The classical Philadelphia-negative myeloproliferative neoplasms (MPNs) are clonal stem cell disorders of the bone marrow with significant niche dysregulation largely driven by abnormal megakaryocytes. The three classical MPN entities are polycythemia vera (PV), essential thrombocythemia (ET) and primary myelofibrosis (PMF), and established morphological differences between megakaryocytes of the three groups aid in their diagnostic classification. The haemodilute and often acellular nature of bone marrow aspirates from MPN patients have previously limited a proteomic analysis of in-vivo differentiated megakaryocytes from MPN samples. We undertook an unbiased proteomic analysis of in situ megakaryocytes and whole trephine sections from the bone marrow of patients with PV, ET and PMF. Using a novel, deep visual proteomics strategy, we dissected and analyzed megakaryocytes from 60 MPN patients and 20 patients with limited stage non-hodgkin’s lymphoma who had uninvolved bone marrows. We proved that megakaryocytes from PMF, PV and ET samples have distinct disease specific signatures and identified novel pathways of disease and biomarkers.