Tandem Mass Spectrometers
Tandem mass spectrometry (MS/MS) is utilized, where a mixture of peptides is used for getting amino acid sequences of peptides one at a time. The first part of tandem spectrometer selects one peptide on the basis of mass, which is then dissociated or fragments by collision with an inert gas like argon or nitrogen. In the second part of tandem mass spectrometer, the resulting fragments are separated and tandem mass spectra or MS/MS spectra are obtained.

Schematic Represention of Tandem Mass Spectrometry for Dtermination of a Peptide Sequence(F1 to F4 peptide fragments Obtained from Peptide P and m1-m4 corresponding Masses Determined by MS2; H, N, S, T and K=Different Amino Acids)

Tandem mass spectra are usually interpreted with computer assistance or are matched against database, while interpreting the data of C-terminal or N-terminal fragments. One will notice that C-terminal fragment starts with masses 147 (lys) or 175 (arg) and the next fragment peak differs by mass of a single second amino acid, which can be identified by mass difference. Consecutive amino acids will be identified using this principle thus giving amino acid sequence of a small peptide. Similar will be the case with the N-terminal ion series.

Other mass spectrometers
In addition to four basic types of mass spectrometers described above, there are other instruments which are relatively less important.