[Massquest-dev] Welcome

Gary Van Domselaar gary@www.bioinformatics.org
Tue, 22 Oct 2002 14:15:17 -0400 (EDT)

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.