Simplified 2‐D CE‐MS mapping: Analysis of proteolytic digests

It has been demonstrated that CE‐MS is a very useful hyphenated technique for proteomic studies. However, the huge amount of data stored in a single CE‐MS run makes it 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 capable of generating a simplified 2‐D 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 mass‐to‐charge (m/z) values, ion intensities and analysis times. It is demonstrated that visualization of CE‐MS data in this simplified 2‐D 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 IT analyzer are used. Moreover, the methodology developed works directly with the CE‐MS raw data, without interference by the user, giving simultaneously a simplified 2‐D 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 2‐D approach allows specific markers for each species to be obtained in a fast and simple way.