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Software for identification of mutant proteins, splicing variants and SNPs in MS/MS data

Mutations cause a wide spectrum of diseases including cancers. Knowledge of mutation profi les allows us to understand which processes are altered and select therapies accordingly. Modern high-throughput methods like SNP chips and NGS are used for alteration screening; however, the mass spectrometry of proteome is not used for this purpose yet.

Software for the identifi cation of mutant, polymorphic and/or alternatively spliced genes on protein level using MS spectra/fragmentation data. It uses a dedicated mutation/SNPs/splice variant database with a unique coverage (number of both mutation and integrated information sources). The search space can be optionally extended beyond the known disease-associated mutations by including in silico generated sets of mutants with predicted impact on protein function (e.g. changes in active sites of enzymes, sites of post-translational modifi cation). A database for the detection of non-canonical splicing variants is also available.

The software allows to software upgrade massspectrometer into a tool for reading of mutations, polymorphisms and protein splicing variants spectra in addition to reference sequence. This type of information is critical in cancer research and diagnostics of somatic mutations, but can be used also in other genetics/ proteomics applications. The advantage of the MS over the standard nucleic acid-based approaches is the possibility to directly observe the effect of mutation on posttranslational modifi cations.

Beta-version of the software, access through the web interface

Palacky University Olomouc – Institute of Molecular and Translational Medicine (IMTM), Faculty of Medicine and Dentistry