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ms_lims

A freely available, open-source system based on a central database to automate data management and processing in mass spectrometry driven proteomics analyses. ms-lims is mainly designed to automate data flow in the high-throughput proteomics lab. Taking spectrum files from a variety of pluggable file formats, it transforms these to the Mascot Generic Format and stores them in the database, retaining LC information if present, and also allowing additional information to be stored for each individual LC run. Another part allows the retrieval of the stored spectra in mergefiles of arbitrary size. These can then be submitted to a search engine, eg. Mascot from Matrix Science. Subsequently, the results of these searches can be parsed and stored in a relational database structure for future reference.

CPAS / Computational Proteomics Analysis System

Contains an entire data analysis and management pipeline for liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics, including experiment annotation, protein database searching and sequence management, and mining LC-MS/MS peptide and protein identifications. CPAS architecture and features, such as a general experiment annotation component, installation software, and data security management, make it useful for collaborative projects across geographical locations and for proteomics laboratories without substantial computational support.

ProSE / Proteios Software Environment

The application features sample tracking, project sharing between multiple users, and automated data merging and analysis. ProSE has built-in support for several quantitative proteomics workflows, and integrates searching in several search engines, automated combination of the search results with predetermined false discovery rates, annotation of proteins and submission of results to public repositories. ProSE also provides a programming interface to enable local extensions, as well as database access using Web services. ProSE provides an analysis platform for proteomics research and is targeted for multiuser projects with needs to share data, sample tracking, and analysis result.

Prequips

Supports interactive data exploration to efficiently interact with the data through graphical viewers and data filters. Prequips is an integrative software platform for comparative proteomics-based systems biology analysis that: (i) integrates all information generated from mass spectrometry (MS)- based proteomics as well as from basic proteomics data analysis tools, (ii) visualizes such information for various proteomic analyses via graphical interfaces and (iii) links peptide and protein abundances to external tools often used in systems biology studies.

LIPAGE

An open source LIMS appropriately customized for 2-D gel electrophoresis-based proteomics workflow. The main features of its design are compactness, flexibility and connectivity to public databases. LIPAGE supports the handling of data imported from mass spectrometry software and 2-D gel image analysis software. The LIMS is equipped with the same input interface for 2-D gel information as a clickable map on public 2DPAGE databases. The LIMS allows researchers to follow their own experimental procedures by reviewing the illustrations of 2-D gel maps and well layouts on the digestion plates and MS sample plates.