Inverse metabolic engineering (IME) provides a strategy to rapidly identify the genetic elements responsible for the desired phenotype of a chosen target organism. This methodology has been successfully applied towards enhancing the N-linked glycosylation efficiency of Escherichia coli. Here, we describe the generation of differentially sized libraries from the E. coli W3110 genome followed by high-throughput semiquantitative glycan specific screening. DNA sequenced targets demonstrating increased levels of glycan production were selected for forward engineering, protein overexpression, and absolute quantification of glycoproteins.