A web-based database search service for the identification of RNAs using tandem mass spectrometry data.
The Global Proteome Machine - Proteomics data analysis, reuse and validation for biological and biomedical research.
The Global Proteome Machine Database was constructed to utilize the information obtained by GPM servers to aid in the difficult process of validating peptide MS/MS spectra as well as protein coverage patterns. This database has been integrated into GPM server pages, allowing users to quickly compare their experimental results with the best results that have been previously observed by other scientists.
ms-utils.org is a list of free (gratis) software for analysis of mass spectrometry data. It is both a repository and a collection of up-to-date links to different types of freely available software and code snippets for the visualization and analysis of mass spectrometry data with emphasis on automated methods for proteomics and protein analysis.
- ProteinProspector Tools
Proteomics tools for mining sequence databases in conjunction with Mass Spectrometry experiments.
These programs were developed in the UCSF Mass Spectrometry Facility, which is directed by Dr. Alma Burlingame, Professor of Chemistry and Pharmaceutical Chemistry at UCSF and funded by the NIH National Institute for General Medical Sciences.
A collection of proteomic tools - ProFound, ProteinInfo, PeptideMap, PepFrag, developed by Dr. Brian T. Chait Lab at The Rockefeller University.
- X! Hunter
X! Hunter is a search engine that compares experimentally observed spectra directly with consensus mass spectra obtained from the GPMDB. It can identify proteins for human, budding yeast, mouse and thale cress samples. Because the sequence modifications and cleavage sites for the peptides in the sequence library are already known, it is not necessary to specify as many parameters for this type of search as in more conventional search engines.
- X! Tandem
A GPM (Global Proteome Machine) web-based X! Tandem search engine for protein/peptide identification, using mass spectrum files as input. The allowed formats for spectrum files include GAML, mzXML, mzData, DTA, PKL and MGF . The search procedure is controlled by a number of parameters, normally given in an XML file.