The current disclosure provides for specific peptides, and derived
ionization characteristics of the peptides, from the KRT5, KRT7, NapsinA, TTF1, TP63, and / or MUC1 proteins that are particularly advantageous for quantifying the KRT5, KRT7, NapsinA, TTF1, TP63, and / or MUC1 proteins directly in biological samples that have been fixed in formalin by the method of Selected Reaction Monitoring (SRM)
mass spectrometry, or what can also be termed as Multiple Reaction Monitoring (MRM)
mass spectrometry. Such biological samples are chemically preserved and fixed wherein said biological sample is selected from tissues and cells treated 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 sample is prepared from said biological sample using the Liquid Tissue™ reagents and protocol and the KRT5, KRT7, NapsinA, TTF1, TP63, and / or MUC1 proteins are quantitated in the Liquid Tissue™ sample by the method of SRM / MRM
mass spectrometry by quantitating in the
protein sample at least one or more of the peptides described. These peptides can be quantitated if they reside in a modified or an unmodified form. An example of a modified form of a KRT5, KRT7, NapsinA, TTF1, TP63, and MUC1 fragment
peptide is
phosphorylation of a
tyrosine,
threonine,
serine, and / or other
amino acid residues within the
peptide sequence.