Isotopic deconvolution of matrix-assisted laser desorption/ionization massspectra for substance-class specific analysis of complex samples

The theoretical isotopic pattern and its variance was determined for peptid es and other substance classes. The mass-dependent mean pattern was used to isotopically deconvolute matrix-assisted laser desorption/ionization (MALD I) spectra and MALDI post-source decay (PSD) spectra from complex peptide s amples, Application of a slightly modified algorithm to electrospray ioniza tion spectra will be described in a later paper, The method was found to be especially useful in suppressing noise and signals from other substance cl asses, and in separating overlapping isotopic patterns in highly complex sa mples. The method can be used for automatic determination of monoisotopic m asses in, for example, proteomics work and the improvement of graphical qua lity and clarity in presentation and manual evaluation of mass spectra. A f ast computer algorithm was developed to demonstrate the efficiency of the m ethod in data filtering and spectra deconvolution for the case of MHC (majo r histocompatibility complex) peptide identification and PSD analysis. The method has some advantages over other approaches, especially due to its sim plicity, universality and processing speed.