Capillary electrophoresis-mass spectrometry (CE-MS) has demonstrated to be a very useful hyphenated technique for Proteomic studies. However, the huge amount of data stored in a single CE-MS run makes necessary to account with procedures able to extract all the relevant information made available by CE-MS. In this work, we present a new and easy approach able to generate a simplified two-dimensional map from CE-MS raw data. This new approach provides the automatic detection and characterization of the most abundant ions from the CE-MS data including their m/z values, ion intensities and analysis times. It is demonstrated that visualization of CE-MS data in this simplified 2D format allows (i) an easy and simultaneous visual inspection of large datasets, (ii) an immediate perception of relevant differences in closely related samples, (iii) a rapid monitoring of data quality levels in different samples and (iv) a fast discrimination between comigrating polypeptides and ESI-MS fragmentation ions. The strategy proposed in this work does not rely on an excellent mass accuracy for peak detection and filtering since MS values obtained from an ion trap analyzer are used. Moreover, the methodology developed works directly with the CE-MS raw data, without interference by the user, giving simultaneously a simplified 2D map and a much easier and more complete data evaluation. Besides, this procedure can easily be implemented in any CE-MS laboratory. The usefulness of this approach is validated by studying the very similar trypsin digests from bovine, rabbit and horse cytochrome c. It is demonstrated that this simplified 2D approach allows obtaining in a fast and simple way specific markers for each species.

Authors are grateful to the AGL2005-05320-C02-01 Project (Ministerio de Educacion y Ciencia) and the S-505/AGR-0153 Project (Comunidad Autonoma de Madrid, CAM) for financial support of this work.

Peer reviewed