Although heavily concentrated and studied, the statistical accuracy of peptide identification remains challenging. There are many peptide identification methods using database searches and assigning the E-value to peptide hits, however, the E-values reported by different methods do not agree with each other and none of them agree with the textbook definition of the E-value. This obviously hinders the feasibility of combining search results from different methods. In particular, if one wishes to combine methods with user-assigned weights. When prior knowledge is available, it is often desirable to weight search methods differently before combining their search results. We have provided a way to combine search results democratically in one of our 2008 publications. When different weights are present, an instability issue occurs if some of the weights are nearly degenerate. In 2011, we have devised a mathematical framework to completely eliminate the possible instability. This work was published in PLoS One(doi:10.1371/journal.pone.0022647). We have expanded this idea to incorporate the case when the methods being considered are correlated. The manuscript is currently under preparation. Since most interactome data are obtained from pull down experiment analyzed using mass spectrometers to identify co-pull-down partner proteins, our efforts in proteomics also include investigation of protein-protein interaction network as well as interactome data quality issue. Our investigation on these problems has led to development of a few tools that are suitable for network exploration, hypotheses forming and gene enrichment analysis. For the past year, one of our major efforts is to undersatnd physical mechanisms for peptide fragmentation so as to predict the possibility of observing a certain peak. If this works, it can significantly improve peptide scoring by providing a peptide-specific peak filtering. The preliminary results inidicate that the dissociation energy can be a good indicator for the observability of certain peaks, at least for short peptide with non-polar side-chains. The manuscript was recently published in the Rapid Communications in Mass Spectrometry.
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