Biomedical subjects

Weimin Zhu

Publications and source records attributed to Weimin Zhu.

26 records · Page 2Linked to original sources

PubMed2004

Common interchange standards for proteomics data: Public availability of tools and schema.

The Proteomics Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparision, exchange and verification. To this end, a Level 1 Molecular Interaction XML data exchange format has been developed which has been accepted for publication and is freely available at the PSI website (http.//psidev.sf.net/). Several major protein interaction databases are already making data available in this format. A draft XML interchange format for mass spectrometry data has been written and is currently undergoing evaluation whilst work is ongoing to develop a proteomics data integration model, MIAPE.

Computational Biology↗

PubMed2004

A common open representation of mass spectrometry data and its application to proteomics research.

A broad range of mass spectrometers are used in mass spectrometry (MS)-based proteomics research. Each type of instrument possesses a unique design, data system and performance specifications, resulting in strengths and weaknesses for different types of experiments. Unfortunately, the native binary data formats produced by each type of mass spectrometer also differ and are usually proprietary. The diverse, nontransparent nature of the data structure complicates the integration of new instruments into preexisting infrastructure, impedes the analysis, exchange, comparison and publication of results from different experiments and laboratories, and prevents the bioinformatics community from accessing data sets required for software development. Here, we introduce the 'mzXML' format, an open, generic XML (extensible markup language) representation of MS data. We have also developed an accompanying suite of supporting programs. We expect that this format will facilitate data management, interpretation and dissemination in proteomics research.

Database Management Systems↗

PubMed2004

The HUPO PSI's molecular interaction format--a community standard for the representation of protein interaction data.

A major goal of proteomics is the complete description of the protein interaction network underlying cell physiology. A large number of small scale and, more recently, large-scale experiments have contributed to expanding our understanding of the nature of the interaction network. However, the necessary data integration across experiments is currently hampered by the fragmentation of publicly available protein interaction data, which exists in different formats in databases, on authors' websites or sometimes only in print publications. Here, we propose a community standard data model for the representation and exchange of protein interaction data. This data model has been jointly developed by members of the Proteomics Standards Initiative (PSI), a work group of the Human Proteome Organization (HUPO), and is supported by major protein interaction data providers, in particular the Biomolecular Interaction Network Database (BIND), Cellzome (Heidelberg, Germany), the Database of Interacting Proteins (DIP), Dana Farber Cancer Institute (Boston, MA, USA), the Human Protein Reference Database (HPRD), Hybrigenics (Paris, France), the European Bioinformatics Institute's (EMBL-EBI, Hinxton, UK) IntAct, the Molecular Interactions (MINT, Rome, Italy) database, the Protein-Protein Interaction Database (PPID, Edinburgh, UK) and the Search Tool for the Retrieval of Interacting Genes/Proteins (STRING, EMBL, Heidelberg, Germany).

Database Management Systems↗

PubMed2004

Current status of proteomic standards development.

The generation of proteomic data is becoming ever more high throughput. Both the technologies and experimental designs used to generate and analyze data are becoming increasingly complex. The need for methods by which such data can be accurately described, stored and exchanged between experimenters and data repositories has been recognized. Work by the Proteome Standards Initiative of the Human Proteome Organization has laid the foundation for the development of standards by which experimental design can be described and data exchange facilitated. The Minimum Information About a Proteomic Experiment data model describes both the scope and purpose of a proteomics experiment and encompasses the development of more specific interchange formats such as the mzData model of mass spectrometry. The eXtensible Mark-up Language-MI data interchange format, which allows exchange of molecular interaction data, has already been published and major databases within this field are supplying data downloads in this format.

Databases, Protein↗

PubMed2003

Gas chromatography-mass spectrometry with solid-phase microextraction method for determination of methyl salicylate and other volatile compounds in leaves of Lycopersicon esculentum.

Methyl salicylate (MeSA) in many plants is a important signaling compound, which plays an important role in a pathogen-induced defense response. In this paper, gas chromatography-mass spectrometry (GC-MS) with headspace solid-phase microextraction (HS-SPME) was developed for determination of MeSA and other volatile compounds in leaves of a tomato plant (Lycopersicon esculentum). Tomato leaves were ground under liquid nitrogen and sampled by HS-SPME, with a 100 microm polydimethylsiloxane fiber, and finally analyzed by GC-MS. Eighteen compounds in the leaves of tomato plant infested by tobacco mosaic virus (TMV) were separated and identified, among them MeSA, which was quantitatively analyzed by the standard addition method. MeSA concentrations higher than 2.0 microg g(-1) fresh weight accumulated in leaves of TMV-infested tomato plant as the defense response to TMV. A similar concentration of MeSA in the leaves of MeSA-treated tomato plant was also found. No MeSA in leaves of control tomato plant was detected. These findings suggest that MeSA might be a signaling compound in the tomato plant response to TMV. The present method for determination of MeSA required only simple sample preparation and no organic solvent, and provided an excellent relative standard deviation of less than 5.0% and a low detection limit of 10 ng g(-1) fresh weight for MeSA. These results show that GC-MS-HS-SPME is a simple, rapid and sensitive method for determination of MeSA and other plant-signaling compounds in plant tissues.

Gas Chromatography-Mass Spectrometry↗

PubMed2003

Further advances in the development of a data interchange standard for proteomics data.

The Protein Standards Initiative (PSI) aims to define community standards for data representation in proteomics and to facilitate data comparison, exchange and verification. Significant progress was made in advancing the design and implementation of a draft standard for exchanging experimental data from proteomics experiments involving mass spectrometry at the 51st Annual Conference of the American Society for Mass Spectrometry. In collaboration with the American Society for Tests and Measurements, the PSI propose to publish this first draft at the forthcoming HUPO 2nd World Congress in Montreal, 8-11 October 2003.

Computational Biology↗

PubMedDate not supplied

Processing of serum proteins underlies the mass spectral fingerprinting of myocardial infarction.

The MALDI-TOF spectra of peptides from the sera of normal and myocardial infarction patients produced patterns that provided an accurate diagnostic of MI. In myocardial infarction, the spectral pattern originated from the cleavage of complement C3 alpha chain to release the C3f peptide and cleavage of fibrinogen to release peptide A. The fibrinogen peptide A and complement C3f peptide were in turn progressively truncated by aminopeptidases to produce two families of fragments that formed the characteristic spectral pattern of MI. Time course and inhibitor studies demonstrated that the peptide patterns in the serum reflect the balance of disease-specific-protease and aminopeptidase activity ex vivo.

Amino Acid Sequence↗

PubMedDate not supplied

Human serum proteins preseparated by electrophoresis or chromatography followed by tandem mass spectrometry.

Electrophoretic and chromatographic sample preparations were compared and together detected the presence of some 600 types of protein products in human serum. Proteins from crude serum preseparated by ionic electrophoresis, chromatography, or a combination of both were analyzed. Proteins were digested with trypsin or chymotrypsin. Naturally occurring peptides were also collected by reversed-phase chromatography. The resulting peptides were identified by tandem mass spectrometry. The peptides were either desorbed by a laser from a metal chip into a quadrupole-time-of-flight mass spectrometer or ionized as an electro-spray from reversed-phase chromatography via a metal needle under voltage into an ion-trap mass spectrometer. All of the commonly known proteins associated with serum were detected, and the two mass spectrometers agreed on the identity of abundant serum proteins. Preseparation of serum proteins prior to digestion markedly enhanced the capacity to detect un-common proteins from blood. Electrophoretic- and chromatography-based experiments were found to be complementary. Many novel cellular proteins not previously associated with serum were recorded.

Blood Proteins↗