A database application for pre-processing, storage and comparison of mass spectra derived from patients and controls

Scientific Paper

Expression Proteomics

10.1186/1471-2105-7-403

MALDI-TOF

2006

Mark K Titulaer, Ivar Siccama, Lennard J Dekker, Angelique LCT van Rijswijk, Ron MA Heeren, Peter A Sillevis Smitt and Theo M Luider

BMC Bioinformatics

Abstract

Background: Statistical comparison of peptide profiles in biomarker discovery requires fast, userfriendly

software for high throughput data analysis. Important features are flexibility in changing

input variables and statistical analysis of peptides that are differentially expressed between patient

and control groups. In addition, integration the mass spectrometry data with the results of other

experiments, such as microarray analysis, and information from other databases requires a central

storage of the profile matrix, where protein id's can be added to peptide masses of interest.

Results: A new database application is presented, to detect and identify significantly differentially

expressed peptides in peptide profiles obtained from body fluids of patient and control groups. The

presented modular software is capable of central storage of mass spectra and results in fast analysis.

The software architecture consists of 4 pillars, 1) a Graphical User Interface written in Java, 2) a

MySQL database, which contains all metadata, such as experiment numbers and sample codes, 3)

a FTP (File Transport Protocol) server to store all raw mass spectrometry files and processed data,

and 4) the software package R, which is used for modular statistical calculations, such as the

Wilcoxon-Mann-Whitney rank sum test. Statistic analysis by the Wilcoxon-Mann-Whitney test in

R demonstrates that peptide-profiles of two patient groups 1) breast cancer patients with

leptomeningeal metastases and 2) prostate cancer patients in end stage disease can be distinguished

from those of control groups.

Conclusion: The database application is capable to distinguish patient Matrix Assisted Laser

Desorption Ionization (MALDI-TOF) peptide profiles from control groups using large size datasets.

The modular architecture of the application makes it possible to adapt the application to handle

also large sized data from MS/MS- and Fourier Transform Ion Cyclotron Resonance (FT-ICR) mass

spectrometry experiments. It is expected that the higher resolution and mass accuracy of the FTICR

mass spectrometry prevents the clustering of peaks of different peptides and allows the

identification of differentially expressed proteins from the peptide profiles.

link to article (Open Access)

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