The intensity of a peak in an isotope pattern is the superposition of all isotope variants' abundances that have identical nominal mass (nucleon number) [36].
Identification performance can be significantly improved by adding isotope pattern information [27, 30, 41] but this data is not available for the two datasets used here.
An ion at m/ z 721.62 displayed a distinctive isotope pattern of a selenium-containing peptide, suggesting that it is either a SGGDILQSGCUG or RSGGDILQSGCUG peptide.
Our input is a measured isotope pattern from a high resolution mass spectrometer, and we want to find those molecules that best match this pattern.
An example is shown in Figure 2A,B where two ions partially coelute (compound A, monoisotopic m/ z 881.996, fifth isotope at 883.334 and Compound B (target), monoisotopic m/ z 883.663) and produce a multiplexed isotope pattern.
ESI+ mass spectrometry gave m/ z 402.1 (100 %), with an associated 69/71Ga isotope pattern, corresponding to the monocation, [Ga(L)]+.
Modifications on selenium-containing peptides were searched manually by distinctive isotope patterns and confirmed by the critical b and y ions in MS/MS.
Finally, we present the software tool SIRIUS (Sum formula Identification by Ranking Isotope patterns Using mass Spectrometry) that implements all of the above algorithms and combines them with an easy-to-use graphical user interface.
An overview of isotope pattern simulation is given in [36].
Ideally, mass information derived from MS measurements should be complemented by the fragmentation pattern achieved by MS or MSn, and the isotope pattern.
