-
Notifications
You must be signed in to change notification settings - Fork 34
Home
Laurent Gatto edited this page Aug 4, 2014
·
16 revisions
Notes about R/Bioc for proteomics.
Ideas:
- Label-free quantification
- MS QC support (integration with QuaMeter from David Tabb). Related:
qcmetrics
for a general framework to define and bundle QC items andmsQC
. - Better fragmentation pattern prediction for spectra annotation - what is, if any, already available? What do we mean by that? Just masses of b & y, a & x and c & z fragment ions? Or also their relative intensities based on the fragmentation method (CID, HCD, ETD, ECD, IRMPD, ...)? The former is trivial, the latter is challenging. See
MSnbase:::calculateFragments
for the former. - Add handling modifications
- Add deisotoping capability - what is, if any, already available? Need to look up if this capability is available in other packaged. However it is quite unlikely. The good old algorithm for this kind of task is
THRASH
. It has been implemented in this GUI only standalone softwareDecon2LS