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

The theoretical isotopic pattern and its variance was determined for peptides and other substance classes. The mass-dependent mean pattern was used to isotopically deconvolute matrix-assisted laser desorption/ionization (MALDI) spectra and MALDI post-source decay (PSD) spectra from complex peptide samples, Application of a slightly modified algorithm to electrospray ionization spectra will be described in a later paper, The method was found to be especially useful in suppressing noise and signals from other substance classes, and in separating overlapping isotopic patterns in highly complex samples. The method can be used for automatic determination of monoisotopic masses in, for example, proteomics work and the improvement of graphical quality and clarity in presentation and manual evaluation of mass spectra. A fast computer algorithm was developed to demonstrate the efficiency of the method in data filtering and spectra deconvolution for the case of MHC (major histocompatibility complex) peptide identification and PSD analysis. The method has some advantages over other approaches, especially due to its simplicity, universality and processing speed.