Figure 2.
Identification of proteins in a gel band by mass spectrometry. MALDI-TOF mass spectrum of the peptides produced by in-gel trypsin digestion of band no. 217 (molecular mass of ∼100 kD, fraction 35). The peak masses were used to identify proteins present in the band with the protein identification algorithm ProFound. The dominant protein component was Nup120p, which was identified with a probability 5 × 1022 higher than the next most probable protein. The peaks arising from Nup120p were subtracted from the spectrum and a new search was initiated, identifying Kap120p with a probability 3 × 109 higher than the next most probable protein. Finally, the peaks arising from Kap120p were subtracted from the spectrum and a new search was initiated identifying Pdr6p/Kap122p with a probability 1 × 108 higher than the next most probable protein. Colored markers indicate which peaks arise from each of the three identified proteins. The peaks labeled T arise from trypsin self-digestion. Unlabeled peaks likely originate from modified or incompletely digested peptides in Nup120p, Kap120p, and Kap122p, or from additional proteins.