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There are also key chemical compositional differences between apples and pears. These factors play a crucial role in pre-fermentation and fermentation decisions for perry production.

Compared to most apples, pears tend to have more sugar and total phenolic compounds. Main sugars in perry pears are Glucose (192 -284 mg/L), Xylose (140-176 mg/g), and Galacturonic acid (108-118 mg/g). Types of sugar that are present in the juice play an important role in yeast activity and determine the success of fermentation.Therefore, if perry fermentation is being started with inoculated yeast, yeast selection should be done carefully. While there are major similarities between cider and perry fermentations, using cider yeasts might not always yield the best results in perry fermentations. Traditional yeasts used in cider making (s.cervisae strains) are mostly glucophilic, while also being able to ferment fructose and sucrose. In apple juice, fructose is found in abundance, making up to 70% of total fermentable sugars. However, unlike the juice of apples, pear juice contains significant quantities of non-fermentable sugar alcohols, the most abundant being sorbitol. Unfermentable sugars such as sorbitol, which can give the finished drink a residual sweetness. The presence of sorbitol can also give perry a mild laxative effect

Pear juices contain rather low levels of amino acids, sources of nitrogen such as aspargine, aspartic acid and glutamic acid. Due to poor levels of nitrogen based yeast nutrients, additional yeast nutrients like Go-Ferm must be added to the pear juice must before fermentation. Lack of yeast assimilable nitrogen (YAN) can cause a stuck fermentation, as the yeast fails to metabolize all sugar, or at least to do so in a timely manner, and can produce off-aromas- especially H2S. . Therefore, during perry fermentation, it might be necessary to add nutrients like Fermaid-K or Diammonium Phosphate (DAP) to bring YAN concentration to desirable levels and ensure a smooth fermentation.

After initial fermentation, many perrys go through malolactic fermentation. On average, compared to apples, pears have higher levels of titrable acidity, most of it being citric acid. In environments with high levels of malic acid, such as apple must or grape must in winemaking, Malolactic fermentation (MLF) bacteria converts malic acid to lactic acid that reduces perception of acidity and enhances complexity of the finished product. However, if high levels of citric acid is present, like in pear must, MLF bacteria catabolyzes citric acid to acetic acid and oxaloacetic acid, instead of lactic acid. This results in a more floral and citrusy final product that does not have diacethyl (fake movie buttered popcorn) odor that is typical for most products undergone MLF.