Quantification of the Transcript Variants in Cancer Cell Lines by Targeted Absolute Quantitative Proteomics and Correlation with mRNA Expression.

proteins have key roles in nuclear structural integrity and chromosomal stability. cumulative protein expression of all variants is reported by semi-quantitative Western blotting. To date, there have not been specific antibodies for the individual transcript variants. We developed a mass spectrometric approach for the quantification of transcript variants. A signature peptide for each specific splice variant of was selected. A LC-MS/MS assay based on the selected signature peptides and their labeled internal standards was established to measure the expression of transcript variant concentrations. The method validation was carried out according to Food and Drug Administration (FDA) guidelines. The expression levels of the transcript variants were measured in samples derived from MCF7 and U937 cell lines. RT-qPCR assay was also used to quantitate and compare the mRNA expression of splice variants of . The established and validated method showed a great linearity, sensitivity, and precision. The different expressed variants in different cell lines were measured and their levels were in concordance with qRT-PCR results. The developed method is reproducible, reliable, and sensitive for measuring different transcript variants in different cell lines.