Improving mass spectrometry peak detection using multiple peak alignment results

Mass spectrometry data are often corrupted by noise. It is very difficult to simultaneously detect low-abundance peaks and reduce false-positive peak detection caused by noise. In this paper, we propose to improve peak detection using an additional constraint: the consistent appearance of similar true peaks across multiple spectra. We observe that false-positive peaks in general do not repeat themselves well across multiple spectra. When we align all the identified peaks (including false-positive ones) from multiple spectra together, those false-positive peaks are not as consistent as true peaks. Thus, we propose to use information from other spectra in order to reduce false-positive peaks. The new method improves the detection of peaks over the traditional single spectrum based peak detection methods. Consequently, the discovery of cancer biomarkers also benefits from this improvement. Source code and additional data are available at: http://www.ece.ust.hk/similar to eeyu/mspeak.htm.