1 - 29 of 29 results

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.

HPM / Human Proteome Map

An interactive resource to the scientific community by integrating the massive peptide sequencing result from the draft map of the human proteome project. The Human Proteome Map was based on LC-MS/MS by utilizing of high resolution and high accuracy Fourier transform mass spectrometry. This includes 17 adult tissues, 6 primary hematopoietic cells and 7 fetal tissues. The HPM portal provides an interactive web resource by reorganizing the label-free quantitative proteomic data set in a simple graphical view. In addition, the portal provides selected reaction monitoring (SRM) information for all peptides identified.

GPMDB / Global Proteome Machine and Database

Obsolete
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.

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).

Curatr

Simplifies the construction of high quality custom spectral libraries. Curatr is complementary to mass spectrometry visualization tools, spectral matching software, online data analysis and sharing platforms, and repositories. It has several features: (1) it collects information about standards analyzed, (2) it automatically selects candidate tandem mass spectrometry (MS/MS) spectra for standards, (3) it facilitates manual curation of MS/MS spectra through the web-browser, (4) it has a searchable catalogue of all spectra contained in the library, and (5) it provides export compatibility with major repositories and external software applications.

MiCId / Microorganism Classification and Identification

A software tool that processes mass spectrometry tandem spectra (MS/MS) data for identification and classification of microorganisms. We have demonstrated, using MS/MS data of 81 samples, each composed of a single known microorganism, that the proposed pipeline can correctly identify microorganisms at least at the genus and species levels. We have also shown that the proposed pipeline computes accurate statistical significances, i.e., E-values for identified peptides and unified E-values for identified microorganisms.

DeconMSn

Determines the monoisotopic mass and charge state of parent ions from high resolution tandem mass spectrometry data. DeconMSn offers significant improvement for LTQ_FT and LTQ_Orbitrap instruments over the commercially delivered Thermo Fisher Scientific’s extract_msn tool. The software calculates the monoisotopic mass of the parent ion for each MSn spectrum by applying a modified THRASH approach to the parent isotopic distribution. For datasets with low-resolution MS1 spectra, it uses a support-vector machine based charge-detection algorithm to determine parent mass.

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.

ProPepper

A database of cereal prolamin epitopes, peptides and proteins for expert users that are dealing with protein chemistry, proteomics and mass spectrometry, method developments and related applications in food science, agricultural breeding or medical studies. ProPepper™ contains the full scale of currently available prolamin sequences and specific in silico digested peptide entries, links to reference databases (Uniprot, NCBI & IEDB) and cross-referenced connections. The interface allows advanced global and parametric search functions along with a download option, with direct connections to the relevant public databases.

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.

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.