Repository: Freie Universit├Ąt Berlin, Math Department

MSSimulator: Simulation of Mass Spectrometry Data

Bielow, C. and Aiche, S. and Andreotti, S. and Reinert, K. (2011) MSSimulator: Simulation of Mass Spectrometry Data. Journal of Proteome Research, 10 (7). pp. 2922-2929.

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Official URL: http://dx.doi.org/10.1021/pr200155f

Abstract

Mass spectrometry coupled to liquid chromatography (LC-MS and LC-MS/MS) is commonly used to analyze the protein content of biological samples in large scale studies, enabling quantitation and identification of proteins and peptides using a wide range of experimental protocols, algorithms, and statistical models to analyze the data. Currently it is difficult to compare the plethora of algorithms for these tasks. So far, curated benchmark data exists for peptide identification algorithms but data that represents a ground truth for the evaluation of LC-MS data is limited. Hence there have been attempts to simulate such data in a controlled fashion to evaluate and compare algorithms. We present MSSimulator, a simulation software for LC-MS and LC-MS/MS experiments. Starting from a list of proteins from a FASTA file,the simulation will perform in-silico digestion, retention time prediction, ionization filtering, and raw signal simulation (including MS/MS), while providing many options to change the properties of the resultingdata like elution profile shape, resolution and sampling rate. Several protocols for SILAC, iTRAQ or MS(E) are available, in addition to the usual label-free approach, making MSSimulator the most comprehensive simulator for LC-MS and LC-MS/MS data.

Item Type:Article
Subjects:Mathematical and Computer Sciences
Divisions:Department of Mathematics and Computer Science > Institute of Mathematics > Comp. Proteomics Group
Department of Mathematics and Computer Science > Institute of Computer Science > Algorithmic Bioinformatics Group
Department of Mathematics and Computer Science > Institute of Mathematics > BioComputing Group
ID Code:1066
Deposited By: AG Alg BioInf
Deposited On:29 Apr 2011 10:33
Last Modified:03 Mar 2017 14:41

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