Spectrum libraries are an invaluable starting point for developing targeted assays (e.g. SRM, PRM) because they provide information about fragmentation patterns and retention times. When library data are collected under a variety of LC conditions, the use of synthetic peptide standards can greatly improve the ability to accurately predict retention time in new experiments. Unfortunately, any samples not including those peptide standards cannot be used in the predictions. We present a method for selecting peptides endogenous to a sample to act as standards and demonstrate their use for predicting retention times of other peptides including those with chemical modifications, which indicate portability to both unmodified and post-translationally modified peptides.