Peptide mass fingerprinting (PMF) is a powerful technique in which experimentally measured m/z values of peptides that result from a protein digest form the basis for a characteristic fingerprint of the intact protein. Due to its propensity to generate singly-charged ions, along with its relative insensitivity to salts and buffers, matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) is the MS method of choice for PMF. The qualitative features of a MALDI-MS mass spectrum can be selectively tuned by varying the matrix and the solvent system used to prepare the matrix. The selective tuning of MALDI-MS mass spectra in order to optimize PMF results is addressed in this paper. Carbonic anhydrase, hemoglobin alpha- and beta-chain, and myoglobin were digested with trypsin, and the digest was analyzed with MALDI-MS. 2,5-Dihydroxybenzoic acid (2,5-DHB) and alpha-cyano-4-hydroxycinnamic acid were prepared, using five different solvent systems: (A) 99% acetone; (B) 50% acetonitrile (ACN), 0.1% trifluoroacetic acid (TFA); (C) 75% ACN, 0.1% TFA; (D) formic acid:H(2)O: 2-propanol (1:3:2); and (E) H(2)O:MeOH (2:1). Each protein was found to have a different optimum solvent system for PMF. Generally, better PMF results were obtained with 2,5-DHB. The best PMF results were obtained when all of the mass spectral data for a particular protein digest were convolved.