Hosts a library of glycoproteins with their corresponding N-glycosites. SRMAtlas permits users to validate biomarker candidates by providing a collection of selected reaction monitoring (SRM) assays produced through three different mass spectrometric platforms. Users browse the database through five panels allowing transitions querying, transitions lists downloading, the browsing of specific builds and access to PeptideAtlas SRM Experiment Library (PASSEL) data and experiments.
Annotates eukaryotic genomes with peptide sequences obtained from mass spectrometry (MS) experiments. PeptideAtlas is a compendium of observations of peptides and associated annotations, based on a large number of contributed data sets. It also supports targeted proteomics workflows, such as selected reaction monitoring (SRM), by allowing the researcher to identify suitable proteotypic peptides to target and to estimate approximate retention time for the target peptides.
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.
Gathers mass spectrometry (MS)-based proteomics datasets. JPOST consists of two mains modules: (i) jPOSTrepo gathering several proteomics data and; (ii) jPOSTdb providing standardized proteomics data reanalyzed from the published raw data in the jPOSTrepo with a graphical data visualization interfaces for identified proteins. This database displays information in accordance to the ProteomeXchange (PX) consortium international standards.
Gathers information about mass spectrometry (MS)/MS spectra. PepBase is a peptide database that consists in a grouping of experimental data handled by a single analytical platform at the proteomics laboratory of IAB.
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.
Assists users in the exploration of protein detection in public mass spectrometry data sets. ProteinExplorer facilitates the selection and inspection of human proteome project’s (HPP)-compliant peptides whose spectra can be matched to spectra of synthetic peptides. It also allows users to rate spectra and to contribute to a community library of peptides mapping to novel proteins.
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).
An endogenous peptide database to aid mass spectrometric identifications. In the identification process the experimental peptide masses are compared with the peptide masses stored in SwePep both with and without possible post-translational modifications. This intermediate identification step is fast and singles out peptides that are potential endogenous peptides and can later be confirmed with tandem mass spectrometry data.
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.
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.
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.
Assists users with cell analysis. Fluorescence SpectraViewer is an online resource for labeling chemistry. It permits planification of users experiments and analyses. Several modules are available: fluorophores, light sources, excitation filters and emission filters. Some spectral simulations such as relative intensities and compensation matrixes are modeled and not based on observed data.
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.
Covers proteomics data, including protein and peptide identifications, post-translational modifications and supports spectral evidence. PRIDE allows public data deposition of MS proteomics data. It can conduct automatic and manual curation of the related experimental metadata and allows the assessment of data quality. This database can be searched by sample details, instrumentation, keywords and other provided annotations.