Mass spectrometry (MS) has recently played a considerable role in the chemical measurements in clinical laboratories. We have analyzed organic acids for diagnosis of organic acidemias, and tried to report quantitative data measured by GC/MS with 20 kinds of standard compounds of key metabolites labelled with stable isotopes. By ESI/MS/MS acylcarnitine was analyzed accurately and quickly. We found a new acylcarnitine compound in urine from a patient with multiple carboxylase deficiency, which showed m/z 276 ion peak on the spectrum by precursor ion scan of methylated compounds of dried raw urine. This was identified as 3-hydroxyisovalerylcarnitine. By ESI/MS, hemolysate was analyzed and an ion peak of abnormal alpha subunit of hemoglobulin, Hb MBoston, was clearly separated from the normal alpha subunit. Serum transferrin precipitated with anti-transferrin serum was analyzed by MALDI/TOF/MS. The transferrin-antibody complex in the immunoprecipitates was separated into transferrin and IgG in an acidic pH, which is the usual condition of loading on MALDI/TOF/MS. Ions of IgG and other minor components were not superimposed on the transferrin ions. Transferrin isoform with a molecular weight about 2.2kDa smaller than normal transferrin, which is contained in the serum from patients with carbohydrate-deficient glycoprotein syndrome, was identified by this method. The MALDI/TOF/MS analysis of immunoprecipitates may serve as a simple and sensitive method to identify the molecular weight heterogeneity of various biological materials.