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PRIDE / PRoteomics IDEntifications database
A centralized, standards compliant, public data repository for proteomics data, including protein and peptide identifications, post-translational modifications and supporting spectral evidence. PRIDE is a core member in the ProteomeXchange (PX) consortium, which provides a single point for submitting mass spectrometry based proteomics data to public-domain repositories. Datasets are submitted to PRIDE via ProteomeXchange and are handled by expert biocurators.
GPMDB / Global Proteome Machine and Database
A database of proteomics experimental information emphasizing biological context, data reuse & validation. GPMDB is based on a combination of data analysis servers, a user interface, and a relational database. The database was designed to store the minimum amount of information necessary to search and retrieve data obtained from the publicly available data analysis servers. Collectively, this system was referred to as the global proteome machine (GPM). The components of the system have been made available as open source development projects.
ProMEX
A mass spectral reference database. The database consists of tryptic peptide fragmentation mass spectra derived from plants. This release 2.12/2013 contains 116,364 tryptic peptide product ion spectra entries of 48,218 different peptide sequence entries from Medicago truncatula, Chlamydomonas reinhardtii, Bradyrhizobium japonicum, Arabidopsis thaliana, Phaseolus vulgaris, Lotus japonicus, Lotus corniculatus, Lycopersicon esculentum, Solanum tuberosum, Nicotiana tabacum, Sinorhizobium meliloti, Glycine max, Zea mays.
Unimod
A database of protein modifications for use in mass spectrometry applications, especially protein identification and de novo sequencing. Unimod contains accurate and verifiable values, derived from elemental compositions, for the mass differences introduced by both natural and artificial modifications. The entire contents of Unimod are available for download in two formats, with files updated weekly: (i) Complete database dump in XML format, suitable for machine translation into other formats; (ii) Mascot mod_file format.
CPTAC Data Portal
The Clinical Proteomic Tumor Analysis Consortium (CPTAC) analyzes cancer biospecimens by mass spectrometry, characterizing and quantifying their constituent proteins, or proteome. The CPTAC Data Portal is the centralized repository for the dissemination of proteomic data collected by the Proteome Characterization Centers (PCCs) for the CPTAC program. The portal also hosts analyses of the mass spectrometry data (mapping of spectra to peptide sequences and protein identification) from the PCCs and from a CPTAC-sponsored common data analysis pipeline (CDAP).
SECexplorer / Size Exclusion Chromatography explorer
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Serves for the interpretation of quantitative co-fractionation protein profiles generated by SEC-SWATH-MS. SECexplorer permits researchers to take advantage of complex-centric data. It offers a graphical interface allowing to display and investigate the HEK293 proteome modularity. This platform provides several features: (1) testing of novel predicted models on complex formation between candidate proteins; (2) interrogating the profile sets of known modules for evidence pointing towards new variants; and (3) manual refining and extension of results obtained from automated complex-centric profiling.
mzCloud
An extensively curated database of high-resolution tandem mass spectra that are arranged into spectral trees. mzCloud represents a key conceptual shift towards a modern mass spectral database. This tool is a scientifically solid and computationally robust platform for the identification of small molecules using tandem mass spectrometry. It offers a web-based interface providing a number of search, visualization and data processing tools. It also comprises curated databases of high and low resolution MSn spectra acquired under a number of experimental conditions which address the spectra reproducibility problem.
NIST Libraries of Peptide Tandem Mass Spectra
Gives access to comprehensive, annotated mass spectral reference collections from various organisms and proteins. NIST Libraries of Peptide Tandem Mass Spectra are useful for the rapid matching and identification of acquired mass spectrometry (MS)/MS spectra. Peptide mass spectrum libraries can be used for direct peptide identification, validation of peptides identified by sequence search programs, organization and identification of recurring, unidentified spectra, detection of internal standards, biomarkers, and target proteins and subtraction of a component from a mixture spectrum.
MoNA / Mass Bank of North America
Designed for efficient storage and querying of mass spectral records. MoNA intends to serve as a framework for a centralized, collaborative database of metabolite mass spectra, metadata and associated compounds. MoNA currently contains over 200000 mass spectral records from experimental and in-silico libraries as well as from user contributions. MoNA has been redesigned, with significant improvements to server-side architecture, query structure, and search speed.
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