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ProTISA

http://mech.ctb.pku.edu.cn/protisa/

Description :
Translation Initiation Site Annotation in prokaryotic genomes

PTM-Switchboard

http://cagr.pcbi.upenn.edu/PTMswitchboard/

Description :
Post-translational modifications of yeast transcription factors

ExPASy 2-D PAGE databases and services

http://us.expasy.org/ch2d/2d-index.html

Description :
References to known 2-D PAGE database servers, as well as to 2-D PAGE related servers and services.

GELBANK

http://gelbank.anl.gov/

Description :
GELBANK is a database of 2D gel images of proteomes for species with completed genomes. The user can search by sequence description or fragment, or by gel characteristics. Links are made between the sequence and gel when available.

GelScape and GelBank

http://www.gelscape.ualberta.ca/

Description :
GelScape is a platform-independent 1D and 2D gel analysis system that is freely available. Features include the ability to mark spots, to measure spot intensities and to archive gel images and annotations to the public database GelBank. Includes searchable access to GelBank s repository.

JVirGel

http://www.jvirgel.de/

Description :
JVirGel creates a virtual 2-D gel based on theoretical molecular weights and calculated isoelectric points from a set of input proteins or proteomes.

NCI Flicker

http://www.lecb.ncifcrf.gov/flicker/

Description :
Flicker provides the means to compare images from different internet sources using a java-enabled web browser. It was originally designed for the comparison of 2D gels.

SWISS-2DPAGE

http://us.expasy.org/ch2d/

Description :
This is a 2D gel electrophoresis database containing data for proteins identified on SDS-PAGE or 2D-PAGE reference maps.

2D-PAGE

http://www.mpiib-berlin.mpg.de/2D-PAGE

Description :
The publicly available Proteome Database System for Microbial Research 2D-PAGE has been established at the Max Planck Institute for Infection Biology and serves as a template for a prototype of a European Proteome Database of Pathogenic Bacteria. The database system is centrally administrated, and investigators without specific bioinformatics competence in database construction can submit their data. The system comprises four heterogeneous but interconnected databases: (i) 2D-PAGE database for 2-D gel electrophoresis and mass spectrometry data, (ii) Isotope Coded Affinity Tag (ICAT)-LC/MS database, (iii) FUNC_CLASS database for functional classification of proteins, (iv) DIFF database for presentation of differentially regulated proteins detected by quantitative gel image analysis. The database system is hyperlinked with public databases such as SWISS-PROT; NCBI; PEDANT and KEGG. The current public release (May, 2004) contains proteomic information on 11 microorganisms such as Mycobacterium tuberculosis, Helicobacter pylori, Chlamydophila pneumoniae, Borrelia garinii, Francisella tularensis, Mycoplasma pneumoniae and information on Jurkat T-cells and mouse mammary gland. Proteomic data are presented in 18 two-dimensional gels with 2572 identified protein spots. For 254 of these spots peptide mass fingerprints are available. More than 1000 identified spots of further miroorganisms such as Mycobacterium bovis BCG, Salmonella SL-1344, Vibrio cholerae are stored in the internal release of 2D-PAGE which will be publicly accessible after paper submission. The annotated proteome data such as protein name, molecular weight Mr, isoelectric point pI, gene name, ORF, NCBI accession number, identification method, sequence coverage, protein spot number, class (antigen, gastric carcinoma associated antigen etc.) can be retrieved either by clicking on protein spots or by formulating complex queries. Specific data such as pI, Mr-values or codon usage for proteins can be visualized and analyzed on the fly using the statistical software environment R (http://www.r-project.org/) or can be downloaded as spread sheet files. The Proteome Database System for Microbial Research can be accessed from http://www.mpiib-berlin.mpg.de/2D-PAGE.

Aknowledgement :
This work was partially funded by the German Federal Ministry for Eduction and Research (contract number: 031U107C/031U207C) and by the European Union (EBPnetwork - contract number: QLRT-1999-31536).

References :
1. Jungblut, P. R., Schaible, U. E., Mollenkopf, H. J., Zimny-Arndt, U., et al., Mol. Microbiol. 1999,33(6), 1103-1117.

2. Mollenkopf, H. J., Jungblut, P. R., Raupach, B., Mattow, J. et al., Electrophoresis 1999, 20, 2172-2180.

3. Pleissner, K.-P., Eifert, T., Jungblut, P.R., Comp. Funct. Genom. 2002, 3, 97-100.

4. Mollenkopf, H. J., Mattow, J., Schaible,U. E. , Grode, L. et al., Methods Enzymol. 2002 358, 242-256.

5. Pleissner, K.-P., Eifert, T., S. Buettner, S., Schmidt, F., Boehme, M., T.F. Meyer, T. F., Kaufmann, S. H. E., Jungblut. P. R. Proteomics, 2004, 4, 1305-1313.

DynaProt 2D

http://www.wzw.tum.de/proteomik/lactis/

Description :
DynaProt 2D provides dynamic online access to proteomes and 2D gels. The database was designed to administer complete in silico proteomes and links them with experimental proteomic data in the manner of two-dimensional electrophoresis gels (IPG-Dalt). The 2D gels serve as reference maps as well as tools for navigation of the database to switch between experimental and predicted data. Therefore, all identified spots in the gels are clickable and linked with summarized protein information. The protein information tables contain calculated characteristics, which are often used in proteomics, such as the molecular weight, isoelectric point, codon adaptation index, grand average of hydropathicity, predicted cellular localization, etc. Besides navigation via 2D gels, the clear graphical interface permits quick and intuitive searching throughout complete proteomes according to six different parameters. For example the search for proteins can be restricted to molecular mass and pH ranges, 2D gels and protein classes (e.g. ribosomal proteins or transporters). The first organism implemented in the database is Lactococcus lactis. Other model organisms as well as stress related experimental data of L. lactis will follow. Furthermore, the database was designed for continuous extension of the protein characteristics to keep up with the quick developments in proteomics. Therefore, additional proteomic data is welcome and will be referenced.

Aknowledgement :
D Preuss (Daikun Solutions) is sincerely thanked for his help in realization of the dynamic online access to the database.

MAPU

http://www.mapuproteome.com

Description :
Mass spectrometry (MS)-based proteomics has become a powerful technology to map the protein composition of organelles, cell types and tissues. In our department a large-scale effort to map these proteomes is complemented by the Max-Planck Unified (MAPU) Proteome Database. MAPU contains several body fluid proteomes including plasma, urine, and cerebrospinal fluid. Cell lines have been mapped to a depth of several thousand proteins and the red blood cell proteome has also been analyzed in depth. By employing high resolution MS and stringent validation criteria, false positive identification rates in MAPU are lower than 1:100 and usually better than 1:1000. Thus MAPU data sets can serve as reference proteomes in biomarker discovery. Proteome data can be queried by protein name, accession number, peptide sequence and annotation information.

Recent develoments :
The new release addresses MS-specific problems including ambiguous peptide-to-protein assignments and it provides insight into general functional features on the protein level ranging from gene ontology classification to comprehensive SwissProt annotation. Moreover, the derived proteomic data are linked to the genomes using the Distributed Annotation Service (DAS) via Ensembl services. MAPU 2.0 is a model for a database specifically designed for high accuracy proteomics and a member of the ProteomExchange Consortium.

Aknowledgement :
We thank the database group at the Beijing Genome Institute for help, discussion and providing database templates.

OPD - Open Proteomics Database

http://bioinformatics.icmb.utexas.edu/OPD/ Mass-spectrometry-based proteomics data for human, yeast, E.coli and Mycobacterium

PepSeeker

http://nwsr.bms.umist.ac.uk/cgi-bin/pepseeker/pepseek.pl

Description :
Peptide identification and ion information from proteome experiments

PeptideAtlas

http://www.peptideatlas.org/

Description :
The PeptideAtlas (1) is a multi-organism, publicly accessible compendium of peptides identified in a large set of LC-MS/MS proteomics experiments. Some of the experimental data have been already published; many are still unpublished. All results of sequence searching have subsequently been processed through PeptideProphet to derive a probability of correct identification for all results in a uniform manner to insure a high quality database. All peptides have been mapped to Ensembl and can be viewed as custom tracks on the Ensembl Genome Browser.

The PeptideAtlas will continue to grow as more datasets and organisms are added. We welcome data submissions, which we will incorporate into the atlas.

Recent develoments :
PeptideAtlas is a first step towards the goal of fully annotating and validating eukaryotic genomes by using experimentally observed protein-products. PeptideAtlas provides a process and a framework to accommodate proteome information generated by high-throughput proteomics technologies and is able to efficiently disseminate experimental data in the public domain. Its significance continues to grow as more data are submitted from diverse experiments, using different cellular compartments and enrichments methods. PeptideAtlas also provides a resource for the development of new avenues of research. The datasets will provide a rich source of data for computational scientists to develop and test new algorithms for proteomic analysis, gene-discovery and splice variant prediction. The need for public proteomics data repositories is recognized (3) and we intend PeptideAtlas to continue to grow as a public database and resource. We strongly encourage researchers to contribute their own MS/MS data to the PeptideAtlas project. In the near future, we will make builds for organisms such as mouse, Arabidopsis thaliana and Halobacterium sp. NRC-1, and continue to make subsets such as the Human Plasma PeptideAtlas (2). Also in the near future we hope to provide an interface to access representative spectra of peptides, and will provide a way to retrieve information on peptide modifications (such as phosphorylation, etc.).

References :
1. Desiere,F., Deutsch,E.W., Nesvizhskii,A.I., Mallick,P., King,N.L., Eng,J.K., Aderem,A., Boyle,R., Brunner,E., Donohoe,S. et al. (2005) Integration with the human genome of peptide sequences obtained by high-throughput mass spectrometry. Genome Biol., 6, R9. http://genomebiology.com/2004/6/1/R9
2. Deutsch,E.W., Eng,J.K., Zhang,H., King,N.L., Nesvizhskii,A.I., Lin,B., Lee,H., Yi,E.C., Osssola,R. and Aebersold,R. (2005) Human Plasma PeptideAtlas. Proteomics., 5. http://www3.interscience.wiley.com/cgi-bin/abstract/110575153/ABSTRACT
3. Prince,J.T., Carlson,M.W., Wang,R., Lu,P. and Marcotte,E.M. (2004) The need for a public proteomics repository. Nat Biotechnol, 22, 471-472.

PRIDE

http://www.ebi.ac.uk/pride/

Description :
PRIDE, The ‘PRoteomics IDEntifications database’ [1,2] is a database of protein and peptide identifications that have been described in the scientific literature. These identifications will typically be from specific species, tissues and sub-cellular locations, perhaps under specific disease conditions. Any post-translational modifications that have been identified on individual peptides can be described. These identifications may be annotated with supporting mass spectra. Proteomics laboratories are encouraged to submit their identifications and spectra to PRIDE to support their manuscript submissions to proteomics journals. Data can be submitted in PRIDE XML format or mzData format. PRIDE is a web application, so submission, searching and data retrieval can all be performed using an Internet browser. PRIDE can be searched by experiment accession number, protein accession number, literature reference and sample parameters including species, tissue, sub-cellular location and disease state. Data can be retrieved as machine-readable PRIDE or mzData XML (the latter for mass spectra without identifications), or as human-readable HTML. Public PRIDE data sets and the open-source code base are available from http://www.ebi.ac.uk/pride.

Recent develoments :
PRIDE has recently been translated from the default English into French, German and Korean. Language selection is automatic, depending on the locale setting of the users’ Internet browser. At the time of writing, PRIDE contains more than 1600 separate experiments, comprising almost 180,000 protein identifications and approximately 500,000 peptide identifications. PRIDE protein identifications can be queried through a Distributed Annotation System (DAS) [3] that provides details of the coordination of peptides

Aknowledgement :
PRIDE is supported through BBSRC iSPIDER and HUPO Plasma Proteome Project funding as well as a EU Marie Curie fellowship.

References :
1. Martens L, Hermjakob H, Jones P, Adamski M, Taylor C, States D, Gevaert K, Vandekerckhove J, Apweiler R: PRIDE: the proteomics identifications database. Proteomics 2005, 5(13):3537-3545.
2. Jones P, Côté RG, Martens L, Quinn A, Taylor CF, Derache W, Hermjakob H, Apweiler R: PRIDE: A Public Repository of Protein and Peptide Identifications for the Proteomics Community. Nucleic Acids Research, in press.
3. Dowell RD, Jokerst RM, Day A, Eddy SR, Stein L: The distributed annotation system. BMC Bioinformatics 2001, 2:7.

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