Evaluation of Different Interpretation Strategies to Discover PTM in MS/MS Peptide Fragmentation Data

Abstract
The phenomenon of acquired high quality MS/MS spectra that can not be explained within typical sequence database searches is well known. Although protein identification was successful it is manually very laborious and in most cases even impossible to match these spectra with any suggested protein sequence.

The procedure of second pass searches has been developed to overcome this problem. Here we report from our in house developed tool PTM-Explorer (Protagen AG, Dortmund, Germany; Bruker Daltonik GmbH, Bermen, Germany). Two LC-MS/MS datasets of recombinant kinase proteins (MAPK 12 and MAPK 13) have been used for the evaluation.