Examples of mass spectra of purified transthyreting and complex mixtures of proteins. In the upper spectra, purified transthyretin was applied to a CM10 ProteinChip array and spectra at medium (left) and high (right) laser energies were acquired. Peaks for transthyretin with z = 1 and 2, and transthyretin dimers are prominent in the medium laser spectrum, while aggregates of 2–9 transthyretin molecules can be seen at high laser energy. The lower spectra are averaged from 90 individual spectra (45 samples in duplicate) of the pH4 extract from Q anion exchange chromatographed plasma samples applied to CM10 ProteinChip arrays. Peaks for α-globin and albumin that were used to develop mass windows for the algorithm are annotated.