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Post-Translational Modifications (PTMs)

Need for new tool assessment:

The analysis of PTMs is very challenging, as many PTMs are transient or labile with respect to MS analysis and are often present in low abundance resulting in incomplete amino acid sequence coverage and a failure to fully characterize the PTMs.  Biological complexity further impedes analysis as a single protein can have a number of amino acid residues that are modified by one or more different types of PTMs. Furthermore each modified residue may have a different effect on function.  Quantitative data on each modified amino acid residue are needed if we are to understand the dynamic changes of the proteome and the crosstalk and selectivity of different PTMs and their impacts on signaling cascades. Our experience has identified that the best methods for PTM analysis have the following characteristics: i) utilize enrichment to allow for the isolation of low abundance modified proteins (or peptides), ii) allow for the simultaneous identification and quantification of the protein, iii) identify the actual modified amino acid residue, iv) have the ability to quantify the extent of a protein modification under different conditions and v) are able to quantify the relative differences of the modified residue in a protein in with multiple modified residues.