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Can a LC-MS/MS based omic antigen identification method provide reliable results and comply with pharmaceutical regulations? In this study, we performed several assays and evaluations to validate the immunopeptidomic pipeline according to FDA and EMA pharmaceutical guidelines. We performed a validation of the accuracy, precision, specificity, limit of detection and robustness of our LC-MS/MS system using an Orbitrap Fusion Lumos. We present different approaches that could be transferred to other MS-based discovery applications to enhance further personalized clinical therapies.

Personalized multipeptide vaccines are currently being discussed intensively for tumor immunotherapy. In order to identify epitopes—short, immunogenic peptides—suitable for eliciting a tumor-specific immune response, human leukocyte antigen-presented peptides are isolated by immunoaffinity purification from cancer tissue samples and analyzed by liquid chromatography-coupled tandem mass spectrometry (LC–MS/MS). Here, we present MHCquant, a fully automated, portable computational pipeline able to process LC–MS/MS data automatically and generate annotated, false discovery rate-controlled lists of (neo-)epitopes with associated relative quantification information. We could show that MHCquant achieves higher sensitivity than established methods. While obtaining the highest number of unique peptides, the rate of predicted MHC binders remains still comparable to other tools. Reprocessing of the data from a previously published study resulted in the identification of several neoepitopes not detected by previously applied methods. MHCquant integrates tailor-made pipeline components with existing open-source software into a coherent processing workflow. Container-based virtualization permits execution of this workflow without complex software installation, execution on cluster/cloud infrastructures, and full reproducibility of the results. Integration with the data analysis workbench KNIME enables easy mining of large-scale immunopeptidomics data sets. MHCquant is available as open-source software along with accompanying documentation on our website at https://www.openms.de/mhcquant/.

Hematopoietic stem and progenitor cells (HSPCs) are responsible for the production of blood and immune cells. Throughout life, HSPCs acquire oncogenic aberrations that can cause hematological cancers. Although molecular programs maintaining stem cell integrity have been identified, safety mechanisms eliminating malignant HSPCs from the stem cell pool remain poorly characterized. Here, we show that HSPCs constitutively present antigens via major histocompatibility complex class II. The presentation of immunogenic antigens, as occurring during malignant transformation, triggers bidirectional interactions between HSPCs and antigen-specific CD4+T cells, causing stem cell proliferation, differentiation, and specific exhaustion of aberrant HSPCs. This immunosurveillance mechanism effectively eliminates transformed HSPCs from the hematopoietic system, thereby preventing leukemia onset. Together, our data reveal a bidirectional interaction between HSPCs and CD4+T cells, demonstrating that HSPCs are not only passive receivers of immunological signals but also actively engage in adaptive immune responses to safeguard the integrity of the stem cell pool.

The structural and electrical properties of as grown multicrystalline (mc) solar silicon have been characterized with special emphasis on the ingot's edge regions. For this purpose a vertical cross section of an mc-Si Bridgman ingot was investigated by Fourier transform infrared spectroscopy (FTIR), laser scattering tomography (LST), lateral photovoltage scanning (LPS), infrared microscopy and microwave detected photoconductivity decay (&PCD). Images of the distribution of dislocations, grain boundaries, precipitates, impurities (O, N, C) and the minority charge carrier lifetime were obtained, partly differentiating the defects by their electrical activity. In particular the LPS method displays dopant striations indicating the shape of the phase boundary. Deviations of the phase boundary from a slightly convex shape in the middle of the ingot to a concave one in the vicinity of the side walls could be observed. The existence of an horizontal temperature gradient deduced from this shape is the reason for convection in the melt. The influence on the concentration profiles of interstitial oxygen and the correlation with the minority charge carrier lifetime are discussed.

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