BackgroundCorn stover is lignocellulosic biomass that has potential to be used as raw material for bioethanol production. In the current research, dilute ammonia pretreatment was used to improve the accessibility of corn stover carbohydrates to subsequently added hydrolytic enzymes. Some carbohydrates, however, were still present after enzymatic hydrolysis and fermentation. Hence, this research was aimed to characterise the recalcitrant carbohydrates, especially the oligosaccharides that remained after hydrolysis and fermentation of dilute ammonia-pretreated corn stover (DACS).ResultsAbout 35% (w/w) of DACS carbohydrates remained after enzymatic hydrolysis and fermentation of the released monosaccharides. One-third of these recalcitrant carbohydrates were water soluble and composed of diverse oligosaccharides. By using UHPLC-MSn, more than 50 oligosaccharides were detected. Glucurono-xylooligosaccharides (UAXOS) with a degree of polymerisation (DP) less than 5 were the most abundant oligosaccharides. The (4-O-methyl) glucuronosyl substituent was mostly attached onto the terminal xylosyl residue. It was shown that the glucuronosyl substituent in some UAXOS was modified into a hexenuronosyl, a glucuronamide or a hexenuronamide residue due to the dilute ammonia pretreatment. Another group of abundant oligosaccharides comprised various xyloglucan oligosaccharides (XGOS), with a DP 5 annotated as XXG as the most pronounced. In addition, disaccharides annotated as xylosyl-glucose with different β linkages as well as larger carbohydrates were present in the fermentation slurry.ConclusionsAround one-third of the 35% (w/w) recalcitrant DACS carbohydrates remained as water-soluble saccharides. In this study, more than 50 recalcitrant oligosaccharides were detected, which mostly composed of xylosyl and/or glucosyl residues. The most pronounced oligosaccharides were UAXOS and XGOS. Hence, α-glucuronidase and α-xylosidase were suggested to be added to the enzyme mixture to degrade these oligosaccharides further, and hence the fermentation yield is potentially increased.Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-017-0803-3) contains supplementary material, which is available to authorized users.