LC-MSsim - a simulation software for liquid chromatography mass spectrometry data

Background: Mass Spectrometry coupled to Liquid Chromatography (LC-MS) is commonly used to analyze the protein content of biological samples in large scale studies. The data resulting from an LC-MS experiment is huge, highly complex and noisy. Accordingly, it has sparked new developments in Bioinformatics, especially in the fields of algorithm development, statistics and software engineering. In a quantitative label-free mass spectrometry experiment, crucial steps are the detection of peptide features in the mass spectra and the alignment of samples by correcting for shifts in retention time. At the moment, it is difficult to compare the plethora of algorithms for these tasks. So far, curated benchmark data exists only for peptide identification algorithms but no data that represents a ground truth for the evaluation of feature detection, alignment and filtering algorithms. Results: We present LC-MSsim, a simulation software for LC-ESI-MS experiments. It simulates ESI spectra on the M...

• Type: Journal
• Year: 2008
• Where: BMCBI
• Authors: Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gröpl, Oliver Kohlbacher, Knut Reinert
• Keywords: Algorithms, BMCBI 2008, Mass Spectrometry, Retention Time