|No enzyme option||Jason Held||2012-02-25|
I’ve got some data from samples that were digested with less-specific enzymes such as chymotrypsin, pepsin, thermoylsin etc that I’d like to do MS1 filtering analysis on and keep intact the amino acid numbering for each peptide in a protein. No enzyme is completely specific and i'd like to assess the reproducibility of peptide generation, and I think your MS1 platform is ideal for testing these less-specific enzymes with a targeted proteomics approach. For example, chymotrypsin cuts at far more than the 5-6 putative 'specific' cleavage sites that most people use under typical digestion conditions. At the end of the day, targeted proteomics is more about reproducibility than specificity.
I did my mascot searches with 'no enzyme' cleavage and would like to move all my peptides over to Skyline. However, I hadn't realized beforehand that there is no ‘no enzyme’ option in Skyline. I tried putting all amino acids cleavages sites, but then I’m limited to 9mers since I can only have 9 missed cleavages. I then tried making a background proteome and adding spectra from the library explorer, but that requires an enzyme to keep the amino acid info intact. I could make peptide lists and paste them in – however, this loses the amino acid # info and would be a nice feature to have. I'd suggest including a 'no enzyme' option in Skyline.