We are planning to develop a mass spectrometry based quantitative assay for the monitoring of certain proteins/ genes. As part of this, we are working on selecting the best proteotypic peptide for each of our target proteins using Skyline.

There are certain proteins which do not have any unique proteotypic peptide. But when we try to apply uniqueness at the gene level, we could see certain peptides considered as unique to a gene. So, I would like to know whether we can consider such peptides (razor peptides) for our quantitative proteomics?

For example, we are looking for a proteotypic peptide of p40 (deltaNP63alpha). However, the peptide sequence for p40 is present in its multiple isoforms. Hence we are not able to select specific proteotypic peptides for p40 isoform (i.e alpha).

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Jyoti