Regression Analysis Applied to Mass Spectrometry (RAAMS) is an algorithm for interpreting 18O differential proteomics data. It is described in two articles: one accepted in Molecular and Cellular Proteomics, the other accepted in Bioinformatics. On this page you will find binaries and source code for our initial implementation of the RAAMS algorithm. Please note that the current implementation of RAAMS is a command line program and as such is not particularly user-friendly. We are working on a user-interface for RAAMS.
If you have questions about this software or data, please don't hesitate to contact Christopher Mason.
If you use this work in publication, please cite either of the two papers above.
An overview of this implementation of RAAMS is available. RAAMS is implemented as a part of the C++ library libmprc; in addition to RAAMS, libmprc includes, among other things, classes for FT-ICR transient processing and an implementation of Thrash.
The current version of libmprc/raams is 1.5, released 20 October 2006.
For instructions on building this code, please see the libmprc overview documentation.
Two sample datasets are available for testing the algorithm. Both are tryptic digests of human transferrin and albumin; digests were performed both in H216O and in two different purities of H218O (approx. 90% and approx. 99%). The 16O and 18O digests were then mixed in varying ratios. FTICR-MS data and data-dependant linear ion trap MS/MS data were collected in parallel on an LTQ-FT. The data are deposited here as centroided mzXML. For more details please see the forthcoming publication.
A poster (2.2MB) on RAAMS was presented at ASMS 2006.
Two of the ratios were omitted from Figure 3 for clarity; the complete figure is available.
Figure S1 is available, along with it's caption.