Abstract Allogeneic hematopoietic stem cell transplantation (AHSCT) has been shown to provide longterm disease-free survival for otherwise fatal malignant or nonmalignant hematological disorders. Acute and chronic graft-versus-host disease (aGvHD and cGvHD) are a major complication following AHSCT and are associated with a substantial morbidity and mortality. Identification of patients (pts) likely to develop severe forms of GvHD could allow the selection of more aggressive therapeutic regimens for patients assessed to be at high risk. Serum samples and clinical data were available from 124 pts (age 18-70) who had received AHSCT. Five pts suffered no GvHD, 15 de novo cGvHD, 21 aGvHD but no cGvHD and 83 both aGvHD and cGvHD (overlap). Of pts with aGvHD 51% had grade I disease and of pts with cGvHD 53% had limited disease. Matrix assisted laser desorption/ionization (MALDI) mass spectra were acquired from the samples using the deep MALDI method, allowing a deep probing of the proteome. Spectra were preprocessed and spectral features defined. The integrated intensities of these features were combined with the clinical data using deep learning based machine learning to create classifiers able to stratify patients into groups depending on occurrence and severity of GvHD. Classifiers could be developed with significant power to predict occurrence and severity of GvHD. The area under the curves (AUCs) obtained for the clinical questions investigated and examples of the sensitivity and specificity achievable are summarized in the table. AUCSensitivity/SensitivityaGvHD ?0.7463%/80% or 80%/65%Grade II or severe aGvHD?0.6560%/67%cGvHD post aGvHD?0.7563%/75%severe vs mild cGvHD?0.6867%/69% It is possible to provide information on occurrence and severity of GvHD from mass spectral analysis of post-transplant serum samples. If validated, this panel of tests could provide additional information useful for clinicians choosing treatment regimens for pts following AHSCT. Citation Format: Heinrich Roder, Andreas-Claudius Hoffmann, Joanna Roder, Michael Koldehoff. A panel of mass spectrometry based serum protein tests for predicting graft-versus-host disease (GvHD) and its severity. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 599. doi:10.1158/1538-7445.AM2015-599