Facile removal of high mannose structures prior to extracting complex type N-glycans from de-N-glycosylated peptides retained by C18 solid phase to allow more efficient glycomic mapping.

Proteomics

PubMedID: 24174266

Lin CH, Kuo CW, Jarvis DL, Khoo KH. Facile removal of high mannose structures prior to extracting complex type N-glycans from de-N-glycosylated peptides retained by C18 solid phase to allow more efficient glycomic mapping. Proteomics. 2013;.
The relative amount of high mannose structures within an N-glycomic pool differs from one source to another but quite often it predominates over the larger size complex type structures carrying biologically important glyco-epitopes. An efficient method to separate these two classes of N-glycans would significantly aid in detecting the lower abundant components by mass spectrometry. Capitalizing on an initial observation that only high mannose type structures were recovered in the flow through fraction when PNGase F digested peptides were passed through a C18 cartridge in 0.1% formic acid, we demonstrated here that native complex type N-glycans can be retained by C18 cartridge and to be efficiently separated from both the smaller high mannose type structures, as well as de-N-glycosylated peptides by step-wise elution with increasing acetonitrile concentration. The weak retention of the largely hydrophilic N-glycans on C18 resin is dependent not only on size but also increased by the presence of a6-fucosylation. This was shown by comparing the resulting N-glycomic profiles of the washed and low acetonitrile eluted fractions derived from both a human cancer cell line and an insect cell line.