with an experimentally determined spectrum a fragmentation model is used which takes account of all possible fragmentation pathways which a particular sequence of amino acids may undergo a peptide or protein may be identified by comparing an experimentally determined mass spectrum with spectra predicted using such a fragmentation model from a library of known peptides or proteins alternatively a de novo method of determining the amino acid sequence of an unknown peptide using such a fragmentation model may be used application_number US 54414600 A description referring first to fig1 the principal components of a tandem time of flight mass spectrometer suitable for carrying out methods according to the invention are shown in schematic form an unknown peptide sample or a mixture of such samples is introduced into a capillary 17 comprised in an electrospray ion source generally indicated by 1 a jet 18 comprising ions characteristic of said peptide is generated in the source 1 and at least some of these ions pass through an aperture in a sampling cone 2 into a first evacuated chamber 3 from the chamber 3 the ions pass through an aperture in a skimmer cone 4 into a second evacuated chamber 5 and are then transported by means of a hexapole ion guide 6 into a quadrupole mass analyzer 7 disposed in a third evacuated chamber 8 in a spectrometer of the kind illustrated in fig1 the molecular weight of the peptide may be determined by using the mass analyzer 7 in a non mass selective mode while a mass spectrum of the sample is acquired preferably the molecular weight is determined to within u00b1 0 5 daltons in order to record a fragmentation spectrum of.