How should I search for the Pan-Methyl Lysine PTM in LC-MS/MS data when using your PTMScan® Pan-Methyl Lysine Kit #14809?

Our PTMScan Pan-Methyl Lysine Kit #14809 will enrich for all three forms of methylated lysine: mono, di and tri-methyl lysine. To reduce the complexity of the search space, it is necessary to search for each modification separately, then for all three combined for a total of 4 searches. Therefore, we search for mono-methyl lysine alone as a variable modification, di-methyl lysine alone as a variable modification, tri-methyl lysine alone as a variable modification, then all three forms combined. Each search also has oxidized methionine as a variable modification and the alkylation of cysteine as a static modification. Please note that lysine methylation will often block trypsin cleavage and CST allows for 5 mis-cleavages. Following the 4 independent searches, the results can be combined for a final data set.

CST uses the following parameters for the Comet search platform:
Pre-cursor mass tolerance (+/-) 50ppm
Product ion match tolerance (+/-) 0.02Da
Post-search filter on pre-cursor mass (+/-) 5 ppm
FDR cutoff 2%
 

Last updated: February 28, 2024