Abstract
BackgroundIn 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.ResultsWe developed 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. It 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.ConclusionOur new open source LIMS is now available as a basic model for proteome informatics, and is accessible for further improvement. We hope that many research scientists working in the field of proteomics will evaluate our LIMS and suggest ways in which it can be improved.
Highlights
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
Many research scientists working in the field of proteomics are required to manage huge volumes of experimental data, which are obtained by two-dimensional polyacrylamide gel electrophoresis (2-DPAGE), image analysis, mass spectrometry (MS) analysis and related information downloaded from the public databases in field of life science
We have developed an original open source laboratory information management system (LIMS) for 2-D gel electrophoresis-based proteomics workflow on the basis of the above background
Summary
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. As part of the Human Genome Project that was carried out by an international consortium, a laboratory information management system (LIMS) was developed for genome research and evaluated as an essential tool for advanced studies in the life sciences [1,2]. Many research scientists working in the field of proteomics are required to manage huge volumes of experimental data, which are obtained by two-dimensional polyacrylamide gel electrophoresis (2-DPAGE), image analysis, mass spectrometry (MS) analysis and related information downloaded from the public databases in field of life science. The software for mass spectrometry analysis picks out peaks in mass spectra and searches them against a database, the so-called "peptidemass fingerprint", for protein identification
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