You have to calibrate i.e. run series of pectin samples with varied DM... there are two distinctive bands around 1700 cm-1, but you can not just integrate them, there is spectral interference from other compounds. There has been many publications on this subject in Carb Polymers in the 1990's early 2000..
No, there is definitely interference from other compounds including a water signal, you'd have to deconvolute the spectrum Carb polymers 42 (2000) 359-368.