Evaluation of Different Interpretation Strategies to Discover PTM in MS/MS Peptide Fragmentation Data
Poster Apr 05, 2007
Daniel Chamrad, Gerhard Korting, Ken Fantom, Andy West, Klaus Schneider, Ulrike Schweiger-Hufagel, Herbert Thiele and Martin Bluggel
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.
When there is a need to quickly analyze samples using a number of different PCR assays, it is likely that optimal conditions for each assay will not be the same. First, different assays often will require different annealing temperatures for their primers. In addition, amplicons may be designed to be of different lengths and therefore require varying durations of the extension step.READ MORE