Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and peptide mass fingerprint (PMF) are one of the most powerful combined tool for protein identification. Frequently it is the method of choice as it is faster and less expensive than protein sequencing. However, sometimes PMF only allows the identification of a subset of peptides, requiring further MS/MS or Edman degradation to attain unequivocal protein identification. This work describes an approach that combines several matrices to improve the fidelity of the protein identification by MALDI-TOF MS. The matrices used for sample preparation are 2,5-dihydroxybenzoic acid (DHB), 2,6- dihydroxyacetophenone (DHAP), CHCA and 2,4,6-Trihydroxy acetophenone (THAP). We have also developed an algorithm called Matrix Assisted Protein Identification (MAPI) that processes Mascot datasets derived from each one of the four matrix preparations, integrating them and achieving a significant improvement in protein identification.