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Results for “Integrated proteomics”

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PubMed2026

Plasma proteins are integral to cross-tissue gene regulatory networks implicated in cardiometabolic disorders and coronary artery disease.

The plasma proteome has demonstrated promise for identifying diagnostic markers for cardiometabolic disorders (CMDs) and coronary artery disease (CAD). However, identifying the organ of origin for these biomarkers is critical for establishing biological relevance. We performed a multi-omic integrative analysis across multiple tissues from the STARNET study by profiling 974 plasma proteins in 532 CAD patients, integrating RNA sequencing (RNA-seq) data from the arterial wall, major metabolic organs, and blood. We identified 144 cis-protein quantitative trait loci in plasma, colocalizing with tissue cis-expression quantitative trait loci. Additionally, by mapping tissue mRNA "seed genes," we traced 262 plasma proteins to their source organs, primarily the liver. Crucially, we found that 851 plasma proteins are associated with the activity of cross-tissue gene regulatory networks (GRNs), including GRNs implicated in CMD and CAD development. Our findings demonstrate that plasma proteins are integral components of GRNs, with potential for developing reliable diagnostics and precise therapeutic targets. A record of this paper's transparent peer review process is included in the supplemental information.

cardiometabolic disorders↗

PubMed2006

Persistent biases in the amino acid composition of prokaryotic proteins.

Correspondence analysis of 28 proteomes selected to span the entire realm of prokaryotes revealed universal biases in the proteins' amino acid distribution. Integral Inner Membrane Proteins always form an individual cluster, which can then be used to predict protein localisation in unknown proteomes, independently of the organism's biotope or kingdom. Orphan proteins are consistently rich in aromatic residues. Another bias is also ubiquitous: the amino acid composition is driven by the G + C content of the first codon position. An unexpected bias is driven, in many proteomes, by the AAN box of the genetic code, suggesting some functional biochemical relationship between asparagine and lysine. Less-significant biases are driven by the rare amino acids, cysteine and tryptophan. Some allow identification of species-specific functions or localisation such as surface or exported proteins. Errors in genome annotations are also revealed by correspondence analysis, making it useful for quality control and correction.

Amino Acids↗

PubMed2005

The continuing evolution of shotgun proteomics.

Shotgun proteomics has emerged as a powerful approach for the analysis of complex protein mixtures, including biofluids, tissues, cells, organelles or protein complexes. Having evolved from the integration of chromatography and mass spectrometry, innovations in sample preparation, multidimensional chromatography, mass spectrometry and proteomic informatics continually facilitate, enable and challenge shotgun proteomics. As a result, shotgun proteomics continues to evolve and enable new areas of biological research, and is beginning to impact human disease diagnosis and therapeutic intervention.

Chromatography, High Pressure Liquid↗

PubMed2001

Location effects of a reporter gene on expression levels and on native protein synthesis in Lactococcus lactis and Saccharomyces cerevisiae.

The engineering of industrially important genetically modified organisms by the integration of heterologous genes into the chromosome is often the method of choice for several reasons concerned with long-term stability, homogeneous population distribution, and the enabling of selection without the addition of antibiotics. However, integration may disrupt endogenous gene expression, giving rise to increased levels of toxic metabolic byproducts or activating otherwise silent genes. The position of integration of a foreign gene in the chromosome can also influence its expression levels, and this effect will be of relevance in terms of optimizing protein production parameters. In this study, we determine how the random integration of a foreign reporter gene might affect expression levels and assess the use of proteome analysis to investigate possible effects on synthesis of endogenous proteins in two important food-relevant microorganisms, Saccharomyces cerevisiae and Lactococcus lactis. Eleven L. lactis integrants carrying the gusA gene were analyzed, and expression levels were found to vary by a factor of threefold in contrast to expression levels of lacZ in 18 S. cerevisiae integrants, which showed a 14-fold variation. Of relevance to industry is whether any changes in expression levels might occur as a consequence of storage of the modified strains. Here it is also shown that the above differences in expression levels were not significantly affected by storage of frozen cultures over a period of several months. Analysis of the protein composition of the yeast and lactococcal integrant strains by separation on one-dimensional (1D) and 2D gels showed no significant variations in position beyond those observed in control samples.

Bacterial Proteins↗

PubMed2026

A functional atlas of transposon-encoded products and their integration into host networks.

Transposable elements (TEs) are pervasive genomic components that propagate via self-encoded factors, yet the nature, regulation, and function of these factors remain largely unresolved. Here, we integrated extensive long- and short-read transcriptome data, regulatory network analyses, deep proteomics, and structural predictions to construct a comprehensive atlas of TE products in Arabidopsis. We show that TE expression is embedded within host regulatory circuits, with DNA methylation and transcription factors jointly shaping TE transcriptional activity. Proteomic analyses confirm the production of over a hundred of high-confidence TE-encoded proteins, and structure-guided analyses of the transcript-informed TE proteome predict previously uncharacterized structural folds, multimerization capacity, and host protein interaction potential. Structural alignments further uncover cryptic homologies between TE-encoded proteins and host factors, including cases of domestications and co-options. Together, our study reveals the functional integration of TEs into cellular pathways and underscores the role of TEs as active drivers of genome function and innovation.

Arabidopsis↗

PubMed2006

MannDB - a microbial database of automated protein sequence analyses and evidence integration for protein characterization.

BACKGROUND: MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. DESCRIPTION: MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. CONCLUSION: MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high-priority agents on the websites of several governmental organizations concerned with bio-terrorism. MannDB provides the user with a BLAST interface for comparison of native and non-native sequences and a query tool for conveniently selecting proteins of interest. In addition, the user has access to a web-based browser that compiles comprehensive and extensive reports. Access to MannDB is freely available at http://manndb.llnl.gov/.

Algorithms↗

PubMed2003

Integrating 'omic' information: a bridge between genomics and systems biology.

The availability of genome sequences for several organisms, including humans, and the resulting first-approximation lists of genes, have allowed a transition from molecular biology to 'modular biology'. In modular biology, biological processes of interest, or modules, are studied as complex systems of functionally interacting macromolecules. Functional genomic and proteomic ('omic') approaches can be helpful to accelerate the identification of the genes and gene products involved in particular modules, and to describe the functional relationships between them. However, the data emerging from individual omic approaches should be viewed with caution because of the occurrence of false-negative and false-positive results and because single annotations are not sufficient for an understanding of gene function. To increase the reliability of gene function annotation, multiple independent datasets need to be integrated. Here, we review the recent development of strategies for such integration and we argue that these will be important for a systems approach to modular biology.

Computational Biology↗

PubMed2006

Integrating medical and genomic data: a successful example for rare diseases.

The recent advances on genomics and proteomics research bring up a significant grow on the information that is publicly available. However, navigating through genetic and bioinformatics databases can be a too complex and unproductive task for a primary care physician. In this paper we present diseasecard, a web portal for rare disease that provides transparently to the user a virtually integration of distributed and heterogeneous information.

Computational Biology↗

PubMed2003

Gel and polymer-solution mediated separation of biopolymers by capillary electrophoresis.

In the age of genomics and proteomics, high-resolution separation techniques are routinely utilized in an integrated and automated fashion to solve formidable separation problems and provide the means for large-scale analysis of biological samples with excellent resolution. By automating the current manual procedures, capillary gel (CGE) and polymer-solution mediated electrophoresis greatly enhance the productivity of biopolymer analysis while also reducing both analysis time and the human intervention necessary from sample loading to data processing. The advent of this novel and high-performance bioseparation technique has made it possible to sequence the human genome and revealed global changes in the genome and proteome level, bringing about a revolutionary transition in our views of living systems on the molecular basis. CGE and polymer-solution mediated electrophoresis and related microseparation methods (e.g., electrophoresis microchips) are quickly becoming important separation and characterization tools in analytical biochemistry and molecular biology. This review gives an overview of the key application areas of DNA, protein, and complex carbohydrate analysis, and summarizes the latest developments on CGE column technology, including capillary coatings and sieving polymer matrices. Micropreparative aspects and related microseparation techniques are also discussed.

Biopolymers↗

PubMed2004

Monoliths for microfluidic devices in proteomics.

We report here on the preparation of monolithic capillary columns in view to their integration in a microsystem for on-chip sample preparation before their on-line analysis by electrospray and mass spectrometry (ESI-MS). These monolithic columns are based on polymer materials and consist of reverse phases for peptide separation and/or desalting. They were prepared using lauryl methacrylate (LMA), ethylene dimethacrylate (EDMA) as well as a suitable porogenic mixture composed of cyclohexanol and ethylene glycol. The resulting stationary phases present thus a C12-functionality. The LMA-based columns were first prepared in a capillary format using capillary tubing of 75 microm i.d. and tested in nanoLC-MS experiments for the separation of a commercial Cytochrome C digest composed of 12 peptidic fragments whose isoelectric point values and hydrophobic character cover a wide range. The LMA-based columns were capable of separating the peptidic fragments and their performances were seen to be similar as those of standard commercial columns dedicated to proteomic purposes with calculated separation efficiencies up to 145 x 10(3) plates/m. Monolithic LMA-based phases were then successfully polymerized in microchannels fabricated using the negative photoresist SU-8. After the polymerization, the systems were seen to withstand the pressures applied during the nanoLC-MS separation tests that were carried out in the same conditions as for the monolithic capillary columns. The pressure drop during these tests of the in-microchannel monoliths was as high as 50 bar; however, the separation was not as good as for a capillary format which could be accounted for by the monolith dimensions.

Amino Acid Sequence↗

PubMed2005

Glycomics: an integrated systems approach to structure-function relationships of glycans.

In comparison with genomics and proteomics, the advancement of glycomics has faced unique challenges in the pursuit of developing analytical and biochemical tools and biological readouts to investigate glycan structure-function relationships. Glycans are more diverse in terms of chemical structure and information density than are DNA and proteins. This diversity arises from glycans' complex nontemplate-based biosynthesis, which involves several enzymes and isoforms of these enzymes. Consequently, glycans are expressed as an 'ensemble' of structures that mediate function. Moreover, unlike protein-protein interactions, which can be generally viewed as 'digital' in regulating function, glycan-protein interactions impinge on biological functions in a more 'analog' fashion that can in turn 'fine-tune' a biological response. This fine-tuning by glycans is achieved through the graded affinity, avidity and multivalency of their interactions. Given the importance of glycomics, this review focuses on areas of technologies and the importance of developing a bioinformatics platform to integrate the diverse datasets generated using the different technologies to allow a systems approach to glycan structure-function relationships.

Animals↗

PubMed2006

Quantitative proteomics and its applications for systems biology.

Here we discuss the current state of research in the rapidly growing field of quantitative proteomics and its applications to systems biology. Quantitative proteomics can be successfully used for characterizing alterations in protein abundance, finding novel protein-protein and protein-peptide interactions, investigating formation of large macromolecular complexes, and elucidating temporal changes in organellar protein composition and phosphorylation in signal transduction cascades. Further, quantitative proteomics can directly compare activation of entire signaling networks in response to individual stimuli and discover critical differences in their circuits that account for alterations of cell response. Maturation of proteomic bioinformatics applications and continuous improvements in proteomics and related genomics and transcriptomics technologies now allows us to investigate cellular mechanisms at the integrative system level.

Animals↗

PubMed2004

Informatics platform for global proteomic profiling and biomarker discovery using liquid chromatography-tandem mass spectrometry.

We have developed an integrated suite of algorithms, statistical methods, and computer applications to support large-scale LC-MS-based gel-free shotgun profiling of complex protein mixtures using basic experimental procedures. The programs automatically detect and quantify large numbers of peptide peaks in feature-rich ion mass chromatograms, compensate for spurious fluctuations in peptide signal intensities and retention times, and reliably match related peaks across many different datasets. Application of this toolkit markedly facilitates pattern recognition and biomarker discovery in global comparative proteomic studies, simplifying mechanistic investigation of physiological responses and the detection of proteomic signatures of disease.

Algorithms↗

PubMed2026

Enrichment Performance Assessment of Extracellular Vesicles Using Different Functionalized Magnetic Materials and Application in Urinary Proteomics of Prostate Cancer.

Extracellular vesicles (EVs) are lipid bilayer nanovesicles that mediate intercellular communication and hold significant potential for clinical applications. Although material-based isolation strategies offer promising alternatives to conventional methods, their relative performances have not been systematically evaluated. In this study, we conducted a comparative assessment of magnetic nanomaterials with distinct surface functionalities, including metal oxides (TiO2), metal-organic frameworks (UiO-66), biopolymeric materials (chitosan), and lipid probes (DSPE-PEG, DOPE-PEG, and CLS-PEG). A comprehensive evaluation across multiple dimensions including capture capacity, capture rate, sample volume, and product purity reveals that the bifunctional magnetic nanomaterial Fe3O4@UiO-66@DSPE material exhibits superior EV capture performance. This material enables the efficient and stable enrichment of high-purity EVs by synergizing Zr4+-phosphate coordination with lipid bilayer anchoring, and preserves EV biological integrity and activity. Meanwhile, this method could be highly compatible with proteomics, and over 1000 proteins are identified by proteomic analysis of urinary EVs, while 34 proteins are upregulated and 25 proteins are downregulated in prostate cancer patients relative to healthy donors. Notably, the differentially expressed proteins, such as AGT, ITIH4, and PGLYRP2, are associated with disease progression. Overall, this work highlights the superior performance of the Fe3O4@UiO-66@DSPE material for efficient and selective EV isolation. It provides a powerful tool for clinical liquid biopsy and proteomic biomarker discovery, enabling early diagnosis, prognostic evaluation, and precision therapy.

Humans↗

PubMed2006

INTEGRATOR: interactive graphical search of large protein interactomes over the Web.

BACKGROUND: The rapid growth of protein interactome data has elevated the necessity and importance of network analysis tools. However, unlike pure text data, network search spaces are of exponential complexity. This poses special challenges for storing, searching, and navigating this data efficiently. Moreover, development of effective web interfaces has been difficult. RESULTS: We present Integrator, a web-integrated graphical search tool for protein-protein interaction networks across 50+ genomes. CONCLUSION: Integrator provides single and multiple protein searches of the Bioverse database containing experimentally-derived and predicted protein-protein interactions. The interface provides animated local network views, rapid subgraph manipulation, and cross-referencing of functional annotations. Integrator is available at http://bioverse.compbio.washington.edu/integrator.

Algorithms↗

PubMed2004

A proteomic analysis of thioacetamide-induced hepatotoxicity and cirrhosis in rat livers.

Thioacetamide (TAA) administration is an established technique for generating rat models of liver fibrosis and cirrhosis. Oxidative stress is believed to be involved as TAA-induced liver fibrosis is initiated by thioacetamide S-oxide, which is derived from the biotransformation of TAA by the microsomal flavine-adenine dinucleotide (FAD)-containing monooxygense (FMO) and cytochrome P450 systems. A two-dimensional gel electrophoresis-mass spectrometry approach was applied to analyze the protein profiles of livers of rats administered with sublethal doses of TAA for 3, 6 and 10 weeks respectively. With this approach, 59 protein spots whose expression levels changed significantly upon TAA administration were identified, including three novel proteins. These proteins were then sorted according to their common biochemical properties and functions, so that pathways involved in the pathogenesis of rat liver fibrosis due to TAA-induced toxicity could be elucidated. As a result, it was found that TAA-administration down-regulated the enzymes of the primary metabolic pathways such as fatty acid beta-oxidation, branched chain amino acids and methionine breakdown. This phenomenon is suggestive of the depletion of succinyl-CoA which affects heme and iron metabolism. Up-regulated proteins, on the other hand, are related to oxidative stress and lipid peroxidation. Finally, these proteomics data and the data obtained from the scientific literature were integrated into an "overview model" for TAA-induced liver cirrhosis. This model could now serve as a useful resource for researchers working in the same area.

Animals↗

PubMed2002

PATIKA: an integrated visual environment for collaborative construction and analysis of cellular pathways.

MOTIVATION: Availability of the sequences of entire genomes shifts the scientific curiosity towards the identification of function of the genomes in large scale as in genome studies. In the near future, data produced about cellular processes at molecular level will accumulate with an accelerating rate as a result of proteomics studies. In this regard, it is essential to develop tools for storing, integrating, accessing, and analyzing this data effectively. RESULTS: We define an ontology for a comprehensive representation of cellular events. The ontology presented here enables integration of fragmented or incomplete pathway information and supports manipulation and incorporation of the stored data, as well as multiple levels of abstraction. Based on this ontology, we present the architecture of an integrated environment named Patika (Pathway Analysis Tool for Integration and Knowledge Acquisition). Patika is composed of a server-side, scalable, object-oriented database and client-side editors to provide an integrated, multi-user environment for visualizing and manipulating network of cellular events. This tool features automated pathway layout, functional computation support, advanced querying and a user-friendly graphical interface. We expect that Patika will be a valuable tool for rapid knowledge acquisition, microarray generated large-scale data interpretation, disease gene identification, and drug development. AVAILABILITY: A prototype of Patika is available upon request from the authors.

Cell Physiological Phenomena↗

PubMed2003

Proteomics approaches to elucidation of signal transduction pathways.

Recent applications have shown that proteomics can provide crucial new information regarding cellular signaling processes. Bottom-up and small-scale top-down proteomics approaches related to routine biochemical methods have become widely applied to identify new aspects of established signaling pathways. Top-down, global proteomics methods are developing rapidly and are beginning to deliver information on global integration of signaling processes that has been difficult to obtain with conventional approaches.

ErbB Receptors↗