A starlike water-soluble fullerene derivative, hexa(sulfonbutyl)fullerene (C60[(CH2)4SO3-]6; HSBF), consisting of a C60 cage covalently bonded with six negatively charged sulfonate arms, was synthesized and used to selectively precipitate positively charged surfactants, amino acids, peptides, and proteins. The affinity of HSBF to the analytes depends on the charge, structure, and hydrophobic characteristics of the analytes. The ion pair precipitate was easily removed from the solution by centrifugation. After washing, the precipitate was redissolved in the solvent or buffer solution and the analyte was characterized by laser desorption ionization-time-of-flight mass spectrometry (LD-TOF). HSBF shows strong optical absorbance in the UV range, so no additional organic matrix was required to conduct LD-TOF analysis of small analytes. For the solution that contained five quaternary amines differing only in alkyl chain length, HSBF exhibits the highest affinity to the amine with the longest alkyl chain. Only the arginine signal was detected from the solution that contained 14 amino acids. The peptides with arginine as the end groups interacted most strongly with HSBF and could be selectively precipitated from a solution of a mixture of five peptides. The signals associated with a trace amount of charged peptides derived from the digestion of proteins by trypsin were greatly enhanced after concentration with HSBF. Among eight proteins in the sample solution, insulin had the strongest affinity to the HSBF and exhibited the strongest signal on the matrix-assisted laser desorption/ionization mass spectrum.