Computer Science – Computational Engineering – Finance – and Science
Scientific paper
2010-02-19
Journal of Proteomics 73(6) (2010) 1176-1182
Computer Science
Computational Engineering, Finance, and Science
Paper details: 10 pages, 7 figures, 2 tables. To be published in Journal of Proteomics. Source code available at http://www.
Scientific paper
10.1016/j.jprot.2010.02.006
As an emerging field, MS-based proteomics still requires software tools for efficiently storing and accessing experimental data. In this work, we focus on the management of LC-MS data, which are typically made available in standard XML-based portable formats. The structures that are currently employed to manage these data can be highly inefficient, especially when dealing with high-throughput profile data. LC-MS datasets are usually accessed through 2D range queries. Optimizing this type of operation could dramatically reduce the complexity of data analysis. We propose a novel data structure for LC-MS datasets, called mzRTree, which embodies a scalable index based on the R-tree data structure. mzRTree can be efficiently created from the XML-based data formats and it is suitable for handling very large datasets. We experimentally show that, on all range queries, mzRTree outperforms other known structures used for LC-MS data, even on those queries these structures are optimized for. Besides, mzRTree is also more space efficient. As a result, mzRTree reduces data analysis computational costs for very large profile datasets.
Camillo Barbara Di
Nasso Sara
Pietracaprina Andrea
Silvestri Francesco
Tisiot Francesco
No associations
LandOfFree
An Optimized Data Structure for High Throughput 3D Proteomics Data: mzRTree does not yet have a rating. At this time, there are no reviews or comments for this scientific paper.
If you have personal experience with An Optimized Data Structure for High Throughput 3D Proteomics Data: mzRTree, we encourage you to share that experience with our LandOfFree.com community. Your opinion is very important and An Optimized Data Structure for High Throughput 3D Proteomics Data: mzRTree will most certainly appreciate the feedback.
Profile ID: LFWR-SCP-O-363661