Key Publications
Empowered by recent developments in MS instrumentation and experimental protocols, MS researchers now have diverse choices with respect to the questions: “what fragmentation method to use?”, “how accurate should be the measurements of the m/z ratios?”, “what proteases to use?”, and “what PTMs to focus on?”. Unfortunately, popular MS/MS database search tools have not kept pace with the increased diversity of the data. Moreover, since different laboratories employ different combinations of tools, capabilities of analyzing the data vary widely and results obtained in one laboratory are difficult to reproduce in another laboratory. This creates a proteomics version of the Tower of Babel when the tools may become so diverse that different laboratories may loose ability to “speak” the same computational language.
CCMS advocates using universal MS tools that perform well for diverse types of spectral datasets. We emphasize that we do not intend to customize these tools for specific spectral datasets but rather to develop a robust probabilistic model that works well across all datasets.
Similarly to lack of universal tools for identification of linear peptides, there are still no universal tools for analyzing cross-linked peptides. While cross-linking has the potential to construct high-resolution maps of protein interactions, shortage of algorithms for identification of spectra from cross-linked peptides, limits the applicability of cross-links.