A multifactorial differential analysis of serum proteins using mass spectrometry distinguished samples from pregnant women with severe early-onset preeclampsia (n ϭ 11) from those of control individuals with uneventful pregnancies (n ϭ 13). Serum proteins were fractionated by either their affinities to reversed-phase material coated magnetic beads or by fractionated precipitation. The on-average most abundant ion signals were observed at m/z 9390, 9103, and 8886. The best differentiating ion signals between the two sample groups were found at m/z 13,715, 13,834, and 13,891. The normalized intensities of these ion signals were on-average lower in the preeclampsia group than in the control group. The six ion signal intensities enabled sorting of the individual spectra with high accuracy. Sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE) analysis showed that a protein band migrating just above the 14 kDa marker band contained transthyretin (P02766; M r (avg.): 13,761). Densitometric analysis of the transthyretin bands showed lower intensities in the preeclampsia samples with respect to those of the controls. Nephelometric analysis of the serum samples determined the mean concentration of transthyretin in the preeclampsia group were lower (0.16 mg/mL; range: 0.13 to 0.20; SD: 0.03) than that in the control group (0.19 mg/mL; range: 0.14 to 0.22; SD: 0.02), substantiating the role of transthyretin concentration differences in the comparison of the two groups. Altogether, our findings support the theory of preeclampsia being a heterogeneous disorder that might be sub-classified by a defined proteome signature in maternal blood using multifactorial analysis of affinity-fractionated serum samples. (J Am