Peripheral blood mononuclear cells (PBMCs) are an easy accessible cellular part of the blood organ and, along with platelets, represent the only site of active gene expression in blood. These cells undergo immunophenotypic changes in various diseases and represent a peripheral source of monitoring gene expression and posttranslational modifications relevant to many diseases. Little is known about the source of many blood proteins and we hypothesise that release from PBMCs through active and passive mechanisms may account for a substantial part of the plasma proteome. The use of state-of-the-art proteomic profiling methods in PBMCs will enable minimally invasive monitoring of disease progression or response to treatment and discovery of biomarkers. To achieve this goal, detailed mapping of the PBMC proteome using a sensitive, robust, and quantitative methodological setup is required. We have applied an indepth gel-free proteomics approach using tandem mass tags (TMT), unfractionated and SCX fractionated PBMC samples, and LC-MS/MS with various modulations. This study represents a benchmark in deciphering the PBMC proteome as we provide a deep insight by identifying 4129 proteins and 25503 peptides. The identified proteome defines the scope that enables PBMCs to be characterised as cellular major biomarker pool within the blood organ. 1. Introduction Peripheral blood mononuclear cells (PBMCs) constitute the cellular part of the blood organ containing all blood cells with a round nucleus. PBMCs are mainly comprised of monocytes, T cells, B cells, natural killer (NK) cells, and dendritic cells. Thus, the PBMCs contain different cell types that play important roles in the immune system monitoring immune-relevant events and respond in an inflammatory manner [1]. In recent years PBMCs have received growing attention as surrogate markers of several diseases. For example, in vitro data describe the response in PBMCs upon contact with diseased cells [2]. PBMCs can be obtained relatively easy from routinely collected blood samples, and therefore they provide direct access to physiologically relevant (immune) proteins without the well-known analytical difficulties of native human plasma originating from the presence of highly abundant proteins [3]. So far, most Omics studies utilising PBMCs were transcriptional profiling experiments in the context of inflammatory (e.g., preeclampsia, rheumatoid arthritis, and chronic pancreatitis) and malignant (e.g., chronic lymphocytic leukaemia and renal cell carcinoma) diseases [4–8]. Although these studies revealed a number of
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