Bioinformatics Links Directory : Proteomics

This section contains links to general proteomics resources, methods, software, and databases.

Multi-Q - (Found July 2, 2008 )

Multi-Q provides an automated data analysis tool for multiplexed protein quantitation based on iTRAQ labeling.
http://ms.iis.sinica.edu.tw/Multi-Q-Web/

KCaM - (Found July 2, 2008 )

The KEGG Carbohydrate Matcher (KCaM) takes glycan structures as input and returns a list of similar glycan structures using a tree-structure alignment algorithm.
http://glycan.genome.ad.jp/

ISOTOPICA - (Found July 2, 2008 )

Tools developed to aid in the identification of mass spectrum that allow the calculation of mass values with isotopic distributions based on molecular formulas, peptidesproteins, DNARNA, carbohydrate sequences or combinations thereof. A viewer for visualizing results is also available.
http://coco.protein.osaka-u.ac.jp/isotopica/

HUPO Proteomics Standards Initiative - (Found July 2, 2008 )

HUPO Proteomics Standards Initiative (PSI) provides data representation standards to facilitate the exchange, comparison and validation of proteomics data.
http://psidev.sourceforge.net/

Human Protein Reference Database - (Found July 2, 2008 )

The Human Protein Reference Database (HPRD) is a centralized resource for information about human proteins, their interactions with other human proteins, and protein-disease relationships. The information contained in HPRD is curated by experts, who manually extract it from published literature.
http://www.hprd.org/

GFS - (Found July 2, 2008 )

Genome-based Fingerprint Scanning (GFS) takes as input an experimentally obtained peptide mass fingerprint, scans a genome sequence of interest, and outputs the most likely regions of the genome from which the mass fingerprint is derived.
http://gfs.unc.edu/cgi-bin/WebObjects/GFSWeb

ExPASy Proteomics tools - (Found July 2, 2008 )

Various tools for protein identification and characterization, similarity searches, pattern and profile searches, post-translational modification prediction, and more.
http://us.expasy.org/tools/

The Global Proteome Machine - (Found July 2, 2008 )

The Global Proteome Machine (GPM) project facilitates the analysis of proteomes for researchers using tandem mass spectrometry. The aims of the project include providing a common validation and testing platform for results, making the results more portable, and improving the quality of the analysis. The GPM uses the X! TANDEM Spectrum Modeler to match peptide sequences to tandem mass spectra. Both the GPM interface and X! TANDEM are open-source.
http://thegpm.org/