Resources

Data repositories

The RefData resource is a collection of publicly available mass spectrometry datasets (proteomics, metabolomics, lipidomics, etc.) for performance evaluation for a wide range of different methods, such as, for example data processing, quantiation, identification.

ProteomicsDB is a respository for the identification of the human proteome, using information from liquid chromatography coupled with tandem mass spectrometry (LC-MS/MS) experiments on human samples. Information is accessible for individual proteins and for peptides of a protein.

ProteomeXchange is a consortium that facilitates the submission of mass spectrometry data to the PRIDE (for tandem MS/MS data) and PASSEL/PeptideAtlas (for Selected Reaction Monitoring data) databases.

Initiative of the National Cancer Institute (NCI) to accerlate the understanding of the molecular basis of cancer through the application of quantitative proteomics. Identifies cancer-related proteins and provides that information with accompanying assays and protocols to the public.

Software for quantitative proteomics

General purpose software

OMICtools is a free repository of various tools for data analysis in genomics, transcriptomics, proteomics, and metabolomics. Tools are classified by the type of omics technology, e.g., NGS, microarrys, PCR, MS, NMR. Designed for a wide audience: bioinformaticians, experimental researchers, and clinicians.

Bioconductor provides tools based on the R statistical programming language for the analysis of high-throughput genomic data. It is open source and open development and is highly used in the computational biology community.