A DISTRIBUTED ALGORITHM FOR PROTEIN IDENTIFICATION FROM TANDEM MASS SPECTROMETRY DATA
Katarzyna ORZECHOWSKA
orzechowska@ire.pw.edu.plWarsaw University of Technology, Institute of Radioelectronics and Multimedia Technology (Poland)
Tymon RUBEL
Warsaw University of Technology, Institute of Radioelectronics and Multimedia Technology (Poland)
Robert KURJATA
Warsaw University of Technology, Institute of Radioelectronics and Multimedia Technology (Poland)
Krzysztof ZAREMBA
Warsaw University of Technology, Institute of Radioelectronics and Multimedia Technology, (Poland)
Abstract
Tandem mass spectrometry is an analytical technique widely used in proteomics for the high-throughput characterization of proteins in biological samples. Modern in-depth proteomic studies require the collection of even millions of mass spectra representing short protein fragments (peptides). In order to identify the peptides, the measured spectra are most often scored against a database of amino acid sequences of known proteins. Due to the volume of input data and the sizes of proteomic databases, this is a resource-intensive task, which requires an efficient and scalable computational strategy. Here, we present SparkMS, an algorithm for peptide and protein identification from mass spectrometry data explicitly designed to work in a distributed computational environment. To achieve the required performance and scalability, we use Apache Spark, a modern framework that is becoming increasingly popular not only in the field of “big data” analysis but also in bioinformatics. This paper describes the algorithm in detail and demonstrates its performance on a large proteomic dataset. Experimental results indicate that SparkMS scales with the number of worker nodes and the increasing complexity of the search task. Furthermore, it exhibits a protein identification efficiency comparable to X!Tandem, a widely-used proteomic search engine.
Keywords:
proteomics, mass spectrometry, distributed computing, Apache SparkReferences
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Authors
Katarzyna ORZECHOWSKAorzechowska@ire.pw.edu.pl
Warsaw University of Technology, Institute of Radioelectronics and Multimedia Technology Poland
Authors
Tymon RUBELWarsaw University of Technology, Institute of Radioelectronics and Multimedia Technology Poland
Authors
Robert KURJATAWarsaw University of Technology, Institute of Radioelectronics and Multimedia Technology Poland
Authors
Krzysztof ZAREMBAWarsaw University of Technology, Institute of Radioelectronics and Multimedia Technology, Poland
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