of the known mitochondrial proteome. These findings have implications for choosing optimal genome-wide approaches for the study of other cellular systems, including organelles and pathways in various species. Furthermore, our systematic identification of genes involved in mitochondrial function and biogenesis in yeast expands the candidate genes available for mapping Mendelian and complex mitochondrial disorders in humans.
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