Abstract: Methods are provided for quantifying the TYMS, TYMP, UCK1, UCK2, UPP1, OPRT, dCK, TK1, DPYD, CDA, RRM1, and/or RRM2 proteins directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring/Multiple Reaction Monitoring (SRM/MRM). The biological samples are chemically preserved with formaldehyde-containing agents/fixatives including formalin-fixed tissue/cells, formalin-fixed/paraffin embedded (FFPE) tissue/cells, FFPE tissue blocks and cells from those blocks, and tissue culture cells that have been formalin fixed and or paraffin embedded. A protein digest sample is prepared from the biological sample and the TYMS, TYMP, UCK1, UCK2, UPP1, OPRT, dCK, TK1, DPYD, CDA, RRM1, and/or RRM2 proteins are quantitated in the digest by SRM/MRM mass spectrometry.