Proteomic profiling of soft tissue sarcomas with SWATH mass spectrometry

Soft tissue sarcomas (STS) are a group of rare and heterogeneous cancers. While large-scale genomic epigenomic profiling STS have been undertaken, proteomic analysis has thus far limited. Here we utilise sequential window acquisition all theoretical fragment ion spectra mass spectrometry (SWATH-MS) for formalin fixed paraffin embedded (FFPE) specimens from cohort patients ( n = 36) across four histological subtypes (leiomyosarcoma, synovial sarcoma, undifferentiated pleomorphic sarcoma dedifferentiated liposarcoma). We quantified 2951 proteins cases show that there is significant enrichment gene sets associated with smooth muscle contraction in leiomyosarcoma, RNA splicing regulation leukocyte activation sarcoma. further identified subgroup distinct expression profile panel proteins, worse survival outcomes when compared to the rest cohort. Our study highlights value comprehensive characterisation as means identify histotype-specific profiles describe key biological pathways clinical therapeutic relevance; well discovering new prognostic biomarkers this difficult-to-treat diseases. • Proteomic FFPE soft was performed by SWATH MS. Subtype-specific protein-protein interaction networks were identified. A patient outcome defined. subset MS validated orthogonal immunohistochemical analysis.