Flame atmospheric pressure chemical ionization (FAPCI) combined with negative electrospray ionization (ESI) mass spectrometry was developed to detect the ion/molecule reactions (IMRs) products between nitric acid (HNO 3 ) and negatively charged amino acid, angiotensin I (AI) and angiotensin II (AII), and insulin ions. Nitrate and HNO 3 -nitrate ions were detected in the oxyacetylene flame, suggesting that a large quantity of nitric acid (HNO 3 ) was produced in the flame. The HNO 3 and negatively charged analyte ions produced by a negative ESI source were delivered into each arm of a Y-shaped stainless steel tube where they merged and reacted. The products were subsequently characterized with an ion trap mass analyzer attached to the exit of the Y-tube. HNO 3 showed the strongest affinity to histidine and formed (M histidine -H+HNO 3 ) – complex ions, whereas some amino acids did not react with HNO 3 at all. Reactions between HNO 3 and histidine residues in AI and AII resulted in the formation of dominant M AI -H+(HNO 3 ) - and M AII -H+(HNO 3 ) – ions. Results from analyses of AAs and insulin indicated that HNO 3 could not only react with basic amino acid residues, but also with disulfide bonds to form M-3H+(HNO 3 ) n 3- complex ions. This approach is useful for obtaining information about the number of basic amino acid residues and disulfide bonds in peptides and proteins. Graphical Abstract ᅟ