A number of potential matrix candidates were investigated with regard to the importance of the pH in the matrix-assisted laser desorption/ionization mass spectrometry (MALDI/MS) analysis of non-covalently bound protein complexes. The matrices examined were 2,5-dihydroxybenzoic acid (DHB), 4-hydroxy-α-cyanocinnamic acid (HCCA), 2-aminonicotinic acid (ANA), 4-nitroaniline (NA), 2-amino-4-methyl-5-nitropyridine (AMNP) and 3-hydroxypicolinic acid (HPA). In solution these matrix compounds permitted the preparation of MALDI samples at pH in the range 2-7. Among the matrices tested, complex formation, by specific non-covalent interactions, could only be observed when HPA (pH 3.8) was used as the matrix for the MALDI analysis. Under these conditions, specific non-covalent complex formation of recombinant streptavidin and glutathione-S-transferases were observed but not for human hemoglobin. The MALDI spectra obtained with the neutral compounds ANA (pH 4.4), NA (pH 6.4) and AMNP (pH 7.1) as matrices contain only peaks of the subunit with no signal of the non-covalent bound complexes present. Considering the results obtained in this study with basic and acidified matrix materials, there does not appear to be a strong correlation between the pH of the matrix solution and the utility of a matrix for the analysis of non-covalently bound complexes.