Example of MS and MS/MS on the LTQ-FT. (a) A mass spectrum of yeast peptides eluting from the column at a particular time point in the LC gradient and electrosprayed into the LTQ-FT mass spectrometer. The inset is a zoom of the doubly charged peptide ion at m/z 735.929, showing its natural isotope distribution and demonstrating very high resolution. (b) Tandem mass spectrum of the dominant peptide in (a). Peptides fragment on average once at different amide bonds, giving rise to carboxy-terminal containing y-ions or amino-terminal containing b-ions. The prominent y13++ ion is caused by fragmentation at the first amide bond, which is favored here because it is amino-terminal to proline. (See  for an introduction to peptide sequencing and identification by MS.) The mass of the peptide identified is within less than 1 ppm of the calculated value.