Introduction

The dominant ions in MS/MS spectra of peptides, which have been fragmented by low-energy CID, are often b-, y-ions and their derivatives resulting from the cleavage of the peptide bonds. However, MS/MS spectra typically contain many more peaks. These can result not only from isotope variants and multiply charged replicates of the peptide fragmentation products but also from unknown fragmentation pathways, sample-specific or systematic chemical contaminations or from noise generated by the electronic detection system. The presence of this background complicates spectrum interpretation. Besides dramatically prolonged computation time, it can lead to incorrect protein identification, especially in the case of de novo sequencing algorithms.

MS Cleaner implements novel algorithms for detection and transformation of multiply charged peaks into singly charged monoisotopic peaks, removal of heavy isotope replicates and random noise as well as a quantitative criterion for the efficient recognition of non-interpretable spectra. The approach is based on numerical spectral analysis and signal detection methods.