ASCQ_ME is a data mining program for the identification of proteins from mass spectrometry raw data (MS and MS/MS) directly from spectra whithout mass list extraction from proteomics or genomics database.

The most commonly used search engines for peptide mass fingerprinting are based on a list of monoisotopic mass values as input data, so that the search engine relies entirely on the extraction of the monoisotopic mass by the extraction software, which is proprietary software, from the mass spectrometer manufacturer. Only one error of one unit during the extraction of the monoisotopic peak and the data base search is completely wrong. On the other hand, the noisy peaks often carry the information on the most interesting proteins; and in the case of two overlapping isotopic clusters, the extraction software very often gives poor results.

ASCQ_ME (Villeneuve d’ASCQ Mass Engine) is based on an original algorithm for peptide mass fingerprint from mass spectrum without mass list extraction. It is able to compute simulated spectra from protein sequence and can compare directly these spectra to the experimental one.