Protein methylation has been studies for over two decades, mainly in histones but more recently also in non-histone proteins. Despite the great advances in technologies, particularly the application of Orbitrap technology, proteomic analysis of methylation still remains a challenge. This is mainly due to the small size of methylations, their position on fragmented peptides and issue of incorrect identification. A number of different methods have been developed or modified to varying degrees of success in order to enrich for protein methylation prior to mass spectrometric analysis. Despite the availability of different techniques, it is important to understand the underlying strategy employed, the type of sample being analysed and the methylation-related question being investigated. Without such knowledge it is very easy to become lost analysing large volumes of insignificant data or misinterpret the data output.

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Neurofibromatosis type 1 (NF1) is an autosomal dominant RASopathy disease that predisposes individuals to developing benign neurofibromas and malignant peripheral nerve sheath tumors (MPNST). The mechanisms of NF1-tumorigenesis or the radical curatives have not been established. Using a unique transcriptome and proteome integration method, iPEACH^1–4, we previously identified translationally controlled tumor protein (TCTP) as a novel biological target for NF1-associated tumors⁵. To evaluate the function of TCTP in NF1-associated malignant tumor cells, the cellular interactome of TCTP, overexpressed as Flag-tagged protein, was identified by affinity-purification using anti-FLAG antibody coupled with SWATH-MS analysis (AP-SWATH). The data described in this paper have been deposited to jPOST^6,7 with the identifier JPST000107.

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