▁solve ▁the ▁sequ encing ▁of ▁pe pt ides . ▁Gener ally , ▁there ▁are ▁two ▁approaches : ▁database ▁search ▁and ▁de ▁nov o ▁sequ encing . ▁Database ▁search ▁is ▁a ▁simple ▁version ▁as ▁the ▁mass ▁spect ra ▁data ▁of ▁the ▁unknown ▁pe pt ide ▁is ▁submitted ▁and ▁run ▁to ▁find ▁a ▁match ▁with ▁a ▁known ▁pe pt ide ▁sequence , ▁the ▁pe pt ide ▁with ▁the ▁highest ▁matching ▁score ▁will ▁be ▁selected . ▁This ▁approach ▁fails ▁to ▁recognize ▁novel ▁pe pt ides ▁since ▁it ▁can ▁only ▁match ▁to ▁existing ▁sequences ▁in ▁the ▁database . ▁De ▁nov o ▁sequ encing ▁is ▁an ▁assignment ▁of ▁fragment ▁ ions ▁from ▁a ▁mass ▁spectrum . ▁D ifferent ▁algorithms ▁are ▁used ▁for ▁interpretation ▁and ▁most ▁instruments ▁come ▁with ▁de ▁nov o ▁sequ encing ▁programs . ▁ ▁Pe pt ide ▁fragment ation ▁Pe pt ides ▁are ▁pro ton ated ▁in ▁positive - ion ▁mode . ▁The ▁pro ton ▁initially ▁loc ates ▁at ▁the ▁N - ter minus ▁or ▁a ▁basic ▁resid ue ▁side ▁chain , ▁but ▁because ▁of ▁the ▁internal ▁sol v ation , ▁it ▁can ▁move ▁along ▁the ▁back bone ▁breaking ▁at ▁different ▁sites ▁which ▁result ▁in ▁different ▁fragments . ▁The ▁fragment ation ▁rules ▁are ▁well ▁explained ▁by ▁some ▁publications . ▁ ▁Three ▁different ▁types ▁of ▁back bone ▁b onds ▁can ▁be ▁broken ▁to ▁form ▁pe pt ide ▁fragments : ▁alk yl ▁car b ony l ▁( CH R - CO ), ▁pe pt ide ▁am ide ▁bond ▁( CO - N H ), ▁and ▁am ino ▁alk