Welcome to the MassQuest developers list. MassQuest is intended to provide an open source alternative to mass spec-based sequence prediction engines such as Mascot and Sequest. Right now the project is still embryonic. I am currently researching the best way to implement such a system. There are several obstacles to consider for this project: 1. Patents. Several algorithms currently used by commercial programs to predict protein sequence information from MS and MS-MS data are patented and therefore incompatible for an open source project. At this point I think it best to review these existing algorithms and summarize them here. Then a decision can be made on which to best implement, or perhaps create one from scratch. 2. MS File formats. MassQuest will need to be able to read the file formats of the various mass spectrometers in use today. In some cases, these file formats are proprietary. There are legal and technical issues to consider here. A discussion on how best to proceed on this issue is relevant for this list. That is plenty to get started. I hope the members of MassQuest can address and overcome these obstacles so we can create a much needed open source alternative for mass spec-based protein sequence prediction. Regards, g.