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Bioinformatics Advance Access originally published online on September 8, 2005
Bioinformatics 2005 21(21):4054-4059; doi:10.1093/bioinformatics/bti660
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

Data pre-processing in liquid chromatography–mass spectrometry-based proteomics

Xiang Zhang 1,*, John M. Asara 3, Jiri Adamec 1, Mourad Ouzzani 2 and Ahmed K. Elmagarmid 2

1Bindley Bioscience Center, Purdue University West Lafayette, IN, USA
2Department of Computer Science, Purdue University West Lafayette, IN, USA
3Beth Israel Deaconess Medical Center Boston, MA, USA

*To whom correspondence should be addressed.

Motivation: In a liquid chromatography–mass spectrometry (LC–MS)-based expressional proteomics, multiple samples from different groups are analyzed in parallel. It is necessary to develop a data mining system to perform peak quantification, peak alignment and data quality assurance.

Results: We have developed an algorithm for spectrum deconvolution. A two-step alignment algorithm is proposed for recognizing peaks generated by the same peptide but detected in different samples. The quality of LC–MS data is evaluated using statistical tests and alignment quality tests.

Availability: Xalign software is available upon request from the author.

Contact: zhang100{at}purdue.edu

Received on April 13, 2005; revised on August 1, 2005; accepted on September 1, 2005

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