Bioinformatics

Post alignment clustering procedure for comparative quantitative proteomics LC-MS Data

  1. Joost C. W. de Groot,
  2. Mark W. E. J. Fiers,
  3. Roeland C. H. J. van Ham,
  4. Antoine H. P. America Dr.*

Article first published online: 19 DEC 2007

DOI: 10.1002/pmic.200700707

Issue

PROTEOMICS

PROTEOMICS

Volume 8, Issue 1, pages 32–36, No. 1 January 2008

Additional Information

How to Cite

de Groot, J. C. W., Fiers, M. W. E. J., van Ham, R. C. H. J. and America, A. H. P. (2008), Post alignment clustering procedure for comparative quantitative proteomics LC-MS Data. Proteomics, 8: 32–36. doi: 10.1002/pmic.200700707

Author Information

  1. Plant Research International, Wageningen-UR, Wageningen, The Netherlands

*Plant Research International, Wageningen-UR, P. O. Box 16, 6700AA Wageningen, The Netherlands Fax: +31-317-418094

Publication History

  1. Issue published online: 19 DEC 2007
  2. Article first published online: 19 DEC 2007
  3. Manuscript Received: 19 JUL 2007

Funded by

  • The Centre of BioSystems Genomics
  • The Netherlands Proteomics Centre
  • The Celiac Disease Consortium. Grant Number: BSIK03009

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Keywords:

  • Alignment;
  • Data quality;
  • LC-MS;
  • Mass spectrometry;
  • Quantitative Proteomics

Abstract

Comparative LC-MS is a powerful method for detailed quantitative comparison of complex protein mixtures. Dedicated software is required for detection, matching, and alignment of peaks in multiple LC-MS datasets. However, retention time shifts, saturation effects, limitations of experimental accuracy, and possible occurrence of split peaks make it difficult for software to perfectly match all chromatograms. We describe a procedure to assess the above problems and show that dataset quality can be enhanced with the aid of cluster analysis.

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