Accurate peak list extraction from proteomic mass spectra for identification and profiling studies

This paper describes an original algorithm for peak list extraction from low and high resolution mass spectra. It has been developed principally to improve the precision of peak extraction in comparison to other reference algorithms. It contains many innovative features among which a sophisticated method for managing the overlapping isotopic distributions.The performances of the basic version of the algorithm and of its optional functionalities have been evaluated in this paper on both SELDI-TOF, MALDI-TOF and ESI-FTICR ECD mass spectra. Executable files of MassSpec, a MATLAB implementation of the peak list extraction procedure for Windows and Linux systems, can be downloaded free of charge for nonprofit institutions from the following web site: http://aimed11.unipv.it/MassSpec webciteMass spectrometry (MS) has been one of the most used tools to analyze large biological molecules since the introduction of the soft ionization methods, such as electrospray ionization (ESI) and matrix-assisted laser desorption/ionization (MALDI). For this reason MS is increasingly being used in proteomics. In particular, MS is exploited in proteomics to cope with two main tasks: determination of proteomic profiles of several samples for differential studies (profiling - clinical proteomics) and the identification of proteins or characterization of post-translational modifications (PTMs) in a biological sample (identification - biological proteomics) [1].The widely used protocols for protein identification or characterization of PTMs are PMF (Peptide Mass Fingerprinting) and PFF (Peptide Fragment Fingerprinting) [2-4]. MALDI-TOF is the platform generally exploited for PMF, whereas different platforms are used for PFF (e.g., ESI-Q/TOF, MALDI-TOF/TOF or ESI-FTICR) [5-7]. Electron capture dissociation (ECD) combined with ESI-FTICR is the most powerful technique for characterization of intact proteins [8-10]. For all these platforms the determination of the monoisotopic masses of the detect