ProtosLINK: a bioinformatics application to manage protein identifications, annotations, and related sample information

Proteomics is the study and characterization of proteins in organisms, tissues, or cells. Researchers use proteomics to diagnose disease, to develop novel compounds to treat disease, and to identify drug-drug interactions. To perform these tasks, proteomics uses mass spectrometry and protein sequence databases to identify and quantify unknown proteins. Modern mass spectrometers and protein database search algorithms can generate protein identification data very quickly. Because analyzing a single sample may lead to identification of several thousand proteins, the data generated cannot be efficiently analyzed manually. Several commercially available applications can identify proteins, but very few can store protein identifications and their annotations. Programs available are typically integrated with a specific mass spectrometer and cannot be used to store and compare data obtained from other instruments and applications. To aid in the management of these data, a Web-based application, ProstosLINK, was developed to store protein identification data with sample and project information in a universal format that accommodates data from all mass spectrometry analysis comparisons (protein presence or absence) between samples; and provide links to existing, on-line databases.