Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “proteomics database”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 757 records · Page 42Linked to original sources
PubMedDate not supplied

[InterPro as a new tool for whole genome analysis. A comparative analysis of Mycobacterium tuberculosis, Bacillus subtilis and Escherichia coli as a case study].

InterPro was developed as a new integrated documentation resource for protein families, domains and functional sites to rationalize the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects and has applications in computational functional classification of newly determined sequences lacking biochemical characterization and in comparative genome analysis. InterPro contains over 3500 entries, with more than 1000000 hits in SWISS-PROT and TrEMBL. The database is accessible for text- and sequence-based searches at http://www.ebi.ac.uk/interpro/. InterPro was used for whole proteome analysis of the pathogenic microorganism, Mycobacterium tuberculosis, and comparison with the predicted protein coding sequences of the complete genomes of Bacillus subtilis and Escherichia coli. 64.8% of the M. tuberculosis proteins in the proteome matched InterPro entries, and these could be classified according to function. The comparison with B. subtilis and E. coli provided information on the most common protein families and domains, and the most highly represented families in each organism. InterPro thus provides a useful tool for global views of whole proteomes and their compositions.

Bacillus subtilis↗
PubMed2000

The 1999 SWISS-2DPAGE database update.

SWISS-2DPAGE (http://www.expasy.ch/ch2d/ ) is an annotated two-dimensional polyacrylamide gel electro-phoresis (2-DE) database established in 1993. The current release contains 24 reference maps from human and mouse biological samples, as well as from Saccharomyces cerevisiae, Escherichia coli and Dictyostelium discoideum origin. These reference maps have now 2824 identified spots, corresponding to 614 separate protein entries in the database, in addition to virtual entries for each SWISS-PROT sequence or any user-entered amino acids sequence. Last year improvements in the SWISS-2DPAGE database are as follows: three new maps have been created and several others have been updated; cross-references to newly built federated 2-DE databases have been added; new functions to access the data have been provided through the ExPASy proteomics server.

Animals↗
PubMed2005

Silicone/graphite coating for on-target desalting and improved peptide mapping performance of matrix-assisted laser desorption/ionization-mass spectrometry targets in proteomic experiments.

In two-dimensional gel electrophoresis-based proteomic experiments matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS) peptide mass fingerprinting is often the technique of choice in identifying proteins. Here, we present a novel surface coating technique for MALDI-MS targets that improves manual and automatic sample analysis. A mixture of silicone and graphite is spread in the form of a thin layer over the target. Due to the hydrophobicity of the coating, aqueous solutions can be applied to relatively small spots very precisely using a robotic system. At least four times more liquid can be concentrated on the same area compared to uncoated steel targets. alpha-cyano-4-hydrocinnamic acid crystallizes in form of very small crystals evenly distributed over the surface. The search for "hot spots" during the analysis is not necessary, which supports the automatic acquisition of data. The homogeneous crystal layer can be very effectively washed on-target without encountering major sample losses. This efficient washing and the focused application of aqueous samples replace expensive and time-consuming reversed phase micro column based sample clean-ups. When analyzing peptide mixtures, the signal intensities are up to five times higher than with preparations of the same un-desalted samples on steel targets, since four times more sample can be loaded. The mass resolution remains unaffected by the surface coating. After usage the coating can be removed, followed by a new coating avoiding any carry-over of sample to the next analysis. All these properties make the precoating of MALDI-MS targets with a silicone/graphite layer an ideal technique for routine analysis in large-scale proteomic experiments.

Autoanalysis↗
PubMed2003

Toxicogenomic approach for assessing toxicant-related disease.

The problems of identifying environmental factors involved in the etiology of human disease and performing safety and risk assessments of drugs and chemicals have long been formidable issues. Three principal components for predicting potential human health risks are: (1) the diverse structure and properties of thousands of chemicals and other stressors in the environment; (2) the time and dose parameters that define the relationship between exposure and disease; and (3) the genetic diversity of organisms used as surrogates to determine adverse chemical effects. The global techniques evolving from successful genomics efforts are providing new exciting tools with which to address these intractable problems of environmental health and toxicology. In order to exploit the scientific opportunities, the National Institute of Environmental Health Sciences has created the National Center for Toxicogenomics (NCT). The primary mission of the NCT is to use gene expression technology, proteomics and metabolite profiling to create a reference knowledge base that will allow scientists to understand mechanisms of toxicity and to be able to predict the potential toxicity of new chemical entities and drugs. A principal scientific objective underpinning the use of microarray analysis of chemical exposures is to demonstrate the utility of signature profiling of the action of drugs or chemicals and to utilize microarray methodologies to determine biomarkers of exposure and potential adverse effects. The initial approach of the NCT is to utilize proof-of-principle experiments in an effort to "phenotypically anchor" the altered patterns of gene expression to conventional parameters of toxicity and to define dose and time relationships in which the expression of such signature genes may precede the development of overt toxicity. The microarray approach is used in conjunction with proteomic techniques to identify specific proteins that may serve as signature biomarkers. The longer-range goal of these efforts is to develop a reference relational database of chemical effects in biological systems (CEBS) that can be used to define common mechanisms of toxicity, chemical and drug actions, to define cellular pathways of response, injury and, ultimately, disease. In order to implement this strategy, the NCT has created a consortium of research organizations and private sector companies to actively collaborative in populating the database with high quality primary data. The evolution of discrete databases to a knowledge base of toxicogenomics will be accomplished through establishing relational interfaces with other sources of information on the structure and activity of chemicals such as that of the National Toxicology Program (NTP) and with databases annotating gene identity, sequence, and function.

Animals↗
PubMed2005

MOLE: a data management application based on a protein production data model.

MOLE (mining, organizing, and logging experiments) has been developed to meet the growing data management and target tracking needs of molecular biologists and protein crystallographers. The prototype reported here will become a Laboratory Information Management System (LIMS) to help protein scientists manage the large amounts of laboratory data being generated due to the acceleration in proteome research and will furthermore facilitate collaborations between groups based at different sites. To achieve this, MOLE is based on the data model for protein production devised at the European Bioinformatics Institute (Pajon A, et al., Proteins in press).

Algorithms↗
PubMed2003

Protein database of Caenorhabditis elegans.

Whole genome sequencing of the free-living nematode Caenorhabditis elegans is a prominent achievement in genomics and uncovers the existence of enormous known and unknown gene products. Characterization and linking of all gene products are the next challenging theme of biology. Genome-wide researches are already progressing on C. elegans and the fruits of these efforts are accessible through the internet. To link the sequence-function relationship, proteomic research has been applied to provide comprehensive information of the worm proteins. In addition to 2-dimensional gel electrophoresis for visualization of the proteome, recent advances in liquid chromatography (LC)-based technologies have allowed the large-scale analysis of proteins and are at cutting-edge of high-throughput analysis of focused proteome.

Animals↗
PubMedDate not supplied

Defining absolute confidence limits in the identification of Caulobacter proteins by peptide mass mapping.

A derivatization reaction, guanidination, was recently reported that increases MALDI-TOF MS sensitivity toward lysine-terminated peptides. Its application conveys sequence information that can be used as a parameter in peptide mass mapping database searches. This paper presents a systematic study of the impact of guanidination on proteomic analysis of an entire bacterial organelle. Sixty-two 2-D gel isolated proteins from Caulobacter crescentus stalks were studied. A novel computer algorithm, Prodigies, was developed to analyze the data. Absolute confidence limits associated with protein assignments were established using Monte Carlo simulations of database searches. The advantages of guanidination are illustrated using both experimental and theoretical data.

Algorithms↗
PubMed2026

Pathway-driven target prioritisation in drug discovery.

Genome-scale association studies and functional screens routinely implicate hundreds of candidate genes per disease, yet only a few will be clinically validated as drug targets. Choosing which to pursue is a central drug-discovery decision that depends on interpreting each candidate in its biological context. Curated pathway databases provide this context, while enrichment analysis applies it at scale, turning gene-level signals from genome-wide association, transcriptomic, proteomic and CRISPR studies into mechanistic hypotheses for prioritisation. This review examines how pathway-based methods inform target prioritisation, the databases and tools available for this purpose, and why pathway co-membership should be viewed as a starting point for validation rather than as evidence of causal involvement.

CRISPR↗
PubMed2003

Analysis of sequence periodicity in E. coli proteins: empirical investigation of the "duplication and divergence" theory of protein evolution.

Periodicity was quantified in 4289 Escherichia coli K12 confirmed and putative protein sequences, using a simple chi-square technique previously shown to reveal triplet period periodicity in coding DNA. Periodicities were calculated from period n = 2 to period n = 50 in nine different alphabetic representations of the proteins. By comparison with a randomly generated proteome of the same compositional content, the E. coli proteome does not contain a significant excess of periodic proteins. However, 60 proteins do appear to be significantly periodic in at least one alphabetic representation, after Bonferroni correction, at p < 0.01, and 30 at p < 0.001. These are compared with significantly periodic proteins of solved three-dimensional structure, detected by an identical analysis of the sequences from a protein structure database. It is concluded that there is no evidence for the presence of a proteome-wide quasi-periodicity as predicted by the "duplication and divergence" model of protein evolution and that the major periodicity detected is a consequence of the repetitive tendencies within alpha-helices. However, it is not possible to explain all sequence periodicities in terms of observable secondary structure, as in cases where sequence periodicity can be compared to solved structure, there is often no structural regularity that would provide an obvious explanation in terms of natural selection on protein function.

Databases, Protein↗
PubMed2004

Comparative genomics: prediction of the ciliary and basal body proteome.

Defects in mammalian cilia lead to a range of diseases, but our understanding of the composition of these organelles and of the basal bodies from which they arise is limited. Two recent studies used comparative genomics to predict the ciliary and basal body proteomes, providing datasets that are rich sources of human disease gene candidates.

Animals↗
PubMed2006

Application of FTTP to alpha-helix or beta-strand motifs.

Information concerning protein structure is widely dispersed and cannot easily and rapidly be processed by the biological community. We present a database of tendentious factors of three states of tripeptide units from PDB database, called a bank of tendentious factors of three states of three-peptide units (FTTP). The FTTP database was constructed based on conformational dihedral angle (varphi,psi) library of 20(3) peptide triplets by exhaustively searching through PDB databases. We introduce the FTTP database for the analysis of characteristics common to relative conformational biases of all peptide triplets, especially finding some motifs apt to alpha-helix and beta-strand. Our results show that this will provide a platform for studies of short peptide motifs, folding codons, secondary structure and three-dimensional (3D) structure of proteins. Moreover, FTTP is a unique resource that will allow a comprehensive characterization of peptide triplets and thus improve our understanding of sequence-structure relationship, refined domains, 3D structures, and their associated function. We believe the FTTP database will help biologists in increasing the efficiency of finding useful and relevant information regarding structure-function relationship of proteins. Therefore, this approach will play an important role in protein folding, protein engineering, molecular design, and proteomics.

Amino Acid Motifs↗
PubMed2006

Isotope-coded affinity tags for protein quantification.

An important goal in proteomics is to compare the relative amounts of different proteins in biological samples and to try to correlate these differences with changes in physiological state. The isotopecoded affinity tag technique pioneered in Aebersold's laboratory takes advantage of differential tagging of cysteine residues in proteins with stable isotopes to significantly reduce the complexity of peptide mixtures and increase the number of sequences that are identified in a single tandem mass spectrometry experiment. In this approach, two samples are isotopically labeled (one heavy, one light) through a reactive group that specifically binds to cysteine residues; the samples are combined, separated with chromatography, and analyzed by mass spectrometry. The results are then database searched and a list of hundreds of proteins and their heavy:light ratio is obtained.

Avidin↗
PubMed2005

Protein and peptide identification algorithms using MS for use in high-throughput, automated pipelines.

Current proteomics experiments can generate vast quantities of data very quickly, but this has not been matched by data analysis capabilities. Although there have been a number of recent reviews covering various aspects of peptide and protein identification methods using MS, comparisons of which methods are either the most appropriate for, or the most effective at, their proposed tasks are not readily available. As the need for high-throughput, automated peptide and protein identification systems increases, the creators of such pipelines need to be able to choose algorithms that are going to perform well both in terms of accuracy and computational efficiency. This article therefore provides a review of the currently available core algorithms for PMF, database searching using MS/MS, sequence tag searches and de novo sequencing. We also assess the relative performances of a number of these algorithms. As there is limited reporting of such information in the literature, we conclude that there is a need for the adoption of a system of standardised reporting on the performance of new peptide and protein identification algorithms, based upon freely available datasets. We go on to present our initial suggestions for the format and content of these datasets.

Algorithms↗
PubMed2003

Proteomics and transcriptomics analyses of secretagogin down-regulation in human non-functional pituitary adenomas.

In order to explore the presence of, and the potential role of, secretagogin in human pituitary adenomas, an analytical strategy that integrated comparative proteomics and comparative transcriptomics was used to detect the protein and the mRNA expression, respectively, of secretagogin in human non-functional pituitary adenomas compared to controls. Proteomics methods included two-dimensional gel electrophoresis, 2D gel image analysis, mass spectrometry [matrix-assisted laser desorption/ionization-time of flight-peptide mass fingerprinting (MALDI-TOF PMF) and liquid chromatography-electrospray ionization-quadrupole-ion trap tandem mass spectrometry (LC-ESI-Q-IT MS/MS)], and database analysis. Transcriptomics methods included the GeneChip microarray, image processing, and data analysis. The proteomics and transcriptomics data demonstrated that secretagogin was significantly down-regulated at the protein and mRNA levels, respectively, in the human non-functional (NF) pituitary adenomas (NF-, LH+, FSH+, and FSH+ + LH+). For the secretagogin protein, the expression level was NF- < FSH+ + LH+ < FSH+ < LH+ < Control, with a range of down-regulation of 2.2-6.9 fold in non-functional pituitary adenomas compared to controls, with a significant difference (p < 0.001). For secretagogin mRNA, the expression level was NF- < LH+ < FSH+ + LH+ < FSH+ < Control, with a range of down-regulation of 1.8-18.6 fold in non-functional pituitary adenomas compared to controls that was significant (p < 0.05). The secretagogin protein expression correlated significantly with its mRNA expression. Those results suggest that secretagogin might play a role in human non-functional pituitary adenomas. This novel finding may provide clues to clarify the basic molecular mechanisms of pituitary adenoma formation, and to identify new tumor-related markers.

Adenoma↗
PubMed2004

Fine-tuning the prediction of sequences cleaved by signal peptidase II: a curated set of proven and predicted lipoproteins of Escherichia coli K-12.

A curated set of 81 proven and 44 predicted lipoproteins of Escherichia coli K-12 was defined with the combined use of a literature survey, a variety of predictive tools and human expertise. The well-documented Gram-negative proteome of E. coli K-12 was chosen to assess how the different approaches complement each other and to ensure a stable definition of a consistent set of lipoproteins. The results of detailed analysis of such proteins at the level of a single proteome are presented, corroborated and rationalized.

Amino Acid Motifs↗