02. November 2015, 13:00 s.t.

Ernst-Abbe-Platz 2, seminar room 3423

Fragment Rarity-based Clustering of Mass spectra

Dr. Lukas Käll (Royal Institute of Technology, KTH Sweden)

Shotgun proteomics experiments generate large amounts of fragment spectra as primary data normally with high redundancy between and within experiments. Here, we have devised a clustering technique to identify fragment spectra stemming from the same species of peptide. As an aid in this process, we propose a distance calculation relying on the rarity of experimental fragment peaks, following the intuition that peaks shared by only a few spectra offer more evidence than peaks shared by a large number of spectra. We used this distance calculation and a complete-linkage scheme to cluster data from a recent large scale mass spectrometry-based study. The clusterings produced by our method have up to 40% more identified peptides for their consensus spectra compared to the previous state-of-the-art method. Furthermore, the advantage of our method increases the fewer clusters one allows, which is a desirable feature in the construction of spectral libraries.