Development of an open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflow

Abstract

Background: In the post-genome era, most research scientists working in the field of proteomics are confronted with difficulties in management of large volumes of data, which they are required to keep in formats suitable for subsequent data mining. Therefore, a well-developed open source laboratory information management system (LIMS) should be available for their proteomics research studies.

2DB: a Proteomics database for storage, analysis, presentation, and retrieval of information from mass spectrometric experiments

“…PEDRo, intended as a model for capturing all data in gel-based proteomics, has been adopted by proteomics applications, for example MASPECTRAS, and forms the basis of its data model [ 37 ], which is similar to other laboratory information systems [ 38 ]. Recently the proteomics standard initiative formalized the minimum information necessary for a proteomics experiment [ 39 ] which now supersedes the PEDRo model.…”

Clinical proteomic biomarkers: relevant issues on study design & technical considerations in biomarker development

“…An important issue is assigning a unique ID given to a sample [32], an appropriate database structure and management system. Such systems have been currently developed [33–35] mainly as laboratory informatics management applications (LIMS) that are built to tract samples from the initial steps of delivery.…”

Assembling proteomics data as a prerequisite for the analysis of large scale experiments

“…However, this mostly resulted in individual solutions for each company which hampered the exchange of experimental data. However, beside commercial solutions some open LIMS systems such as PROTEIOS [ 5 ] or the open source laboratory information management system for 2-D gel electrophoresis-based proteomics workflows [ 6 ] are available free of charge and some of them were compared in more detail by Piggee et al [ 7 ]. The representation of protein data must be standardized to compare proteomics results worldwide.…”