Although great success of microvascular free-flap transplantation surgery has been achieved in recent years, between 1.5% and 15% of flaps are still lost due to vascular occlusion. The clinical challenge remains to salvage a transplant in the case of vascular complications. Since flap loss is devastating for the patient, it is of utmost importance to detect signs of complications or of conspicuities as soon as possible. Rescue success rates highly depend on early revision. In this study, we collected blood samples during transplantation surgery from either the contributory artery or the effluent vein of the flap and applied a targeted mass spectrometry-based approach to quantify 24 acute phase proteins, cytokines, and growth factors in 63 plasma samples from 21 hospitalized patients, generating a dataset with 9450 protein concentration values. Biostatistical analyses of the targeted plasma protein concentrations in all 63 plasma samples showed that venous concentrations of macrophage colony-stimulating factor (M-CSF) provided the highest accuracy for discriminating patients with either clinical conspicuities or complications from control individuals. Using 21.33ng/mL of M-CSF as the diagnostic threshold when analyzing venous blood plasma samples, the assay obtained a sensitivity of 0.93 and a specificity of 0.85 with an area under the curve value of 0.902 in the receiver operating characteristic analysis. Overall, our results indicate that M-CSF is a potential molecular marker for early risk prognosis of free-flap transplant failure.